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.gitattributes

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+
+# Python caches
+__pycache__/
+*.py[cod]
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
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+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Other
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+# Runtime outputs
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README.md

@@ -0,0 +1,375 @@
+---
+frameworks:
+- JAX
+language:
+- en
+license: apache-2.0
+tags:
+- OneScience
+- bioscience
+- protein-complex-structure-prediction
+- CombFold
+- AlphaFold-Multimer
+- ColabFold
+tasks: []
+datasets: []
+---
+
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">CombFold</span>
+  </strong>
+</p>
+
+# Model Introduction
+
+CombFold is an open-source pipeline developed by dina-lab3D for predicting the structures of large protein complexes. Starting from the amino acid sequences of the individual chains in a complex, CombFold uses AlphaFold-Multimer to predict multiple candidate subcomplexes and then applies combinatorial assembly algorithms to construct the complete protein complex.
+
+The original publication reports support for complexes containing at least 18,000 amino acids and up to 32 subunits.
+
+Paper: [Assembly of protein complexes by combining AlphaFold and combinatorial optimization](https://www.nature.com/articles/s41592-024-02174-0)
+
+# Model Description
+
+CombFold consists of four main stages:
+
+1. Define subunits according to protein domains and chain composition and generate `subunits.json`;
+2. Generate FASTA files for all subunit pairs and predict pairwise subcomplexes using AlphaFold-Multimer;
+3. Optionally predict candidate subcomplexes containing more than two subunits;
+4. Extract relative transformations between subunits from the predicted PDB structures and use a C++ combinatorial optimization algorithm to assemble the complete complex.
+
+The main components included in the Hugging Face model package are:
+
+- `model/CombinatorialAssembler/`: C++17 combinatorial assembler and the `AF2trans` structural transformation tool;
+- `scripts/prepare_fastas.py`: generates FASTA files for pairwise or larger subunit combinations;
+- `scripts/inference.py`: unified assembly entry point for the Hugging Face model package;
+- `scripts/run_on_pdbs.py`: original upstream entry point for assembly from predicted PDB structures;
+- `weight/`: official pretrained AlphaFold-Multimer parameters used for offline ColabFold inference;
+- `requirements.txt`: additional dependencies required on top of the OneScience base environment.
+
+CombFold itself is not a trainable neural network. Neural-network inference is performed by pretrained AlphaFold-Multimer models, while CombFold is responsible for extracting structural transformations and performing combinatorial assembly.
+
+# Use Cases
+
+| Use Case | Description |
+| :---: | :--- |
+| Large protein complex prediction | Combine multiple AlphaFold-Multimer subcomplex predictions into a complete complex structure. |
+| Homomer prediction | Assemble complexes containing multiple copies of the same unique subunit according to the specified stoichiometry. |
+| Heteromer prediction | Integrate predictions from different subunit pairs or groups to construct the complete structure. |
+| Assembly from existing AFM results | Directly use existing AlphaFold-Multimer PDB predictions without rerunning AlphaFold-Multimer. |
+| Crosslink-guided assembly | Optionally incorporate crosslinking restraints to constrain candidate complex structures. |
+
+# Usage
+
+## 1. OneCode
+
+You can use the OneCode online environment for an intelligent one-click AI4S programming experience:
+
+[Try OneCode for AI4S Programming](https://web-2069360198568017922-iaaj.ksai.scnet.cn:58043/home)
+
+## 2. Manual Installation
+
+**Hardware Requirements**
+
+- The CombFold C++ combinatorial assembly stage requires only CPU resources;
+- Local AlphaFold-Multimer subcomplex prediction typically requires an accelerator;
+- Memory usage for long-sequence and multi-model inference increases with the total number of residues, MSA depth, number of models, and number of recycles;
+- PyTorch is not a direct runtime dependency of CombFold or the current ColabFold inference pipeline.
+
+### Download the Model Package
+
+Install the Hugging Face command-line tool and download the model repository:
+
+```bash
+pip install -U huggingface_hub
+
+hf download OneScience-Group/CombFold --local-dir ./CombFold
+cd CombFold
+```
+
+### Install the Runtime Environment
+
+**OneScience DCU Base Environment**
+
+```bash
+conda create -n onescience311 python=3.11 -y
+conda activate onescience311
+
+python -m pip install onescience[bio-dcu] \
+  -i http://mirrors.onescience.ai:3141/pypi/simple/ \
+  --trusted-host mirrors.onescience.ai
+```
+
+Install the additional dependencies:
+
+```bash
+python -m pip install --no-deps -r requirements.txt
+```
+
+### Compile the Combinatorial Assembler
+
+The combinatorial assembly stage of CombFold is implemented in C++17 and requires the following system-level components. These components cannot be installed through `requirements.txt`.
+
+| Component | Purpose | Description |
+| --- | --- | --- |
+| C++17 compiler | Compile the C++ source code | `g++` is commonly used on Linux |
+| GNU Make | Execute the Makefile | GNU Make 4.2.1 has been validated |
+| Boost headers | Compile-time headers | The directory must contain `boost/algorithm/string.hpp` |
+| Boost program_options | Link-time runtime library | Usually provided as `libboost_program_options.so` on Linux |
+
+Boost headers are generally portable across Linux distributions, but compiled Boost libraries depend on the operating system, CPU architecture, compiler, and `libstdc++` ABI. Therefore, compiled Boost libraries should not be copied directly between Linux, macOS, Windows, or different CPU architectures.
+
+It is recommended to use Boost headers and runtime libraries from the same Boost version.
+
+The upstream Makefile is configured primarily for macOS Homebrew. On Linux, the following command can be used directly only when Boost is already available in the compiler's default search paths:
+
+```bash
+cd model/CombinatorialAssembler
+make
+cd ../..
+```
+
+#### Specify a Custom Boost Path
+
+If Boost is not installed in the default compiler search paths, define the following environment variables:
+
+```bash
+export COMBFOLD_BOOST_INCLUDE="<Boost source or include directory>"
+export COMBFOLD_BOOST_LIB="<Boost library directory>"
+```
+
+`COMBFOLD_BOOST_INCLUDE` must point to a directory that directly contains the `boost/` subdirectory.
+
+`COMBFOLD_BOOST_LIB` must point to a directory that directly contains the `libboost_program_options` library.
+
+Before compilation, you can verify the paths using:
+
+```bash
+test -f "${COMBFOLD_BOOST_INCLUDE}/boost/algorithm/string.hpp" \
+  && echo "Boost headers OK"
+
+find "${COMBFOLD_BOOST_LIB}" -maxdepth 1 \
+  -name 'libboost_program_options*' -print
+```
+
+Compile the assembler:
+
+```bash
+cd model/CombinatorialAssembler
+
+make -j4 \
+  BOOST_INCLUDE="${COMBFOLD_BOOST_INCLUDE}" \
+  BOOST_LIB="${COMBFOLD_BOOST_LIB}"
+
+cd ../..
+```
+
+### Weights and Data Preparation
+
+The CombFold combinatorial assembler itself does not require model weights.
+
+Local generation of AlphaFold-Multimer subcomplex predictions requires the five official AlphaFold-Multimer v3 parameter files:
+
+| Asset | Location in the Model Package | Purpose |
+| --- | --- | --- |
+| `params_model_1_multimer_v3.npz` | `weight/alphafold/params/` | AFM v3 model 1 |
+| `params_model_2_multimer_v3.npz` | `weight/alphafold/params/` | AFM v3 model 2 |
+| `params_model_3_multimer_v3.npz` | `weight/alphafold/params/` | AFM v3 model 3 |
+| `params_model_4_multimer_v3.npz` | `weight/alphafold/params/` | AFM v3 model 4 |
+| `params_model_5_multimer_v3.npz` | `weight/alphafold/params/` | AFM v3 model 5 |
+
+Use the following ColabFold data path:
+
+```text
+--data weight/alphafold
+```
+
+If you only use existing AlphaFold-Multimer PDB predictions for combinatorial assembly, AlphaFold-Multimer weights and a DCU device are not required.
+
+### Define Subunits
+
+The input `subunits.json` is a JSON dictionary keyed by unique subunit names.
+
+Each subunit contains the following fields:
+
+- `name`: unique subunit name;
+- `sequence`: amino acid sequence;
+- `chain_names`: chain names corresponding to this subunit in the complete complex. The number of entries also defines its stoichiometry;
+- `start_res`: starting residue index of the sequence in the original chain.
+
+Example:
+
+```json
+{
+  "A0": {
+    "name": "A0",
+    "chain_names": ["A", "B"],
+    "start_res": 1,
+    "sequence": "MKDILEKLEERRAQARLGGGEKRLEAQHKRGKLTARERIELLLDHGSFEE"
+  }
+}
+```
+
+The Hugging Face model package provides a complete example:
+
+```text
+scripts/example/subunits.json
+scripts/example/pdbs/
+```
+
+### Quick Inference: CPU Assembly from Existing PDB Files
+
+This is the shortest CombFold inference path and does not run AlphaFold-Multimer:
+
+```bash
+python scripts/inference.py \
+  --subunits scripts/example/subunits.json \
+  --pdbs scripts/example/pdbs \
+  --output output/example_assembly
+```
+
+The output directory must either not exist or be empty before execution.
+
+After successful execution, the main results are located at:
+
+```text
+output/example_assembly/assembled_results/output_clustered_0.pdb
+output/example_assembly/assembled_results/confidence.txt
+```
+
+You can also use the original upstream positional-argument entry point:
+
+```bash
+python scripts/run_on_pdbs.py \
+  scripts/example/subunits.json \
+  scripts/example/pdbs \
+  output/example_assembly
+```
+
+### Generate Pairwise FASTA Files
+
+Generate FASTA files for every pair of unique subunits defined in `subunits.json`:
+
+```bash
+python scripts/prepare_fastas.py \
+  scripts/example/subunits.json \
+  --stage pairs \
+  --output-fasta-folder output/pair_fastas \
+  --max-af-size 1800
+```
+
+The output directory must not already exist.
+
+The official example generates files such as:
+
+```text
+A0_A0.fasta
+A0_G0.fasta
+G0_G0.fasta
+```
+
+### Minimal DCU Pairwise Inference
+
+For an offline smoke test on a compute node, you can use `single_sequence`, one model, and one recycle:
+
+```bash
+colabfold_batch \
+  output/pair_fastas \
+  output/colabfold_pairs \
+  --data weight/alphafold \
+  --model-type alphafold2_multimer_v3 \
+  --model-order 1 \
+  --num-models 1 \
+  --num-recycle 1 \
+  --num-relax 0 \
+  --msa-mode single_sequence \
+  --disable-unified-memory
+```
+
+The configuration:
+
+```text
+single_sequence + 1 model + 1 recycle
+```
+
+is intended only to verify parameter loading, JAX/DCU forward execution, and PDB output generation.
+
+It should not be used to evaluate formal prediction accuracy.
+
+For production-quality predictions, prepare appropriate MSA features and increase the number of models and recycles according to available memory and runtime constraints.
+
+### End-to-End DCU-to-CPU Inference
+
+At least one predicted PDB structure must be selected for each pair.
+
+To select the top-ranked ColabFold structure:
+
+```bash
+mkdir -p output/combfold_pdbs
+
+find output/colabfold_pairs -maxdepth 1 \
+  -type f -name '*rank_001*.pdb' \
+  -exec cp {} output/combfold_pdbs/ \;
+```
+
+Then run the CombFold combinatorial assembly stage:
+
+```bash
+python scripts/inference.py \
+  --subunits scripts/example/subunits.json \
+  --pdbs output/combfold_pdbs \
+  --output output/end2end_assembly
+```
+
+The unified inference entry point also outputs a machine-readable summary, for example:
+
+```text
+COMBFOLD_INFERENCE_RESULT={"assembled_structures": 5, "format": "pdb", "status": "PASS", ...}
+```
+
+### Use Crosslinking Restraints
+
+Use the `--crosslinks` option to provide a crosslink restraint file:
+
+```bash
+python scripts/inference.py \
+  --subunits scripts/example/example_xlinks/subunits.json \
+  --pdbs scripts/example/example_xlinks/pdbs \
+  --crosslinks scripts/example/example_xlinks/crosslinks.txt \
+  --output output/crosslink_assembly
+```
+
+### Optional Prediction of Larger Subcomplexes
+
+After completing pairwise prediction, larger subcomplex FASTA files can be generated based on the pairwise results:
+
+```bash
+python scripts/prepare_fastas.py \
+  scripts/example/subunits.json \
+  --stage groups \
+  --output-fasta-folder output/group_fastas \
+  --max-af-size 1800 \
+  --input-pairs-results output/combfold_pdbs
+```
+
+### Training
+
+CombFold is an inference algorithm that performs combinatorial assembly using predictions generated by pretrained AlphaFold-Multimer models.
+
+CombFold itself does not contain a trainable neural network, training entry point, optimizer, or training-data pipeline. Therefore, this Hugging Face model package does not provide training commands.
+
+Retraining AlphaFold-Multimer is a separate upstream large-scale model-training task and is not part of the CombFold combinatorial assembly workflow.
+
+# OneScience Official Resources
+
+| Platform | OneScience Main Repository | Skills Repository |
+| --- | --- | --- |
+| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
+| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |
+
+# Citation and License
+
+- Paper: [Assembly of protein complexes by combining AlphaFold and combinatorial optimization](https://www.nature.com/articles/s41592-024-02174-0)
+- Official implementation: https://github.com/dina-lab3D/CombFold
+- The CombFold source code is provided under the Apache License 2.0 according to the upstream repository.
+- AlphaFold, AlphaFold-Multimer, ColabFold, pretrained parameters, and other third-party components are subject to their respective original copyright notices, model terms, and licenses.

conf/config.json

@@ -0,0 +1,11 @@
+{
+  "assembler_dir": "model/CombinatorialAssembler",
+  "weight_dir": "weight/alphafold/params",
+  "model_type": "alphafold2_multimer_v3",
+  "msa_mode": "single_sequence",
+  "num_models": 1,
+  "num_recycle": 1,
+  "num_relax": 0,
+  "max_results": 5,
+  "output_cif": false
+}

configuration.json

@@ -0,0 +1,14 @@
+{
+  "model_name": "CombFold",
+  "framework": "C++/Python/JAX",
+  "task": "protein-complex-structure-prediction",
+  "entry_points": {
+    "inference": "scripts/inference.py",
+    "prepare_fastas": "scripts/prepare_fastas.py",
+    "assemble": "scripts/run_on_pdbs.py"
+  },
+  "source_package": "model",
+  "config": "conf/config.json",
+  "weight_dir": "weight",
+  "license": "Apache-2.0"
+}

model/CombinatorialAssembler/AF2trans/AF2trans.cc

@@ -0,0 +1,134 @@
+#include "Atom.h"
+#include "Match.h"
+#include "Molecule.h"
+
+#include <fstream>
+#include <string>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/program_options.hpp>
+
+namespace po = boost::program_options;
+
+/* float calculateRMSD(Molecule<Atom>& origMol, Molecule<Atom>& transMol) {
+  float square_rmsd =0;
+  if((origMol.size() != transMol.size()) || (origMol.size() == 0)) {
+    std::cerr << "different molecules " << origMol.size() << " " << transMol.size()<< std::endl;
+    exit(1);
+  }
+  for(unsigned int i=0; i<origMol.size();i++) {
+    square_rmsd+=origMol(i).dist2(transMol(i));
+  }
+  return sqrt(square_rmsd/origMol.size());
+} */
+
+double getTempPercentile(Molecule<Atom> &mol1, Molecule<Atom> &mol2, float percentile) {
+    std::vector<double> temps1, temps2;
+    for (unsigned int i = 0; i < mol1.size(); i++) {
+        temps1.push_back(mol1[i].getTempFactor());
+        temps2.push_back(mol2[i].getTempFactor());
+    }
+
+    std::sort(temps1.begin(), temps1.end());
+    std::sort(temps2.begin(), temps2.end());
+    int index1 = std::max((int)(percentile * mol1.size() - 1), 0);
+    int index2 = std::max((int)(percentile * mol1.size() - 1), 0);
+    return std::min(temps1[index1], temps2[index2]);
+}
+
+Match calculateTrans(Molecule<Atom> &origMol, Molecule<Atom> &transMol) {
+    if ((origMol.size() != transMol.size()) || (origMol.size() == 0)) {
+        std::cerr << "different molecules " << origMol.size() << " " << transMol.size() << std::endl;
+        exit(1);
+    }
+    Match match;
+    float tempThreshold = std::min(80.0, getTempPercentile(origMol, transMol, 0.5));
+    for (unsigned int i = 0; i < origMol.size(); i++) {
+        if (origMol[i].getTempFactor() < tempThreshold || transMol[i].getTempFactor() < tempThreshold)
+            continue;
+        match.add(i, i);
+    }
+    match.calculateBestFit(origMol, transMol);
+    // std::cout << "Got rmsd: " << match.rmsd() << std::endl;
+    return match;
+}
+
+Molecule<Atom> readMolecule(std::string molName, bool all_atoms) {
+    Molecule<Atom> mol;
+    std::ifstream molFile(molName);
+    if (!molFile) {
+        std::cerr << "Can't open file " << molName << std::endl;
+        exit(0);
+    }
+
+    if (!all_atoms) {
+        mol.readPDBfile(molFile, PDB::CAlphaSelector());
+        // try nucleic acids
+        if (mol.size() == 0) {
+            molFile.clear();
+            molFile.seekg(0, std::ios::beg);
+            mol.readPDBfile(molFile, PDB::PSelector());
+        }
+    }
+
+    // in case no CA were read, we use all atoms
+    if (all_atoms || mol.size() == 0) {
+        molFile.clear();
+        molFile.seekg(0, std::ios::beg);
+        mol.readAllPDBfile(molFile);
+    }
+    molFile.close();
+
+    return mol;
+}
+
+int main(int argc, char **argv) {
+    // output arguments
+    for (int i = 0; i < argc; i++)
+        std::cerr << argv[i] << " ";
+    std::cerr << std::endl;
+
+    bool all_atoms = false;
+    po::options_description desc(
+        "Usage: AF2trans <receptorRef> <ligandRef> <receptorAF2_1> <ligandAF2_1> <receptorAF2_2> <ligandAF2_2> ...\n "
+        "translates AF2 complexes into transformations of the ligandRef onto the receptorRef\n");
+    desc.add_options()("help",
+                       "AF2mer2trans - produces ligand onto receptor docking like transformations from AF2 models\n")(
+        "input-files", po::value<std::vector<std::string>>(), "input files")("all,a",
+                                                                             "all atoms rmsd (default = false)");
+
+    po::positional_options_description p;
+    p.add("input-files", -1);
+    po::variables_map vm;
+    po::store(po::command_line_parser(argc, argv).options(desc).positional(p).run(), vm);
+    po::notify(vm);
+
+    std::vector<std::string> files;
+    if (vm.count("input-files")) {
+        files = vm["input-files"].as<std::vector<std::string>>();
+    }
+    if (vm.count("help") || files.size() < 4) {
+        std::cout << desc << "\n";
+        return 0;
+    }
+    if (vm.count("all_atoms")) {
+        all_atoms = true;
+    }
+
+    Molecule<Atom> receptorRef = readMolecule(files[0], all_atoms);
+    Molecule<Atom> ligandRef = readMolecule(files[1], all_atoms);
+
+    std::cout.precision(4);
+    for (unsigned int i = 2; i < files.size(); i += 2) {
+        Molecule<Atom> receptorAF2 = readMolecule(files[i], all_atoms);
+        Molecule<Atom> ligandAF2 = readMolecule(files[i + 1], all_atoms);
+        Match m1 = calculateTrans(receptorRef, receptorAF2);
+        Match m2 = calculateTrans(ligandRef, ligandAF2);
+        RigidTrans3 T = m1.rigidTrans() * (!m2.rigidTrans());
+        std::cout << i / 2 << " | " << m1.rmsd() << "_" << files[i] << " | " << m2.rmsd() << "_" << files[i + 1]
+                  << " | " << T << std::endl;
+        //    std::cout << rms << std::endl;
+    }
+
+    return 0;
+}

model/CombinatorialAssembler/BB.cc

@@ -0,0 +1,178 @@
+#include "BB.h"
+
+#include <Common.h>
+#include <connolly_surface.h>
+
+BB::BB(int id, const std::string pdbFileName, int groupID, const ChemLib &lib, float gridResolution, float gridMargins,
+       float minTempFactor)
+    : id_(id), groupId_(groupID), pdbFileName_(pdbFileName) {
+    // read atoms
+    Common::readChemMolecule(pdbFileName_, allAtoms_, lib);
+    std::cout << "Done reading ChemMolecule " << allAtoms_.size() << std::endl;
+    // read backbone atoms
+    std::ifstream pdb2(pdbFileName_);
+    backBone_.readPDBfile(pdb2, PDB::BBSelector());
+    pdb2.close();
+    cm_ = backBone_.centroid();
+    numOfAtoms_ = allAtoms_.size();
+
+    // read CA atoms
+    std::ifstream pdb3(pdbFileName_);
+    caAtoms_.readPDBfile(pdb3, PDB::CAlphaSelector());
+    pdb3.close();
+
+    // compute ms surface
+    msSurface_ = get_connolly_surface(allAtoms_, 10, 1.8);
+    std::cout << "Surface size " << msSurface_.size() << std::endl;
+
+    // compute grid
+    grid_ = new BBGrid(msSurface_, gridResolution, gridMargins, 1.5);
+    grid_->computeDistFromSurface(msSurface_);
+    grid_->markTheInside(allAtoms_);
+    grid_->markResidues(backBone_);
+    std::cout << "Done compute grid " << pdbFileName_ << std::endl;
+
+    std::vector<Atom *> atomsMap;
+    atomsMap.push_back(&(*allAtoms_.begin()));
+    for (ChemMolecule::iterator i = allAtoms_.begin(); i != allAtoms_.end(); i++) {
+        atomsMap.push_back(&(*i));
+    }
+
+    computeFragments(minTempFactor); // get the endpoints
+
+    for (Molecule<Atom>::const_iterator it = caAtoms_.begin(); it != caAtoms_.end(); it++) {
+        resIndexToCAAtom[it->residueIndex()] = *it;
+    }
+
+    maxRadius_ = 0.0;
+    for (Molecule<Atom>::const_iterator it = caAtoms_.begin(); it != caAtoms_.end(); it++) {
+        float r = (it->position() - cm_).norm();
+        if (r > maxRadius_)
+            maxRadius_ = r;
+    }
+    std::cout << "Max radius: " << maxRadius_ << std::endl;
+
+    std::cout << " done reading BB " << pdbFileName_.c_str() << std::endl;
+}
+
+void BB::computeFragments(float minTempFactor) {
+    // calculate endpoints
+    char currChain;
+    int firstResIndex, prevResIndex;
+    bool currChainSet = false;
+    for (auto i = allAtoms_.begin(); i != allAtoms_.end(); i++) {
+        // only CA atoms are considered
+        if (!i->isCA())
+            continue;
+        if (i->getTempFactor() < minTempFactor)
+            continue;
+        char chain = i->chainId();
+        int resIndex = i->residueIndex();
+        // one more residue of the same chain - advance
+        // if over 20 residues diff - new fragment
+        if (currChainSet && currChain == chain && resIndex - prevResIndex <= 20) {
+            prevResIndex = resIndex;
+        } else {                // new chain
+            if (currChainSet) { // save currChain
+                ResidueRange range(firstResIndex, prevResIndex);
+                fragmentEndpoints_.push_back(std::make_pair(currChain, range));
+            }
+            // update
+            currChain = chain;
+            firstResIndex = prevResIndex = resIndex;
+            currChainSet = true;
+        }
+    }
+    // save last fragment
+    if (currChainSet) { // save currChain
+        ResidueRange range(firstResIndex, prevResIndex);
+        fragmentEndpoints_.push_back(std::make_pair(currChain, range));
+    }
+
+    for (int i = 0; i < (int)fragmentEndpoints_.size(); i++) {
+        std::cout << "Fragment " << i << " chainId " << fragmentEndpoints_[i].first << " range "
+                  << fragmentEndpoints_[i].second.first << ":" << fragmentEndpoints_[i].second.second << std::endl;
+    }
+}
+
+void BB::getChainConnectivityConstraints(const BB &otherBB,
+                                         std::vector<std::pair<char, std::pair<int, int>>> &constraints) const {
+    for (int i = 0; i < (int)fragmentEndpoints_.size(); i++) {
+        char chainId1 = fragmentEndpoints_[i].first;
+        int resIndex1N = fragmentEndpoints_[i].second.first;
+        int resIndex1C = fragmentEndpoints_[i].second.second;
+
+        for (int j = 0; j < (int)otherBB.fragmentEndpoints_.size(); j++) {
+            char chainId2 = otherBB.fragmentEndpoints_[j].first;
+            if (chainId1 != chainId2)
+                continue;
+            int resIndex2N = otherBB.fragmentEndpoints_[j].second.first;
+            int resIndex2C = otherBB.fragmentEndpoints_[j].second.second;
+            if (resIndex1N < resIndex2N) { // add constraint on 1C and 2N
+                constraints.push_back(std::make_pair(chainId1, std::make_pair(resIndex1C, resIndex2N)));
+            } else { // add constraint on 2C and 1N
+                constraints.push_back(std::make_pair(chainId1, std::make_pair(resIndex1N, resIndex2C)));
+            }
+        }
+    }
+}
+
+bool BB::isPenetrating(const RigidTrans3 &trans, const BB &other, float threshold) const {
+    for (Surface::const_iterator it = other.surface_.begin(); it != other.surface_.end(); it++) {
+        float penetration = getDistFromSurface(trans * it->position());
+        if (threshold > penetration) {
+            // cerr << "trans " << trans << " penetrates " << penetration << endl;
+            return true;
+        }
+    }
+    return false;
+}
+
+float BB::maxPenetration(const RigidTrans3 &trans, const BB &other) const {
+    float max = 1000;
+    for (Surface::const_iterator it = other.surface_.begin(); it != other.surface_.end(); it++) {
+        float penetration = getDistFromSurface(trans * it->position());
+        if (max > penetration) {
+            max = penetration;
+        }
+    }
+    return max;
+}
+
+bool BB::isIdent(const BB &otherBB) const {
+    if (getNumOfAtoms() != otherBB.getNumOfAtoms()) {
+        std::cout << "different num of atoms" << std::endl;
+        return false;
+    }
+    for (unsigned int i = 0; i < allAtoms_.size(); i++) {
+        if (!(allAtoms_[i].position() - otherBB.allAtoms_[i].position()).isZero()) {
+            std::cout << "different atom position" << i << std::endl;
+            return false;
+        }
+    }
+    if (groupId_ != otherBB.groupId_) {
+        std::cout << "different group id" << std::endl;
+        return false;
+    }
+    std::cout << "checking transforms" << std::endl;
+    if (trans_.size() != otherBB.trans_.size())
+        return false;
+    for (unsigned int i = 0; i < trans_.size(); i++) {
+        if (i == id_ || i == otherBB.id_)
+            continue;
+
+        if (trans_[i].size() != otherBB.trans_[i].size()) {
+            std::cout << "different number of trans " << i << " " << trans_[i].size()
+                      << " != " << otherBB.trans_[i].size() << std::endl;
+            return false;
+        }
+
+        for (unsigned int j = 0; j < trans_[i].size(); j++) {
+            if (trans_[i][j]->score() != otherBB.trans_[i][j]->score()) {
+                std::cout << "different trans score" << i << std::endl;
+                return false;
+            }
+        }
+    }
+    return true;
+}

model/CombinatorialAssembler/BB.h

@@ -0,0 +1,106 @@
+#ifndef BB_H
+#define BB_H
+
+#include "BBGrid.h"
+#include "TransformationAndScore.h"
+#include "BitId.h"
+
+#include <ChemMolecule.h>
+#include <GeomScore.h>
+#include <RigidTrans3.h>
+#include <Surface.h>
+#include <Vector3.h>
+
+#include <vector>
+
+class BBConstructor {
+    // idea taken from
+    // https://stackoverflow.com/questions/3220009/is-this-key-oriented-access-protection-pattern-a-known-idiom
+  private:
+    friend class BBContainer;
+    BBConstructor() {}
+};
+
+class BB {
+  public:
+    friend class SuperBB;
+
+    BB(int id, const std::string pdbFilename, int groupID, const ChemLib &lib, float gridResolution, float gridMargins,
+       float minTempFactor);
+
+    // access
+    int getID() const { return id_; }
+    BitId bitId() const { return BitId(id_); }
+    int groupId() const { return groupId_; }
+    std::string getPDBFileName() const { return pdbFileName_; }
+
+    unsigned int getNumOfAtoms() const { return numOfAtoms_; }
+    const Vector3 &getCM() const { return cm_; }
+    const float getRadius() const { return maxRadius_; }
+
+    const ChemAtom &getChemAtom(int atomIndex) const { return allAtoms_.getChemAtom(atomIndex); }
+    const ChemAtom &getChemAtomByIndex(int atomIndex) const { return allAtoms_[atomIndex]; }
+    const Atom &getAtomByResId(unsigned int resId) const { return resIndexToCAAtom.at(resId); }
+
+    unsigned int getSurfaceSize() const { return surface_.size(); }
+    float getDistFromSurface(const Vector3 &v) const { return grid_->getDist(v); }
+
+
+    // This uses BBConstructor to make sure that only BBContainer can call this
+    void putTransWith(int bbIndex, const std::shared_ptr<TransformationAndScore> &t1, const BBConstructor &) const {
+        trans_[bbIndex].push_back(t1);
+    }
+    void initTrans(unsigned int numberOfBBs, const BBConstructor &) const {
+        trans_.insert(trans_.begin(), numberOfBBs, std::vector<std::shared_ptr<TransformationAndScore>>());
+    }
+
+    // TODO: do we still need isPenetrating/maxPenetration ?
+    bool isPenetrating(const RigidTrans3 &trans, const BB &other, float threshold) const;
+    float maxPenetration(const RigidTrans3 &trans, const BB &other) const;
+
+    void getChainConnectivityConstraints(const BB &bb,
+                                         std::vector<std::pair<char, std::pair<int, int>>> &) const; // update
+
+    const std::vector<std::shared_ptr<TransformationAndScore>> &getTransformations(int bbIndex) const {
+        return trans_[bbIndex];
+    }
+
+    bool isIdent(const BB &otherBB) const;
+    
+  private:
+    // after BB is initialized, compute chains and fragment ranges
+    void computeFragments(float minTempFactor);
+
+  private:
+    // surface points
+    // Different methods for computing collision
+    Surface surface_;                  // shuo
+    Surface msSurface_;                // connolly - dense
+
+    // BB id
+    unsigned int id_;
+
+    // transformations to other BBs
+    // This is the edge in a graph - The result of a patch dock calculation
+    mutable std::vector<std::vector<std::shared_ptr<TransformationAndScore>>> trans_;
+
+    int groupId_;
+    std::string pdbFileName_;
+    int numOfAtoms_;
+
+    Vector3 cm_;
+    float maxRadius_;
+
+    // chain id and residue numbers for each chain fragment in BB
+    typedef std::pair<int, int> ResidueRange;
+    std::vector<std::pair<char, ResidueRange>> fragmentEndpoints_;
+
+  public: // TODO
+    BBGrid *grid_;
+    ChemMolecule backBone_;
+    ChemMolecule allAtoms_;
+    Molecule<Atom> caAtoms_;
+    std::map<unsigned int, Atom> resIndexToCAAtom;
+};
+
+#endif /* BB_H */

model/CombinatorialAssembler/BBContainer.cc

@@ -0,0 +1,132 @@
+#include "BBContainer.h"
+#include <boost/algorithm/string.hpp>
+
+namespace {
+std::string trim_extension(const std::string file_name) {
+    if (file_name[file_name.size() - 4] == '.')
+        return file_name.substr(0, file_name.size() - 4);
+    return file_name;
+}
+} // namespace
+
+BBContainer::BBContainer(const std::string SUFileName, std::string chemLibFileName, float minTempFactor) {
+    readSUFile(SUFileName);
+
+    // prepare ChemLib
+    ChemLib chemLib(chemLibFileName);
+
+    // read the building blocks
+    bbs_.reserve(numOfBBs_);
+    for (unsigned int i = 0; i < numOfBBs_; i++) {
+        bbs_.push_back(std::make_shared<BB>(i, pdbs_[i], groupIDs_[i], chemLib, 0.5, 5.0, minTempFactor));
+    }
+}
+
+void BBContainer::readTransformationFiles(std::string transFilePrefix, unsigned int transNumToRead) {
+    // init transformations vector
+    for (unsigned int i = 0; i < numOfBBs_; i++) {
+        bbs_[i]->initTrans(numOfBBs_, {});
+    }
+
+    // read the files
+    for (size_t i = 0; i < numOfBBs_; i++) {
+        for (size_t j = 0; j < numOfBBs_; j++) {
+            if (i == j)
+                continue;
+            std::string inFileName = transFilePrefix + trim_extension(pdbs_[i]) + "_plus_" + trim_extension(pdbs_[j]);
+            std::ifstream inS(inFileName);
+            std::cerr << "Opening transformation file " << inFileName << std::endl;
+            if (!inS) {
+                std::cerr << "Problem opening transformation file " << inFileName << std::endl;
+                continue;
+            }
+
+            unsigned int counter = 0;
+            while (!inS.eof() && counter < transNumToRead) {
+                TransformationAndScore *t1 = new TransformationAndScore();
+                if (readTrans(*t1, inS)) {
+                    std::shared_ptr<TransformationAndScore> t2 = std::make_shared<TransformationAndScore>(*t1);
+                    t2->refFrame_ = !t2->refFrame_;
+                    bbs_[i]->putTransWith(j, std::make_shared<TransformationAndScore>(*t1), {});
+                    bbs_[j]->putTransWith(i, t2, {});
+                    counter++;
+                }
+            }
+            std::cerr << counter << " transforms were read from file " << inFileName << std::endl;
+            inS.close();
+        }
+    }
+}
+
+int BBContainer::readSUFile(const std::string SUFileName) {
+    numOfBBs_ = 0;
+    std::ifstream SUFile(SUFileName);
+    if (!SUFile) {
+        std::cerr << "Can't open SU file" << SUFileName << std::endl;
+        exit(1);
+    }
+    while (!SUFile.eof()) {
+        std::string line;
+        getline(SUFile, line);
+        boost::trim(line);
+        if (line.length() > 0) {
+            std::vector<std::string> split_results;
+            boost::split(split_results, line, boost::is_any_of(" "), boost::token_compress_on);
+            std::string pdbName(split_results[0]);
+            std::cout << "PDBname " << pdbName << ":" << line << std::endl;
+            numOfBBs_++;
+            pdbs_.push_back(pdbName);
+            // group assignment
+            int groupID = 0;
+            if (split_results.size() == 2) {
+                groupID = stoi(split_results[1]);
+                if (groupID <= 0) {
+                    std::cerr << "Group ID must be positive" << std::endl;
+                }
+            }
+            groupIDs_.push_back(groupID);
+        }
+    }
+    return numOfBBs_;
+}
+
+bool BBContainer::readTrans(TransformationAndScore &trans, std::ifstream &transFile) {
+    std::string line;
+    if (!transFile.eof()) {
+        getline(transFile, line);
+        boost::trim(line); // remove all spaces
+        // skip comments
+        if (line[0] == '#' || line[0] == '\0')
+            return false;
+
+        std::vector<std::string> split_results;
+        boost::split(split_results, line, boost::is_any_of(":|\t"), boost::token_compress_on);
+        if (split_results.size() != 4) {
+            std::cerr << "Wrong number of fields in transformation file, should be: "
+                      << "index(int) | score(float) | comment | transformation(space seperated 6 floats)" << std::endl;
+            return false;
+        }
+
+        boost::trim(split_results[3]);
+        std::vector<std::string> splitted_transformation;
+        boost::split(splitted_transformation, split_results[3], boost::is_any_of(" "), boost::token_compress_on);
+
+        if (splitted_transformation.size() != 6)
+            return false;
+
+        // extract trans
+        RigidTrans3 tr(Vector3(std::stof(splitted_transformation[0].c_str()),
+                               std::stof(splitted_transformation[1].c_str()),
+                               std::stof(splitted_transformation[2].c_str())),
+                       Vector3(std::stof(splitted_transformation[3].c_str()),
+                               std::stof(splitted_transformation[4].c_str()),
+                               std::stof(splitted_transformation[5].c_str())));
+        trans.refFrame_ = tr;
+        trans.score_.totalScore_ = 1.0;
+        trans.dist_ = 1.0;
+
+        trans.score_.totalScore_ = std::stof(split_results[1].c_str());
+        std::cout << "loaded score: " << trans.score_.totalScore_ << std::endl;
+    }
+    return !transFile.eof();
+}

model/CombinatorialAssembler/BBContainer.h

@@ -0,0 +1,43 @@
+//
+// Created by dina on 8/1/18.
+//
+
+#ifndef BB_CONTAINER_H
+#define BB_CONTAINER_H
+
+#include "BB.h"
+#include <memory>
+
+class BBContainer {
+  public:
+    // Constructor
+    BBContainer(std::string SUFileName, std::string chemLibFileName, float minTempFactor);
+
+    // Group: access
+    std::shared_ptr<const BB> getBB(unsigned int bbIndex) const { return bbs_[bbIndex]; }
+    const std::vector<std::shared_ptr<const BB>> &getBBs() const { return bbs_; }
+    unsigned int getBBsNumber() const { return numOfBBs_; }
+
+    void readTransformationFiles(std::string transFilePrefix, unsigned int transNumToRead);
+
+  private:
+    int readSUFile(const std::string SUFileName);
+    bool readTrans(TransformationAndScore &trans, std::ifstream &transFile);
+
+  private:
+    // PDB filenames
+    std::vector<std::string> pdbs_;
+
+    // BBs
+    std::vector<std::shared_ptr<const BB>> bbs_;
+
+    // total bbs num
+    unsigned int numOfBBs_;
+
+    // BBs can be grouped according to a number provided by the user in SUlist
+    // BBs in the same group will be assembled first
+    // if no number is given, all the BBs are considered a group
+    std::vector<int> groupIDs_;
+};
+
+#endif // BBCONTAINER_H

model/CombinatorialAssembler/BBGrid.cc

@@ -0,0 +1,51 @@
+#include "BBGrid.h"
+
+void BBGrid::markResidues(const ChemMolecule &M) {
+    std::vector<float> weights;
+    weights.insert(weights.end(), maxEntry, 0.0);
+    for (Molecule<ChemAtom>::const_iterator it = M.begin(); it != M.end(); it++) {
+        float atomRadius = it->getRadius() + radiusAdition_;
+        float radius = atomRadius * 2; // may be +1 is enouph
+        // cout << " atomRadius " << atomRadius << endl;
+        int centerIndex = getIndexForPoint(it->position());
+        if (!isValidIndex(centerIndex)) {
+            std::cerr << "Error: Point out of grid" << std::endl;
+            exit(1);
+        }
+
+        int intRadius = getIntGridRadius(radius);
+        int radius2 = intRadius * intRadius;
+
+        int i_bound, j_bound, k_bound;
+        i_bound = intRadius;
+        for (int i = -i_bound; i <= i_bound; i++) {
+            j_bound = (int)sqrt(radius2 - i * i);
+            for (int j = -j_bound; j <= j_bound; j++) {
+                k_bound = (int)sqrt(radius2 - i * i - j * j);
+                for (int k = -k_bound; k <= k_bound; k++) {
+                    int index = centerIndex + i + xGridNum * j + xyGridNum * k;
+                    if (isValidIndex(index) && grid[index] <= 0) {
+                        Vector3 point = getPointForIndex(index);
+                        float dist = point.dist(it->position());
+                        if (dist == 0.0) {
+                            if (it->isBackbone())
+                                residues[index] = it->residueIndex() * -1;
+                            else
+                                residues[index] = it->residueIndex();
+                            continue;
+                        }
+                        float weight = atomRadius / dist;
+                        if (weight <= weights[index])
+                            continue;
+                        weights[index] = weight;
+                        if (it->isBackbone())
+                            residues[index] = it->residueIndex() * -1;
+                        else
+                            residues[index] = it->residueIndex();
+                    }
+                }
+            }
+        }
+    }
+    weights.clear();
+}

model/CombinatorialAssembler/BBGrid.h

@@ -0,0 +1,25 @@
+/**
+ * \file BBGrid.h
+ * \brief
+ *
+ * \authors Dina Schneidman
+ *
+ *
+ */
+#ifndef BBGRID_H
+#define BBGRID_H
+
+#include <ChemMolecule.h>
+#include <prGrid.h>
+
+class BBGrid : public ResidueGrid {
+  public:
+    BBGrid(const Surface &surface, const float inDelta, const float maxRadius, float radiusAdition)
+        : ResidueGrid(surface, inDelta, maxRadius), radiusAdition_(radiusAdition){};
+    void markResidues(const ChemMolecule &M);
+
+  private:
+    float radiusAdition_;
+};
+
+#endif /* BBGRID_H */

model/CombinatorialAssembler/BestK.cc

@@ -0,0 +1,82 @@
+#include "BestK.h"
+
+
+bool BestK::push(std::shared_ptr<SuperBB> in) {
+    std::lock_guard<std::mutex> locker(_mu);
+    if (size() < k_) {
+        insert(in);
+        return true;
+    } else {
+
+        if (internalMinScore() < score(in)) {
+            erase(begin());
+            insert(in);
+            curMinScore = score(*begin());
+            return true;
+        }
+    }
+
+    return false;
+}
+
+bool BestK::push_cluster(std::shared_ptr<SuperBB> in, double rmsd, std::vector<std::vector<unsigned int>> &identGroups) {
+    std::lock_guard<std::mutex> locker(_mu);
+
+    if (internalMinScore() > score(in))
+        return false;
+
+    for (auto it = begin(); it != end(); it++) {
+        if (score(in) <= score(*it) && (*it)->calcRmsd(*in, identGroups) < rmsd)
+            return false;
+    }
+
+    for (auto it = begin(); it != end();) {
+        if (score(in) > score(*it) && (*it)->calcRmsd(*in, identGroups) < rmsd) {
+            erase(it++);
+        } else {
+            ++it;
+        }
+    }
+
+    if (size() >= k_) {
+        erase(begin());
+    }
+
+    insert(in);
+    curMinScore = score(*begin());
+    return true;
+}
+
+void BestK::cluster(BestK &clusteredBest, double rmsd, std::vector<std::vector<unsigned int>> &identGroups) const {
+    if (size() == 0)
+        return;
+    const std::shared_ptr<SuperBB> firstSBB = *rbegin();
+    if (firstSBB->size() == 2) { // don't cluster
+        for (auto it = rbegin(); it != rend(); it++) {
+            clusteredBest.insert(*it);
+        }
+    } else {
+        std::vector<bool> clustered(size(), false);
+        int i = 0;
+
+        for (auto it = rbegin(); it != rend(); it++, i++) {
+            const std::shared_ptr<SuperBB> refSBB = *it;
+            // std::cout << "clustering " << i << " clsutered:" << clustered[i] << std::endl;
+            if (!clustered[i]) {
+                clustered[i] = true;
+                clusteredBest.insert(refSBB);
+            }
+
+            // TODO: maybe shouldn't cluster more if already clustered (can lead to drift)
+
+            // cluster to other SBBs
+            int j = 0;
+            // for(auto it2 = begin(); it2!= end(); it2++, j++) {
+            for (auto it2 = rbegin(); it2 != rend(); it2++, j++) {
+                if (!clustered[j] && (*it2)->calcRmsd(*refSBB, identGroups) < rmsd) {
+                    clustered[j] = true;
+                }
+            }
+        }
+    }
+}

model/CombinatorialAssembler/BestK.h

@@ -0,0 +1,63 @@
+#ifndef BESTK_H
+#define BESTK_H
+
+#include "SuperBB.h"
+#include <mutex>
+
+static float scoreSuperBB(const std::shared_ptr<SuperBB> &sbb) {
+    // return sbb->getRestraintsRatio();
+    // return sbb->weightedTransScore_;
+
+    // Note: if you change this, you also needs to change in HierarchicalFold::tryToConnect which optimizes by 
+    // summing and comparing trans scores before trying to connect
+    // return sbb->transScore_;
+    return sbb->transScore_ * sbb->getRestraintsRatio();
+}
+struct comp {
+    bool operator()(const std::shared_ptr<SuperBB> &lhs, const std::shared_ptr<SuperBB> &rhs) const {
+        return scoreSuperBB(lhs) < scoreSuperBB(rhs);
+    }
+};
+
+/**
+   This class stores the best k permutations of a specific size
+   implemented as inheriting from a multiset with shapred_ptr and
+   the comp struct
+*/
+class BestK : public std::multiset<std::shared_ptr<SuperBB>, comp> {
+
+  public:
+    BestK(unsigned int k, bool toDel = true) : k_(k), curMinScore(-1) {}
+
+    float score(const std::shared_ptr<SuperBB> &sbb) const { return scoreSuperBB(sbb); }
+
+    float minScore() const { return curMinScore; }
+    float maxScore() const { 
+        if (size() == 0)
+            return 0;
+        return score(*rbegin()); 
+    }
+
+    void setK(int k) { k_ = k; }
+
+    bool push(std::shared_ptr<SuperBB> in);
+
+    bool push_cluster(std::shared_ptr<SuperBB> in, double rmsd, std::vector<std::vector<unsigned int>> &identGroups);
+
+    void cluster(BestK &clusteredBest, double rmsd, std::vector<std::vector<unsigned int>> &identGroups) const;
+    virtual ~BestK() {}
+
+  private:
+    float internalMinScore() {
+        if (size() < k_)
+            return -1;
+        return score(*begin());
+    }
+
+  private:
+    std::mutex _mu;
+    unsigned int k_;
+    float curMinScore;
+};
+
+#endif /* BESTK_H */

model/CombinatorialAssembler/BestKContainer.h

@@ -0,0 +1,50 @@
+/**
+ * \file BestKContainer.h
+ * \brief
+ *
+ * \authors Dina Schneidman
+ *
+ */
+#ifndef BESTKCONTAINER_H
+#define BESTKCONTAINER_H
+
+#include <unordered_map>
+#include "BestK.h"
+
+class BestKContainer : private std::vector<BestK *> {
+  public:
+    // N - subunit number
+    BestKContainer(int K) : K_(K) {}
+
+    ~BestKContainer() {
+        for (auto it = begin(); it != end(); it++)
+            delete *it;
+    }
+
+    BestK *newBestK(BitId set) {
+        BestK *best = new BestK(K_);
+        push_back(best);
+        set2index_[set] = size() - 1;
+        return best;
+    }
+
+    bool isEmpty(const BitId set) const { return (set2index_.find(set) == set2index_.end()); }
+
+    // assumes BestK for set exists, can be checked with isEmpty
+    const BestK &operator[](const BitId set) const {
+        unsigned int index = set2index_.find(set)->second;
+        return *((std::vector<BestK *>)(*this))[index];
+    }
+
+    // assumes BestK for set exists
+    BestK &operator[](const BitId set) { return *((std::vector<BestK *>)(*this))[set2index_[set]]; }
+
+  private:
+    int K_;
+    // The long is a unique representation key for each SBB
+    // And it is the long type because we want to support more than 32 subunits
+    // int corresponds to an index in the vector that holds the BestK
+    std::unordered_map<BitId, unsigned int> set2index_;
+};
+
+#endif /* BESTKCONTAINER_H */

model/CombinatorialAssembler/BitId.h

@@ -0,0 +1,48 @@
+#ifndef BITID_H
+#define BITID_H
+
+#include <ostream>
+#include <bitset>
+
+
+template <size_t N>
+class CustomBitset : public std::bitset<N> {
+public:
+    CustomBitset() : std::bitset<N>() {}
+
+    CustomBitset(const std::bitset<N>& b) : std::bitset<N>(b) {}
+
+    // assert val < n and then set the val bit, this is different from std::bitset
+    CustomBitset(unsigned long long val) : std::bitset<N>(0) {
+        assert(val < N);
+        this->set(val);
+    }
+
+    // don't print leading zeros
+    std::string to_string() const {
+        std::string str = std::bitset<N>::to_string();
+        size_t first_one = str.find('1');
+        return first_one == std::string::npos ? "0" : str.substr(first_one);
+    }
+};
+
+template <size_t N>
+std::ostream& operator<<(std::ostream& os, const CustomBitset<N>& b) {
+    os << b.to_string();
+    return os;
+}
+
+
+namespace std {
+    template <size_t N>
+    struct hash<CustomBitset<N>> {
+        size_t operator()(const CustomBitset<N>& b) const {
+            return std::hash<std::string>()(b.to_string());
+        }
+    };
+}
+
+
+typedef CustomBitset<128> BitId;
+
+#endif /* BITID_H */

model/CombinatorialAssembler/ComplexDistanceConstraint.cc

@@ -0,0 +1,189 @@
+#include "ComplexDistanceConstraint.h"
+
+#include "BB.h"
+
+void ComplexDistanceConstraint::addConstraint(int suInd1, int suInd2, Vector3 receptorAtom, Vector3 ligandAtom,
+                                              float maxDistance, float minDistance) {
+    int ind = suInd1 * noOfSUs_ + suInd2;
+    constraints_[ind].push_back(DistanceRestraint(receptorAtom, ligandAtom, maxDistance, minDistance));
+}
+
+bool ComplexDistanceConstraint::areConstraintsSatisfied(int suInd1, int suInd2, RigidTrans3 &trans2) const {
+    int ind = suInd1 * noOfSUs_ + suInd2;
+    for (unsigned int index = 0; index < constraints_[ind].size(); index++) {
+        bool sat = constraints_[ind][index].isSatisfied(trans2);
+        if (!sat) {
+            return false;
+        }
+    }
+    return true;
+}
+
+int ComplexDistanceConstraint::addChainConnectivityConstraints() {
+    for (int suInd1 = 0; suInd1 < noOfSUs_; suInd1++) {
+        for (int suInd2 = suInd1 + 1; suInd2 < noOfSUs_; suInd2++) {
+            std::vector<std::pair<char, std::pair<int, int>>> constraints;
+            int counter = 0;
+            float epsilon = 20.0; // for shorter connections
+            bbs_[suInd1]->getChainConnectivityConstraints(*bbs_[suInd2], constraints);
+            for (int i = 0; i < (int)constraints.size(); i++) {
+                int su1resIndex = constraints[i].second.first;
+                int su2resIndex = constraints[i].second.second;
+
+                int receptorAtomIndex = bbs_[suInd1]->allAtoms_.getFirstAtomEntryForResIndex(
+                    constraints[i].first, std::to_string(su1resIndex));
+                int ligandAtomIndex = bbs_[suInd2]->allAtoms_.getFirstAtomEntryForResIndex(constraints[i].first,
+                                                                                           std::to_string(su2resIndex));
+
+                Vector3 receptorAtom = bbs_[suInd1]->getChemAtomByIndex(receptorAtomIndex).position();
+                Vector3 ligandAtom = bbs_[suInd2]->getChemAtomByIndex(ligandAtomIndex).position();
+
+                int sequenceDist = std::fabs(su1resIndex - su2resIndex);
+                if (sequenceDist < 100) {
+                    float maxDist = sequenceDist * 2.0;
+                    if (sequenceDist <= 5)
+                        maxDist += epsilon;
+                    addConstraint(suInd1, suInd2, receptorAtom, ligandAtom, maxDist);
+                    addConstraint(suInd2, suInd1, ligandAtom, receptorAtom, maxDist);
+                    std::cerr << "DISTANCE CONSTRAINT ADDED: " << constraints[i].first << " su1 endpoint "
+                              << su1resIndex << " su2 endpoint " << su2resIndex << " " << maxDist << std::endl;
+                    counter++;
+                }
+            }
+            numberOfConstraints_ += counter;
+        }
+    }
+    return numberOfConstraints_;
+}
+
+std::set<int> ComplexDistanceConstraint::getSUs(const std::string residueSequenceID, const std::string chains,
+                                                int maxOffset) const {
+
+    int rOffset = 0;
+    std::set<int> ret;
+    // iterate chains
+    for (unsigned int chainIndex = 0; chainIndex < chains.size(); chainIndex++) {
+        // for each chain find corresponding SU
+        for (int suIndex = 0; suIndex < noOfSUs_; suIndex++) {
+            int atomIndex = bbs_[suIndex]->allAtoms_.getClosestAtomEntryForResIndex(
+                chains[chainIndex], residueSequenceID, maxOffset, rOffset);
+            if (atomIndex != -1) { // found
+                ret.insert(suIndex);
+                continue;
+            }
+        }
+    }
+    return ret;
+}
+
+int ComplexDistanceConstraint::readRestraintsFile(const std::string fileName) {
+    // read cross links
+    std::vector<CrossLink> crosslinks;
+    int xnum = readCrossLinkFile(fileName, crosslinks);
+    Logger::infoMessage() << "# of xlinks " << xnum << " read from file" << fileName << std::endl;
+    int MAX_OFFSET = 20;
+
+    crosslinkIndToWeight_ = std::vector<float>(crosslinks.size());
+
+    // map them to BB pairs
+    for (unsigned int i = 0; i < crosslinks.size(); i++) {
+        crosslinkIndToWeight_[i] = crosslinks[i].getWeight();
+
+        // SUs that have xlinks endpoints (sus1, sus2)
+        std::string residueSequenceID1 = std::to_string(crosslinks[i].getResidue1());
+        std::set<int> sus1 = getSUs(residueSequenceID1, crosslinks[i].getChain1());
+        if (sus1.size() == 0)
+            sus1 = getSUs(residueSequenceID1, crosslinks[i].getChain1(), MAX_OFFSET);
+        std::string residueSequenceID2 = std::to_string(crosslinks[i].getResidue2());
+        std::set<int> sus2 = getSUs(residueSequenceID2, crosslinks[i].getChain2());
+        if (sus2.size() == 0)
+            sus2 = getSUs(residueSequenceID2, crosslinks[i].getChain2(), MAX_OFFSET);
+
+        // iterate over all pairs of SUs
+        for (auto suIndexIter1 = sus1.begin(); suIndexIter1 != sus1.end(); suIndexIter1++) {
+            for (unsigned int chainIndex1 = 0; chainIndex1 < crosslinks[i].getChain1().size(); chainIndex1++) {
+                char chainId1 = crosslinks[i].getChain1()[chainIndex1];
+                int rOffset = 0;
+                int receptorAtomIndex = bbs_[*suIndexIter1]->allAtoms_.getClosestAtomEntryForResIndex(
+                    chainId1, residueSequenceID1, MAX_OFFSET, rOffset);
+                if (rOffset < 0)
+                    rOffset = -1 * rOffset;
+                if (receptorAtomIndex == -1)
+                    continue;
+                Vector3 rcoord = bbs_[*suIndexIter1]->getChemAtomByIndex(receptorAtomIndex).position();
+
+                for (auto suIndexIter2 = sus2.begin(); suIndexIter2 != sus2.end(); suIndexIter2++) {
+                    for (unsigned int chainIndex2 = 0; chainIndex2 < crosslinks[i].getChain2().size(); chainIndex2++) {
+                        char chainId2 = crosslinks[i].getChain2()[chainIndex2];
+                        int lOffset = 0;
+                        int ligandAtomIndex = bbs_[*suIndexIter2]->allAtoms_.getClosestAtomEntryForResIndex(
+                            chainId2, residueSequenceID2, MAX_OFFSET, lOffset);
+                        if (ligandAtomIndex == -1)
+                            continue;
+                        if (lOffset < 0)
+                            lOffset = -1 * lOffset;
+
+                        Vector3 lcoord = bbs_[*suIndexIter2]->getChemAtomByIndex(ligandAtomIndex).position();
+
+                        float maxDistance = crosslinks[i].getMaxDistance() + (rOffset + lOffset) * 3.0;
+                        float minDistance = crosslinks[i].getMinDistance();
+
+                        int ind1 = *suIndexIter1 * noOfSUs_ + *suIndexIter2;
+                        DistanceRestraint d1(rcoord, lcoord, maxDistance, minDistance, crosslinks[i].getWeight());
+                        restraintIndsToCrosslinkInds_[ind1].push_back(i);
+                        restraints_[ind1].push_back(d1);
+
+                        int ind2 = *suIndexIter2 * noOfSUs_ + *suIndexIter1;
+                        DistanceRestraint d2(lcoord, rcoord, maxDistance, minDistance, crosslinks[i].getWeight());
+                        restraintIndsToCrosslinkInds_[ind2].push_back(i);
+                        restraints_[ind2].push_back(d2);
+
+                        std::cout << " adding restraint to " << *suIndexIter1 << "x" << *suIndexIter2 << " :"
+                                  << residueSequenceID1 << chainId1 << " : " << residueSequenceID2 << chainId2
+                                  << " dist " << maxDistance << " " << minDistance << " indexes " << ind1 << " : "
+                                  << ind2 << std::endl;
+                    }
+                }
+            }
+        }
+    }
+    return crosslinks.size();
+}
+
+float ComplexDistanceConstraint::getRestraintsRatio(const std::vector<std::shared_ptr<const BB>> &bbs,
+                                                    const std::vector<RigidTrans3> &trans) const {
+    std::set<unsigned int> totalSeenCrosslinks;
+    std::set<unsigned int> satisfiedCrosslinks;
+    for (int suInd1 = 0; suInd1 < (int)bbs.size(); suInd1++) {
+        for (int suInd2 = 0; suInd2 < (int)bbs.size(); suInd2++) {
+            int index1 = bbs[suInd1]->getID();
+            int index2 = bbs[suInd2]->getID();
+            if (index1 == index2)
+                continue;
+            int suPairIndex = index1 * noOfSUs_ + index2;
+            for (unsigned int restraintIndex = 0; restraintIndex < restraints_[suPairIndex].size(); restraintIndex++) {
+                unsigned int crosslinkIndex = restraintIndsToCrosslinkInds_[suPairIndex][restraintIndex];
+                if (satisfiedCrosslinks.find(crosslinkIndex) != satisfiedCrosslinks.end()) {
+                    continue;
+                }
+                totalSeenCrosslinks.insert(crosslinkIndex);
+                if (restraints_[suPairIndex][restraintIndex].isSatisfied(trans[suInd1], trans[suInd2]))
+                    satisfiedCrosslinks.insert(crosslinkIndex);
+            }
+        }
+    }
+    if (totalSeenCrosslinks.size() == 0)
+        return 1.0;
+
+    float satisfiedWeight = 0.0;
+    float totalWeight = 0.0;
+    for (auto it = satisfiedCrosslinks.begin(); it != satisfiedCrosslinks.end(); it++) {
+        satisfiedWeight += crosslinkIndToWeight_[*it];
+    }
+    for (auto it = totalSeenCrosslinks.begin(); it != totalSeenCrosslinks.end(); it++) {
+        totalWeight += crosslinkIndToWeight_[*it];
+    }
+
+    return satisfiedWeight / totalWeight;
+    // return (float)satisfiedCrosslinks.size() / (float)totalSeenCrosslinks.size();
+}

model/CombinatorialAssembler/ComplexDistanceConstraint.h

@@ -0,0 +1,63 @@
+#ifndef DistanceConstraint_H
+#define DistanceConstraint_H
+
+#include <fstream>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include <Molecule.h>
+// #include <DistanceConstraint.h>
+#include <CrossLink.h>
+#include <DistanceRestraint.h>
+
+#include "BB.h"
+
+class ComplexDistanceConstraint {
+  public:
+    ComplexDistanceConstraint(const std::vector<std::shared_ptr<const BB>> &bbs)
+        : bbs_(bbs), noOfSUs_(bbs.size()), constraints_(noOfSUs_ * noOfSUs_), restraints_(noOfSUs_ * noOfSUs_),
+          restraintIndsToCrosslinkInds_(noOfSUs_ * noOfSUs_) {}
+
+    int readRestraintsFile(const std::string fileName);
+    int addChainConnectivityConstraints();
+
+    int numberOfRestraints(int suInd1, int suInd2) const {
+        int ind = suInd1 * noOfSUs_ + suInd2;
+        return restraints_[ind].size();
+    }
+
+    int numberOfConstraints(int suInd1, int suInd2) const {
+        int ind = suInd1 * noOfSUs_ + suInd2;
+        return constraints_[ind].size();
+    }
+
+    // constraints satisfaction: every constraint needs to be satisfied
+    bool areConstraintsSatisfied(int suInd1, int suInd2, RigidTrans3 &trans2) const;
+
+    // restraints satisfaction: a predefined ratio needs to be satisfied
+    float getRestraintsRatio(const std::vector<std::shared_ptr<const BB>> &bbs,
+                             const std::vector<RigidTrans3> &trans) const;
+
+  private:
+    void addConstraint(int suInd1, int suInd2, Vector3 receptorAtom, Vector3 ligandAtom, float maxDistance,
+                       float minDistance = 0);
+
+    void addRestraint(int suInd1, int suInd2, Vector3 receptorAtom, Vector3 ligandAtom, float maxDistance,
+                      float minDistance = 0);
+
+    // find all SUs with residueSequenceID and chains, maxoffset is +/- few residues
+    std::set<int> getSUs(const std::string residueSequenceID, const std::string chains, int maxoffset = 0) const;
+
+  private:
+    const std::vector<std::shared_ptr<const BB>> &bbs_;
+    int noOfSUs_;
+    std::vector<std::vector<DistanceRestraint>> constraints_;
+    std::vector<std::vector<DistanceRestraint>> restraints_;
+    int numberOfConstraints_ = 0;
+    int numberOfRestraints_ = 0;
+    std::vector<std::vector<unsigned int>> restraintIndsToCrosslinkInds_;
+    std::vector<float> crosslinkIndToWeight_;
+};
+
+#endif

model/CombinatorialAssembler/DOCK.conf

@@ -0,0 +1,21 @@
+#Model
+MODEL_BUCKET_SIZE 0.5
+MODEL_QUERY_RADIUS 1.5
+HINGE_BUCKET_SIZE 0.5
+HINGE_QUERY_RADIUS 6.0
+TRIANGLE_SIZE_DIST 2.5
+TRIANGLE_SIZE_DIST_WH 4.0
+PROBABILITY 0.05
+PROBABILITY_WH 0.2
+CLUSTER_RADIUS 4.0
+CLUSTER_RADIUS_WH 1.0
+THRESHOLD 300
+THRESHOLD_WH -100
+GRID_RESOLUTION 0.5
+GRID_MARGINS 5.0
+#TriangleIterator
+TRIANGLE_MAX_SEG_SIZE 12.0
+TRIANGLE_MIN_SEG_SIZE 2.0
+TRIANGLE_SEG_RATIO 4.0
+#Cluster
+CLUSTER_RADIUS_RATIO 3.0

model/CombinatorialAssembler/FoldStep.h

@@ -0,0 +1,34 @@
+#ifndef FOLDSTEP_H
+#define FOLDSTEP_H
+
+#include <algorithm>
+
+class FoldStep {
+  public:
+    // Constructors
+    FoldStep(unsigned int i, unsigned int j, RigidTrans3 trans) : i_(i), j_(j), trans_(trans) {}
+    FoldStep(unsigned int i, unsigned int j) : i_(i), j_(j) {}
+    FoldStep(unsigned int i, unsigned int j, float score) : i_(i), j_(j), tScore_(score) {}
+
+    // bool operator < (const FoldStep& s2) const { return ((i_ < s2.i_) || (i_ == s2.i_ && j_ < s2.j_)); }
+
+    friend bool operator<(const FoldStep &s1, const FoldStep &s2) {
+        unsigned int max1 = std::max(s1.i_, s1.j_);
+        unsigned int max2 = std::max(s2.i_, s2.j_);
+        return (max1 < max2 || (max1 == max2 && std::min(s1.i_, s1.j_) < std::min(s2.i_, s2.j_)));
+    }
+
+    static void outputFoldSteps(std::ostream &out, const std::vector<FoldStep> &foldSteps) {
+        out << "foldSteps:";
+        for (unsigned int i = 0; i < foldSteps.size(); i++) {
+            out << " (" << foldSteps[i].i_ << ", " << foldSteps[i].j_ << ")-" << foldSteps[i].tScore_;
+        }
+    }
+
+  public:
+    unsigned int i_, j_;
+    float tScore_;
+    RigidTrans3 trans_;
+};
+
+#endif /* FOLDSTEP_H */

model/CombinatorialAssembler/HierarchicalFold.cc

@@ -0,0 +1,730 @@
+#include "HierarchicalFold.h"
+
+#include <boost/graph/adjacency_list.hpp>
+#include <boost/graph/connected_components.hpp>
+
+Timer HierarchicalFold::timer_;
+Timer HierarchicalFold::timerAll_;
+unsigned int HierarchicalFold::countResults_(0);
+
+std::vector<std::vector<unsigned int>> createIdentGroups(unsigned int N_, BestKContainer &bestKContainer_) {
+    std::vector<bool> addedToGroup(N_, false);
+    std::vector<std::vector<unsigned int>> identGroups;
+    for (unsigned int i = 0; i < N_; i++) {
+        std::shared_ptr<SuperBB> sbbI = *(bestKContainer_[BitId(i)].begin());
+        const std::shared_ptr<const BB> bbI = sbbI->bbs_[0];
+
+        if (addedToGroup[i])
+            continue;
+        addedToGroup[i] = true;
+        std::vector<unsigned int> identical;
+
+        for (unsigned int j = i + 1; j < N_; j++) {
+            std::cout << "checking ident " << i << " & " << j << std::endl;
+            std::shared_ptr<SuperBB> sbbJ = *(bestKContainer_[BitId(j)].begin());
+
+            const std::shared_ptr<const BB> bbJ = sbbJ->bbs_[0];
+
+            if (bbI->isIdent(*bbJ)) {
+                addedToGroup[j] = true;
+                std::cout << "found ident " << i << " " << j << std::endl;
+                identical.push_back(j);
+            }
+        }
+        if (identical.size() > 0) {
+            identical.insert(identical.begin(), i);
+            identGroups.push_back(identical);
+        }
+    }
+    std::cout << "---- ident groups " << std::endl;
+    for (std::vector<unsigned int> identGroup : identGroups) {
+        std::cout << "ident group: ";
+        for (unsigned int i : identGroup) {
+            std::cout << i << " ";
+        }
+        std::cout << std::endl;
+    }
+
+    return identGroups;
+}
+
+std::map<unsigned int, std::vector<unsigned int>> createAssemblyGroupsMap(unsigned int N_,
+                                                                          BestKContainer &bestKContainer_) {
+    std::map<unsigned int, std::vector<unsigned int>> assemblyGroupsMap;
+    for (unsigned int i = 0; i < N_; i++) {
+        std::shared_ptr<SuperBB> sbbI = *(bestKContainer_[BitId(i)].begin());
+        const std::shared_ptr<const BB> bbI = sbbI->bbs_[0];
+        if (assemblyGroupsMap.count(bbI->groupId()) == 0) {
+            std::vector<unsigned int> newGroup;
+            assemblyGroupsMap[bbI->groupId()] = newGroup;
+        }
+        assemblyGroupsMap[bbI->groupId()].push_back(i);
+    }
+    std::cout << "---- assembly groups " << std::endl;
+    // std::vector<std::vector<unsigned int>> assemblyGroups;
+    for (const auto &[groupId, groupBBIds] : assemblyGroupsMap) {
+        std::cout << "assembly group " << groupId << ":";
+        for (unsigned int i : groupBBIds) {
+            std::cout << i << " ";
+        }
+        std::cout << std::endl;
+        // assemblyGroups.push_back(groupBBIds);
+    }
+    return assemblyGroupsMap;
+}
+
+void printBestK(unsigned int N_, BestK *bestK) {
+    // just for print
+    std::map<unsigned int, unsigned int> count_new_kept_by_bb;
+    std::unordered_map<BitId, unsigned int> count_new_kept_by_resSet;
+    for (unsigned int bit_index = 0; bit_index < N_; bit_index++)
+        count_new_kept_by_bb[bit_index] = 0;
+    for (auto it1 = bestK->begin(); it1 != bestK->end(); it1++) {
+        if (count_new_kept_by_resSet.count((**it1).bitIds()) == 0)
+            count_new_kept_by_resSet[(**it1).bitIds()] = 0;
+        count_new_kept_by_resSet[(**it1).bitIds()] += 1;
+        for (unsigned int bit_index = 0; bit_index < N_; bit_index++)
+            if ((**it1).bitIds().test(bit_index)) {
+                count_new_kept_by_bb[bit_index] += 1;
+            }
+    }
+
+    std::cout << "scores of saved " << bestK->minScore() << ":" << bestK->maxScore() << std::endl;
+    std::cout << "new kept results by chain ";
+    for (const auto &elem : count_new_kept_by_bb)
+        std::cout << elem.first << ":" << elem.second << ", ";
+    std::cout << std::endl << "new kept results by resSet ";
+    for (const auto &elem : count_new_kept_by_resSet)
+        std::cout << elem.first << ":" << elem.second << ", ";
+    std::cout << std::endl;
+}
+
+bool isValidBasedOnAssembly(std::map<unsigned int, std::vector<unsigned int>> assemblyGroupsMap,
+                            BitId currResSet) {
+    if (assemblyGroupsMap.size() <= 1)
+        return true;
+
+    bool seenPartialGroup = false;
+    int numberOfGroups = 0;
+
+    bool seenGroupZero = false;
+
+    for (const auto &[groupId, assemblyGroup] : assemblyGroupsMap) {
+        bool seenZero = false;
+        bool seenOne = false;
+
+        for (unsigned int i = 0; i < assemblyGroup.size(); i++) {
+            if (currResSet.test(assemblyGroup[i]))
+                seenOne = true;
+            else
+                seenZero = true;
+        }
+        if (groupId == 0) {
+            // assembly group 0 is special, this group should not be assembled before joining others
+            // so we never treat it as partial, but it can't be with another partial group
+            if (seenOne)
+                seenGroupZero = true;
+        } else {
+            if (seenOne)
+                numberOfGroups++;
+
+            if (seenZero && seenOne) {
+                seenPartialGroup = true;
+            }
+        }
+    }
+    if (numberOfGroups >= 1 && seenPartialGroup && seenGroupZero)
+        return false;
+
+
+    if (numberOfGroups > 1 && seenPartialGroup)
+        return false;
+
+    return true;
+}
+
+void HierarchicalFold::fold(const std::string &outFileNamePrefix) {
+    std::vector<std::vector<unsigned int>> identGroups = createIdentGroups(N_, bestKContainer_);
+    std::map<unsigned int, std::vector<unsigned int>> assemblyGroupsMap = createAssemblyGroupsMap(N_, bestKContainer_);
+
+    std::map<unsigned int, BestK *> precomputedResults;
+    for (unsigned int i = 2; i <= N_; i++)
+        precomputedResults[i] = new BestK(K_);
+
+    // populate with homomers subunits
+    for (std::vector<unsigned int> identGroup : identGroups) {
+        for (unsigned int groupDivider = 1; (identGroup.size() / groupDivider) >= 5; groupDivider++) {
+        if ((identGroup.size() % groupDivider) != 0)
+            continue;
+        unsigned int groupSize = identGroup.size() / groupDivider;
+        std::vector<std::shared_ptr<SuperBB>> groupSBBs;
+        for (unsigned int j = 0; j < groupSize; j++) {
+            groupSBBs.push_back(*(bestKContainer_[BitId(identGroup[j])].begin()));
+        }
+        std::cout << "searching for size " << groupSBBs.size() << " has " << precomputedResults.count(groupSBBs.size())
+                  << std::endl;
+        createSymmetry(groupSBBs, *precomputedResults[groupSBBs.size()]);
+        }
+    }
+
+    // Hierarchical Assembly
+    for (unsigned int length = 2; length <= N_; length++) { // # subunits iteration
+        std::cout << "*** running iteration " << length
+                  << " prev kept results: " << keptResultsByLength[length - 1]->size() << std::endl;
+        std::unordered_map<BitId, BestK *> best_k_by_id;
+
+        // populate with precomputedResults
+        for (auto it1 = precomputedResults[length]->begin(); it1 != precomputedResults[length]->end(); it1++) {
+            BitId currResSet = (**it1).bitIds();
+            if (best_k_by_id.count(currResSet) == 0)
+                best_k_by_id[currResSet] = new BestK(K_);
+            best_k_by_id[currResSet]->push(*it1);
+        }
+
+        // try to assemble from each pair of kept results that together have (length) subunits
+        for (unsigned int firstResultSize = 1; firstResultSize <= length / 2; firstResultSize++) {
+            unsigned int secondResultSize = length - firstResultSize;
+            std::cout << "** running sub-iteration " << firstResultSize << " " << secondResultSize << std::endl;
+            std::cout << "counters " << countFilterTrasSkipped_ << "/" << countFilterTras_ << std::endl;
+
+            for (auto it1 = keptResultsByLength[firstResultSize]->begin();
+                 it1 != keptResultsByLength[firstResultSize]->end(); it1++) {
+                SuperBB sbb1 = **it1;
+                BitId setA = sbb1.bitIds();
+
+                for (auto it2 = keptResultsByLength[secondResultSize]->begin();
+                     it2 != keptResultsByLength[secondResultSize]->end(); it2++) {
+
+                    if (firstResultSize == secondResultSize &&
+                        std::distance(keptResultsByLength[firstResultSize]->begin(), it1) >
+                            std::distance(keptResultsByLength[secondResultSize]->begin(), it2))
+                        continue; // Since in this case there are 2 identical loops, don't do things twice
+
+                    // If there are identical subunits in both results, rewrite the second result to not have the same
+                    std::shared_ptr<SuperBB> sbb2Pointer = getMatchingSBB(sbb1, **it2, identGroups);
+                    if (sbb2Pointer == NULL)
+                        continue;
+                    SuperBB sbb2 = *sbb2Pointer;
+
+                    // make sure that the two results can be connected
+                    BitId setB = sbb2.bitIds();
+                    if ((setA & setB) != 0)
+                        continue;
+                    BitId currResSet = setA | setB;
+                    if(!isValidBasedOnAssembly(assemblyGroupsMap, currResSet)){
+                        std::cout << "invalid assembly " << currResSet << std::endl;
+                        continue;
+                    }
+
+                    // connect the two results and add all new combined results to best_k_by_id[currResSet]
+                    if (best_k_by_id.count(currResSet) == 0)
+                        best_k_by_id[currResSet] = new BestK(K_);
+
+                    unsigned int resCountBefore = best_k_by_id[currResSet]->size();
+                    float minScoreBefore = best_k_by_id[currResSet]->minScore();
+
+                    std::promise<int> promise1;
+                    this->tryToConnect(1, sbb1, sbb2, *best_k_by_id[currResSet], (length < N_), promise1, identGroups);
+
+                    if (resCountBefore < best_k_by_id[currResSet]->size() ||
+                        minScoreBefore != best_k_by_id[currResSet]->minScore())
+                        std::cout << "found more for " << currResSet << " based on " << setA << " and " << setB
+                                  << " before: " << resCountBefore << " after: " << best_k_by_id[currResSet]->size()
+                                  << " scores " << best_k_by_id[currResSet]->minScore() << ":"
+                                  << best_k_by_id[currResSet]->maxScore() << std::endl;
+                }
+            }
+        }
+
+        // cluster results and save them
+        std::map<unsigned int, BestK *> bestForSubunitId;
+        keptResultsByLength[length] = new BestK(K_);
+
+        for (const auto &[currResSet, currBestK] : best_k_by_id) {
+            if (currBestK->size() > 0) {
+                BestK *clusteredBestK = bestKContainer_.newBestK(currResSet);
+                currBestK->cluster(*clusteredBestK, 1.0, identGroups);
+
+                std::cerr << "clustering resSet " << currResSet << " before: " << currBestK->size() << " after "
+                          << bestKContainer_[currResSet].size() << " scores " << bestKContainer_[currResSet].minScore()
+                          << ":" << bestKContainer_[currResSet].maxScore() << std::endl;
+
+                for (unsigned int i = 0; i < N_; i++) {
+                    if (currResSet.test(i)) {
+                        if (bestForSubunitId.count(i) == 0) {
+                            bestForSubunitId[i] = new BestK(1);
+                        }
+                        bestForSubunitId[i]->push(*clusteredBestK->rbegin());
+                    }
+                }
+
+                unsigned int count = 0;
+                for (auto it1 = bestKContainer_[currResSet].rbegin(); it1 != bestKContainer_[currResSet].rend(); it1++) {
+                    keptResultsByLength[length]->push(*it1);
+                    count += 1;
+                    if (count >= maxResultPerResSet)
+                        break;
+                }
+            }
+            delete currBestK;
+        }
+
+        // save best from each subunit
+        keptResultsByLength[length]->setK(K_ + bestForSubunitId.size());
+        for (const auto &[subunitId, currBestK] : bestForSubunitId) {
+            keptResultsByLength[length]->push(*currBestK->rbegin());
+            delete currBestK;
+        }
+
+        printBestK(N_, keptResultsByLength[length]);
+    }
+
+    // output fully assembled results or largest subsets
+    if (keptResultsByLength[N_]->size() != 0) {
+        std::string outFileName = outFileNamePrefix + ".res";
+        std::ofstream outFile(outFileName);
+        std::ofstream outFileClustered(outFileNamePrefix + "_clustered.res");
+        BestK clusteredBestK(finalSizeLimit_); // TODO: this should also change on the best_k_by_id level
+
+        for (auto it = keptResultsByLength[N_]->rbegin(); it != keptResultsByLength[N_]->rend(); it++)
+            (*it)->fullReport(outFile);
+        // output after clustering
+        keptResultsByLength[N_]->cluster(clusteredBestK, 5.0, identGroups);
+        for (auto it = clusteredBestK.rbegin(); it != clusteredBestK.rend(); it++)
+            (*it)->fullReport(outFileClustered);
+        outFile.close();
+        outFileClustered.close();
+    } else {
+        // output largest subsets
+        for (unsigned int i = N_; i > 1; i--) {
+            if (keptResultsByLength[i]->size() == 0)
+                continue;
+            std::string outFileName = "cb_" + std::to_string(i) + "_" + outFileNamePrefix + ".res";
+            std::ofstream outFile(outFileName);
+            for (auto it = keptResultsByLength[i]->rbegin(); it != keptResultsByLength[i]->rend(); it++)
+                (*it)->fullReport(outFile);
+            outFile.close();
+            break;
+        }
+    }
+
+    // cleanup
+    for (const auto &[length, currBestK] : precomputedResults) {
+        delete currBestK;
+    }
+    for (const auto &[length, currBestK] : keptResultsByLength) {
+        delete currBestK;
+    }
+}
+
+void HierarchicalFold::tryToConnect(int id, const SuperBB &sbb1, const SuperBB &sbb2, BestK &results, bool toAdd,
+                                    std::promise<int> &output, std::vector<std::vector<unsigned int>> &identGroups) {
+    // iterate over pairs of BBs os SuperBB1 and SuperBB2
+    for (int i = 0; i < (int)sbb1.bbs_.size(); i++) {
+        int firstBB = sbb1.bbs_[i]->getID();
+        for (int j = 0; j < (int)sbb2.bbs_.size(); j++) {
+            int secondBB = sbb2.bbs_[j]->getID();
+
+            // loop over possible transformations between BBs
+            for (TransIterator2 it(sbb1, sbb2, firstBB, secondBB); !it.isAtEnd(); it++) {
+                // optimization - check that the score is not lower than the minimum in the current bestK
+                if((it.getScore() + sbb1.transScore_ + sbb2.transScore_) < results.minScore()){
+                    continue;
+                }
+
+                // discard any invalid transformations
+                bool filtered = filterTrans(sbb1, sbb2, it.transformation());
+                if (filtered)
+                    continue;
+
+                FoldStep step(firstBB, secondBB, it.getScore());
+                std::shared_ptr<SuperBB> theNew = createJoined(sbb1, sbb2, it.transformation(), 0, step, it.getScore());
+
+                if (theNew->getRestraintsRatio() < restraintsRatioThreshold_) {
+                    //            std::cout << "not enough restraints " << theNew->getRestraintsRatio() << " : " <<
+                    //            complexConst_.getDistanceRestraintsRatioThreshold();
+                    continue;
+                }
+
+                // results.push(theNew);
+                results.push_cluster(theNew, 1, identGroups);
+            }
+        }
+    }
+    output.set_value(1);
+}
+
+bool HierarchicalFold::filterTrans(const SuperBB &sbb1, const SuperBB &sbb2, const RigidTrans3 &trans) const {
+
+    // check distance constraints & restraints
+    for (unsigned int i = 0; i < sbb1.size_; i++) {
+        const BB &bb1 = *sbb1.bbs_[i];
+        RigidTrans3 t = (!sbb1.trans_[i]) * trans;
+        for (unsigned int j = 0; j < sbb2.size_; j++) {
+            const BB &bb2 = *sbb2.bbs_[j];
+            RigidTrans3 t2 = t * sbb2.trans_[j];
+            // check constraints first
+            if (!complexConst_.areConstraintsSatisfied(bb1.getID(), bb2.getID(), t2))
+                return true;
+        }
+    }
+
+    // backbone penetrations for each pair of BBs
+    for (unsigned int i = 0; i < sbb1.size_; i++) {
+        const BB &bb1 = *sbb1.bbs_[i];
+        RigidTrans3 t = (!sbb1.trans_[i]) * trans;
+
+        for (unsigned int j = 0; j < sbb2.size_; j++) {
+            const BB &bb2 = *sbb2.bbs_[j];
+            RigidTrans3 t2 = t * sbb2.trans_[j];
+
+            const BB *pBB1 = &bb1, *pBB2 = &bb2;
+            if (bb2.getSurfaceSize() > bb1.getSurfaceSize()) {
+                pBB1 = &bb2;
+                pBB2 = &bb1;
+                t2 = !t2;
+            }
+
+            countFilterTras_ = countFilterTras_ + 1;
+
+            // optimization - check if radiuses are too far apart and if so, skip check
+            if ((pBB1->getRadius() + pBB2->getRadius()) < (pBB1->getCM() - t2*pBB2->getCM()).norm()) {
+                countFilterTrasSkipped_ = countFilterTrasSkipped_ + 1;
+                continue;
+            }
+
+            unsigned int bbPenetrations = 0;
+            unsigned int totalUsedAtoms = 0;
+
+            // TODO: maybe should save Weighted bbPen using pBB1->grid_->getDist(v) as weight
+            for (Molecule<Atom>::const_iterator it = pBB2->caAtoms_.begin(); it != pBB2->caAtoms_.end(); it++) {
+                if (it->getTempFactor() < minTemperatureToConsiderCollision) {
+                    continue;
+                }
+                totalUsedAtoms++;
+
+                Vector3 v = t2 * it->position();
+                if (pBB1->getDistFromSurface(v) < 0) {
+                    // getResidueEntry(v) when used in BBGrid.h will return -1*res_index if res_index is backbone
+                    if (pBB1->grid_->getResidueEntry(v) < 0 && pBB1->grid_->getDist(v) < penetrationThreshold_) {
+                        int resEntry = pBB1->grid_->getResidueEntry(v) * -1;
+                        if (pBB1->getAtomByResId(resEntry).getTempFactor() < minTemperatureToConsiderCollision)
+                            continue;
+
+                        bbPenetrations++;
+                    }
+                }
+            }
+            float bbPenChangePercent = (float)(bbPenetrations) / (float)totalUsedAtoms;
+            if (bbPenChangePercent > maxBackboneCollisionPercentPerChain) {
+                return true;
+            }
+        }
+    }
+
+    return false;
+}
+
+void HierarchicalFold::createSymmetry(std::vector<std::shared_ptr<SuperBB>> identBBs, BestK &results) {
+    unsigned int transCount = 0;
+    std::cout << "started trans check, bb_size:" << identBBs.size() << std::endl;
+    for (TransIterator2 it(*identBBs[0], *identBBs[1], identBBs[0]->bbs_[0]->getID(), identBBs[1]->bbs_[0]->getID());
+         !it.isAtEnd(); it++)
+        transCount++;
+
+    std::cout << "number of transformations:" << transCount << std::endl;
+    unsigned int addedSymCount = 0;
+    for (unsigned int transNum = 0; transNum < transCount; transNum++) {
+        std::cout << "checking trans indexed" << transNum << std::endl;
+        // create symSBB for a trans, this is cumbersome because I don't really know how to handle transformations
+        std::shared_ptr<SuperBB> symSBB = identBBs[0];
+        for (unsigned int i = 1; i < identBBs.size(); i++) {
+            unsigned int count = -1;
+
+            // There is a memory issue here, I create TransIterator2 with symSBB as bb1, but then I override it
+            // and freeing the memory(?) of bb1_, so it is important to break after chanigng symSBB
+            for (TransIterator2 it(*symSBB, *identBBs[i], symSBB->bbs_[i - 1]->getID(), identBBs[i]->bbs_[0]->getID());
+                 !it.isAtEnd(); it++) {
+                count++;
+                if (count != transNum)
+                    continue;
+                float transScore = it.getScore() + it.getScore() * ((100 - it.getScore()) / 100);
+
+                FoldStep step(symSBB->bbs_[i - 1]->getID(), identBBs[i]->bbs_[0]->getID(), transScore);
+                std::cout << "adding trans " << it.transformation() << " **** " << it.getScore() << std::endl;
+                symSBB = createJoined(*symSBB, *identBBs[i], it.transformation(), 0, step, transScore);
+                break;
+            }
+        }
+        std::cout << "created possibly symSBB" << std::endl;
+
+        // check bb penetration between each 2 chains
+        double maxPenetration = 0;
+        bool shouldContinuePen = false;
+        for (unsigned int i = 0; i < symSBB->size_; i++) {
+            const BB &bb1 = *symSBB->bbs_[i];
+            RigidTrans3 t1 = (!symSBB->trans_[i]);
+            for (unsigned int j = i + 1; j < symSBB->size_; j++) {
+                const BB &bb2 = *symSBB->bbs_[j];
+                RigidTrans3 t2 = t1 * symSBB->trans_[j];
+
+                const BB *pBB1 = &bb1, *pBB2 = &bb2;
+                unsigned int totalUsedAtoms = 0;
+                unsigned int bbPenetrations = 0;
+
+                for (Molecule<Atom>::const_iterator it = pBB2->caAtoms_.begin(); it != pBB2->caAtoms_.end(); it++) {
+                    if (it->getTempFactor() < minTemperatureToConsiderCollision) {
+                        continue;
+                    }
+                    totalUsedAtoms++;
+
+                    Vector3 v = t2 * it->position();
+                    if (pBB1->getDistFromSurface(v) < 0) {
+                        // getResidueEntry(v) when used in BBGrid.h will return -1*res_index if res_index is backbone
+                        if (pBB1->grid_->getResidueEntry(v) < 0 && pBB1->grid_->getDist(v) < -1.0) {
+                            int resEntry = pBB1->grid_->getResidueEntry(v) * -1;
+                            if (pBB1->getAtomByResId(resEntry).getTempFactor() < minTemperatureToConsiderCollision)
+                                continue;
+                            bbPenetrations++;
+                        }
+                    }
+                }
+
+                if ((bbPenetrations / (1.0 * totalUsedAtoms)) > 0.2) {
+                    std::cout << "dropping " << identBBs.size() << " because penetration "
+                              << bbPenetrations / (1.0 * totalUsedAtoms) << std::endl;
+                    shouldContinuePen = true;
+                    break;
+                }
+
+                maxPenetration = std::max(maxPenetration, bbPenetrations / (1.0 * totalUsedAtoms));
+            }
+            if (shouldContinuePen)
+                break;
+        }
+        if (shouldContinuePen)
+            continue;
+        std::cout << "checked penetrations ratio max: " << maxPenetration << std::endl;
+        // if above some TH (for everything, not per chain) (20%) - drop
+
+        // if last and first centers are the farthest - drop
+        std::vector<Vector3> centroids;
+        for (unsigned int i = 0; i < symSBB->size_; i++) {
+            centroids.push_back(symSBB->trans_[i] * symSBB->bbs_[i]->getCM());
+        }
+        std::cout << "centroids distance " << (centroids[0] - centroids[1]).norm2() << " : "
+                  << (centroids[0] - centroids.back()).norm2() << std::endl;
+
+        float allowedDistFactor = 1.5 + (symSBB->size_ - 3) * 0.25;
+        if ((centroids[0] - centroids[1]).norm2() * allowedDistFactor < (centroids[0] - centroids.back()).norm2()) {
+            std::cout << "dropping " << identBBs.size() << " because centroids distance "
+                      << (centroids[0] - centroids[1]).norm2() << " : " << (centroids[0] - centroids.back()).norm2()
+                      << std::endl;
+            continue;
+        }
+
+        // verify that centroids are first all increasing distance from first centroid and then all decreasing distance
+        // from first centroid
+        bool increasing = true;
+        bool shouldContinue = false;
+        for (unsigned int i = 1; i < centroids.size(); i++) {
+            if (increasing) {
+                if ((centroids[i] - centroids[0]).norm2() < (centroids[i - 1] - centroids[0]).norm2()) {
+                    increasing = false;
+                }
+            } else {
+                if ((centroids[i] - centroids[0]).norm2() > (centroids[i - 1] - centroids[0]).norm2()) {
+                    std::cout << "dropping " << identBBs.size() << " because centroids not increasing and decreasing"
+                              << std::endl;
+                    shouldContinue = true;
+                    break;
+                }
+            }
+        }
+        if (shouldContinue)
+            continue;
+        if (increasing) {
+            std::cout << "dropping " << identBBs.size() << " because centroids only increasing " << std::endl;
+            continue;
+        }
+
+        std::cout << "added with score " << symSBB->weightedTransScore_ << std::endl;
+        results.push(symSBB);
+        addedSymCount++;
+    }
+
+    BitId groupIdentifier;
+    for (unsigned int i = 0; i < identBBs.size(); i++) {
+        groupIdentifier |= identBBs[i]->bbs_[0]->bitId();
+    }
+    std::cout << "Created " << addedSymCount << " Symmetrical for " << groupIdentifier << std::endl;
+}
+
+// utils
+std::shared_ptr<SuperBB> HierarchicalFold::createJoined(const SuperBB &sbb1, const SuperBB &sbb2, RigidTrans3 &trans,
+                                                        int bbPen, FoldStep &step, float transScore) const {
+    std::shared_ptr<SuperBB> theNew = std::make_shared<SuperBB>(sbb1);
+    theNew->join(trans, sbb2, bbPen, step, transScore);
+    theNew->setRestraintsRatio(complexConst_.getRestraintsRatio(theNew->bbs_, theNew->trans_));
+    return theNew;
+}
+
+std::shared_ptr<SuperBB> HierarchicalFold::getMatchingSBB(SuperBB sbb1, SuperBB sbb2,
+                                                          std::vector<std::vector<unsigned int>> &identGroups) {
+    /*
+    This function recieves two SuperBBs and checks if they have common BBs that are a part of the same ident group.
+    If so, it checks wether the total amount of BBs from the same ident group is smaller than the size of the ident 
+    group. If so, It return a new SuperBB based on sbb2, but with the BBs from the ident group that are not in sbb1.
+    
+    It also validates that in both sbb1&sbb2, the BBs from the ident group are the smallest BBs in the ident group (This
+    prevents duplications of results). If they are not valid - returns NULL.
+    */
+    std::map<unsigned int, unsigned int> bbIdToNewId;
+    for (std::vector<unsigned int> identGroup : identGroups) {
+        // verify sbb1 is valid (mostly needed to ignore initial structures of BBs that are not first in group) 
+        bool flag = false;
+        int maxIdInSbb1 = -1;
+        for (unsigned int i = 0; i < identGroup.size(); i++) {
+            if (!sbb1.bitIds().test(identGroup[i])) // ident_group[i] not in currResSet
+                flag = true;
+            else if (flag) {
+                if (sbb1.bbs_.size() != 1)
+                    std::cout << "sbb1 not valid " << sbb1.bitIds() << ":" << sbb2.bitIds() << std::endl;
+                return NULL;
+            } else {
+                maxIdInSbb1 = i;
+            }
+        }
+
+        // compute mapping from sbb2 bb ids to new bb ids
+        int maxIdInSbb2 = -1;
+        flag = false;
+        for (unsigned int i = 0; i < identGroup.size(); i++) {
+            if (!sbb2.bitIds().test(identGroup[i])) // ident_group[i] not in currResSet
+                flag = true;
+            else if (flag) {
+                if (sbb2.bbs_.size() != 1)
+                    std::cout << "sbb2 not valid " << sbb1.bitIds() << ":" << sbb2.bitIds() << std::endl;
+                return NULL;
+            } else {
+                maxIdInSbb2 = i;
+            }
+        }
+
+        if (maxIdInSbb1 == -1 || maxIdInSbb2 == -1)
+            continue;
+
+        // check if there are more copies in sbb1 and sbb2 than the size of the ident group
+        if ((maxIdInSbb1 + 1) + (maxIdInSbb2 + 1) > identGroup.size()) { 
+            return NULL;
+        }
+
+        for (unsigned int i = 0; i < maxIdInSbb2 + 1; i++) {
+            bbIdToNewId[identGroup[i]] = identGroup[i + maxIdInSbb1 + 1];
+        }
+    }
+
+    // create new SuperBB with new ids
+    if (bbIdToNewId.size() == 0)
+        return std::make_shared<SuperBB>(sbb2);
+
+    // std::cout << "converting " << sbb1.bitIds() << ":" << sbb2.bitIds() << " with " << bbIdToNewId.size() <<
+    // std::endl;
+    std::shared_ptr<SuperBB> newSbb = std::make_shared<SuperBB>(sbb2);
+
+    for (auto iter = bbIdToNewId.rbegin(); iter != bbIdToNewId.rend(); ++iter) {
+        unsigned int oldId = iter->first;
+        unsigned int newId = iter->second;
+        newSbb->replaceIdentBB(BitId(oldId), (*(bestKContainer_[BitId(newId)].begin()))->bbs_[0]);
+    }
+
+    return newSbb;
+}
+
+void HierarchicalFold::checkConnectivity() const {
+    typedef boost::adjacency_list<boost::vecS,        // edge list
+                                  boost::vecS,        // vertex list
+                                  boost::undirectedS, // directedness
+                                  float>              // property associated with vertices
+        Graph;
+
+    Graph g(N_);
+    for (unsigned int suIndex = 0; suIndex < N_; suIndex++) {
+        BitId index = BitId(suIndex);
+        std::cerr << "isEmpty " << suIndex << " " << bestKContainer_.isEmpty(index) << std::endl;
+        std::cerr << "SBB " << suIndex << " size " << bestKContainer_[index].size() << std::endl;
+        if (bestKContainer_[index].size() >= 1) {
+            std::shared_ptr<SuperBB> sbb = *(bestKContainer_[index].rbegin());
+            std::shared_ptr<const BB> bb = sbb->bbs_[0];
+
+            for (unsigned int suIndex2 = 0; suIndex2 < N_; suIndex2++) {
+                unsigned int transSize = bb->getTransformations(suIndex2).size();
+                std::cerr << suIndex << " " << suIndex2 << " trans size " << transSize << std::endl;
+                if (transSize > 0)
+                    boost::add_edge(suIndex, suIndex2, g);
+                std::cerr << "done add_edge" << std::endl;
+            }
+        }
+    }
+
+    std::vector<int> component(boost::num_vertices(g));
+    size_t num_components = boost::connected_components(g, &component[0]);
+    std::cerr << "Num of components " << num_components << std::endl;
+    if (num_components != 1) {
+        for (size_t i = 0; i < boost::num_vertices(g); ++i)
+            std::cerr << "SU " << i << " component " << component[i] << std::endl;
+        std::cerr << "Not enough transformations between subunits, there should be one connected component!"
+                  << std::endl;
+        exit(1);
+    }
+}
+
+void HierarchicalFold::outputConnectivityGraph(std::string outFileName) const {
+    std::ofstream outFile(outFileName);
+    outFile << "SU1 Prot1 size1 SU2 Prot2 size2 Restraints" << std::endl;
+    for (unsigned int suIndex = 0; suIndex < N_; suIndex++) {
+        BitId set = BitId(suIndex);
+        std::cerr << "SBB " << suIndex << " set " << set << " isEmpty " << bestKContainer_.isEmpty(set) << std::endl;
+        std::cerr << "SBB " << suIndex << " size " << bestKContainer_[set].size() << std::endl;
+        if (bestKContainer_[set].size() >= 1) {
+            std::shared_ptr<SuperBB> sbb = *(bestKContainer_[set].rbegin());
+            std::shared_ptr<const BB> bb = sbb->bbs_[0];
+
+            for (unsigned int suIndex2 = suIndex + 1; suIndex2 < N_; suIndex2++) {
+                unsigned int transSize = bb->getTransformations(suIndex2).size();
+                BitId set2 = BitId(suIndex2);
+                std::cerr << suIndex << " " << suIndex2 << " trans size " << transSize << " " << set2 << std::endl;
+                std::shared_ptr<SuperBB> sbb2 = *(bestKContainer_[set2].rbegin());
+                std::shared_ptr<const BB> bb2 = sbb2->bbs_[0];
+
+                if (transSize > 0) {
+                    std::vector<std::string> results1, results2;
+                    std::string PDBFileName1 = bb->getPDBFileName();
+                    boost::split(results1, PDBFileName1, [](char c) { return c == '_'; });
+                    std::string PDBFileName2 = bb2->getPDBFileName();
+                    boost::split(results2, PDBFileName2, [](char c) { return c == '_'; });
+
+                    unsigned int xlinkNumber = complexConst_.numberOfRestraints(suIndex, suIndex2);
+                    unsigned int connectivityConstraintsNumber = complexConst_.numberOfConstraints(suIndex, suIndex2);
+
+                    if (xlinkNumber > 0) {
+                        outFile << bb->getPDBFileName() << " " << results1[0] << " " << bb->backBone_.size() / 4 << " ";
+                        outFile << bb2->getPDBFileName() << " " << results2[0] << " " << bb2->backBone_.size() / 4
+                                << " ";
+                        outFile << complexConst_.numberOfRestraints(suIndex, suIndex2) << std::endl;
+                    }
+                    if (connectivityConstraintsNumber > 0) {
+                        outFile << bb->getPDBFileName() << " " << results1[0] << " " << bb->backBone_.size() / 4 << " ";
+                        outFile << bb2->getPDBFileName() << " " << results2[0] << " " << bb2->backBone_.size() / 4
+                                << " ";
+                        outFile << complexConst_.numberOfConstraints(suIndex, suIndex2) << std::endl;
+                    }
+                    /*outFile << bb->getPDBFileName() << " "
+                            << complexConst_.numberOfRestraints(suIndex, suIndex2) << " "
+                            << bb2->getPDBFileName() << std::endl;*/
+                }
+            }
+        }
+    }
+    outFile.close();
+}

model/CombinatorialAssembler/HierarchicalFold.h

@@ -0,0 +1,86 @@
+#ifndef HIERARCHICALFOLD_H
+#define HIERARCHICALFOLD_H
+
+#include "BestK.h"
+#include "BestKContainer.h"
+#include "ComplexDistanceConstraint.h"
+#include "BBContainer.h"
+#include <future>
+#include <memory>
+
+// TODO: should this class just be a namespace? because each function is called once...
+class HierarchicalFold {
+  public:
+    // N - number of subunits, k - best solutions to save at each step
+    HierarchicalFold(BBContainer& bbContainer, unsigned int k, unsigned int maxResultPerResSet,
+                     float minTemperatureToConsiderCollision, float maxBackboneCollisionPercentPerChain,
+                     float penetrationThreshold, float restraintsRatio)
+        : countFilterTras_(0), countFilterTrasSkipped_(0), N_(bbContainer.getBBs().size()), K_(k),
+          maxResultPerResSet(maxResultPerResSet), minTemperatureToConsiderCollision(minTemperatureToConsiderCollision),
+          maxBackboneCollisionPercentPerChain(maxBackboneCollisionPercentPerChain),
+          restraintsRatioThreshold_(restraintsRatio), penetrationThreshold_(penetrationThreshold),
+          finalSizeLimit_(k * N_), bestKContainer_(k), complexConst_(bbContainer.getBBs()) {
+
+        // initialize keptResultsByLength and bestKContainer_
+        keptResultsByLength[1] = new BestK(N_);
+        for (unsigned int i = 0; i < bbContainer.getBBsNumber(); i++) {
+            std::shared_ptr<SuperBB> sbb = std::make_shared<SuperBB>(bbContainer.getBB(i));
+
+            keptResultsByLength[1]->push(sbb);
+            BitId set = BitId(i);
+            BestK *cb = bestKContainer_.newBestK(set);
+            cb->push(sbb);
+        }
+    }
+    
+
+    void fold(const std::string &outFileNamePrefix);
+
+    void tryToConnect(int id, const SuperBB &sbb1, const SuperBB &sbb2, BestK &results, bool toAdd,
+                      std::promise<int> &output, std::vector<std::vector<unsigned int>> &identGroups);
+    
+    bool filterTrans(const SuperBB &sbb1, const SuperBB &sbb2, const RigidTrans3 &trans) const;
+
+    void createSymmetry(std::vector<std::shared_ptr<SuperBB>> identBBs, BestK &results);
+
+    // utils
+    std::shared_ptr<SuperBB> createJoined(const SuperBB &sbb1, const SuperBB &sbb2, RigidTrans3 &trans, int bbPen,
+                                          FoldStep &step, float transScore) const;
+
+    std::shared_ptr<SuperBB> getMatchingSBB(SuperBB sbb1, SuperBB sbb2,
+                                            std::vector<std::vector<unsigned int>> &identGroups);
+
+    void readConstraints(const std::string fileName) {
+        complexConst_.readRestraintsFile(fileName);
+        complexConst_.addChainConnectivityConstraints();
+    }
+
+    void checkConnectivity() const;
+
+    void outputConnectivityGraph(std::string outFileName = "graph.sif") const;
+
+    // members
+    static Timer timer_, timerAll_;
+    static unsigned int countResults_;
+
+
+    mutable unsigned int countFilterTras_;
+    mutable unsigned int countFilterTrasSkipped_;
+
+  private:
+    const unsigned int N_;                 // number of subunits
+    const unsigned int K_;                 // number of solutions to save at each stage
+    const unsigned int maxResultPerResSet; // number of solutions to save for each resSet
+    const float minTemperatureToConsiderCollision;
+    const float maxBackboneCollisionPercentPerChain;
+    const float restraintsRatioThreshold_;
+
+    float penetrationThreshold_; // this is ignored for now
+
+    int finalSizeLimit_;
+    BestKContainer bestKContainer_;
+    std::map<unsigned int, BestK *> keptResultsByLength;
+    ComplexDistanceConstraint complexConst_;
+};
+
+#endif /* HIERARCHICALFOLD_H */

model/CombinatorialAssembler/MainCombDock.cc

@@ -0,0 +1,140 @@
+#include "BBContainer.h"
+#include "HierarchicalFold.h"
+
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <stdio.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <vector>
+// #include <memory>
+
+#include <boost/program_options.hpp>
+namespace po = boost::program_options;
+
+// #include <gperftools/profiler.h>
+
+int main(int argc, char *argv[]) {
+    // output arguments
+    for (int i = 0; i < argc; i++)
+        std::cout << argv[i] << " ";
+    std::cout << std::endl;
+
+    // input parsing
+    double penetrationThr;
+    float maxBackboneCollisionPerChain;
+    float minTemperatureToConsiderCollision;
+    unsigned int maxResultPerResSet;
+
+    std::string outFileNamePrefix;
+    double restraintsRatio;
+    double clusterRMSD;
+
+    // positional
+    std::string suFileName;
+    std::string transFilesPrefix;
+    int transNumToRead;
+    int bestK;
+    std::string constraintsFileName;
+
+    po::options_description desc("Usage: <subunitsFileList> <transFilesPrefix> \
+<transNumToRead> <bestKeachStep> <constraintsFile>");
+
+    // optional
+    desc.add_options()("help,h", "Combinatoral Assembly help")("version", "CombFold 1.0 2022")(
+        "penetrationThr,p", po::value<double>(&penetrationThr)->default_value(-1.0),
+        "maximum allowed penetration between subunit surfaces (default = -1.0)")(
+        "restraintsRatio,r", po::value<double>(&restraintsRatio)->default_value(0.1),
+        "constraints ratio (default = 0.1)")("clusterRMSD,c", po::value<double>(&clusterRMSD)->default_value(5.0),
+                                             "final clustering RMSD (default = 5.0)")
+
+        ("maxBackboneCollisionPerChain,b", po::value<float>(&maxBackboneCollisionPerChain)->default_value(0.1),
+         "Max percentage(0 to 1) of backbone atoms of a chain that can collide with another chain(default=0.1)")(
+            "minTemperatureToConsiderCollision,t",
+            po::value<float>(&minTemperatureToConsiderCollision)->default_value(0),
+            "Minimal Bfactor required for atom to be considered when calculating collisions(default=0)")(
+            "maxResultPerResSet,j", po::value<unsigned int>(&maxResultPerResSet)->default_value(0),
+            "number of results saved for each calculated combination of subunits (default=k)")
+
+            ("outputFileNamePrefix,o", po::value<std::string>(&outFileNamePrefix)->default_value("output"),
+             "output file name, default name output.res");
+
+    // required options: currently 5
+    po::options_description hidden("Hidden options");
+    hidden.add_options()("SUlist", po::value<std::string>(&suFileName)->required(), "SU list file name")(
+        "transFilesPrefix", po::value<std::string>(&transFilesPrefix)->required(),
+        "Trans files prefix")("transNumToRead", po::value<int>(&transNumToRead)->required(),
+                              "# of tranformations")("bestK", po::value<int>(&bestK)->required(), "bestK")(
+        "constraintsFile", po::value<std::string>(&constraintsFileName)->required(), "constraints file name");
+
+    po::options_description cmdline_options;
+    cmdline_options.add(desc).add(hidden);
+
+    po::positional_options_description p;
+    p.add("SUlist", 1);
+    p.add("transFilesPrefix", 1);
+    p.add("transNumToRead", 1);
+    p.add("bestK", 1);
+    p.add("constraintsFile", 1);
+
+    po::variables_map vm;
+
+    try {
+        po::store(po::command_line_parser(argc, argv).options(cmdline_options).positional(p).run(), vm);
+
+        if (vm.count("help")) {
+            std::cout << desc << "\n";
+            return 0;
+        }
+        po::notify(vm);
+    } catch (po::required_option &e) {
+        std::cout << desc << "\n";
+        return 0;
+    } catch (po::error &e) {
+        std::cout << desc << "\n";
+        return 0;
+    }
+
+    if (maxResultPerResSet == 0)
+        maxResultPerResSet = bestK;
+
+    // done parsing
+
+    auto start = std::chrono::high_resolution_clock::now();
+    HierarchicalFold::timerAll_.reset();
+
+    std::cerr << "Before process input" << std::endl;
+    std::string argv_str(argv[0]);
+    std::string base = argv_str.substr(0, argv_str.find_last_of("/"));
+    std::string chemLibFileName = base + "/chem_params.txt";
+    BBContainer bbContainer(suFileName, chemLibFileName, minTemperatureToConsiderCollision);
+    bbContainer.readTransformationFiles(transFilesPrefix, transNumToRead);
+
+    std::cout << "Starting HierarchicalFold" << std::endl;
+    HierarchicalFold hierarchalFold(bbContainer, bestK, maxResultPerResSet, minTemperatureToConsiderCollision,
+                                    maxBackboneCollisionPerChain, penetrationThr, restraintsRatio);
+
+    // read constraints
+    hierarchalFold.readConstraints(constraintsFileName);
+
+    HierarchicalFold::timer_.reset();
+
+    hierarchalFold.outputConnectivityGraph("graph.txt");
+    hierarchalFold.checkConnectivity();
+    //    ProfilerStart("nameOfProfile.log");
+    auto startBeforeFold = std::chrono::high_resolution_clock::now();
+    hierarchalFold.fold(outFileNamePrefix);
+    //    ProfilerStop();
+    auto end = std::chrono::high_resolution_clock::now();
+    std::chrono::duration<double> diff = end - start;
+    std::chrono::duration<double> diffFold = end - startBeforeFold;
+    std::cout << "Overall time " << diff.count() << " s\n";
+    std::cout << "only fold time " << diffFold.count() << " s\n";
+    std::cerr << "countResults_ " << HierarchicalFold::countResults_ << std::endl;
+    std::cerr << "timer_ " << HierarchicalFold::timer_ << std::endl;
+    std::cerr << "timerAll_ " << HierarchicalFold::timerAll_ << std::endl;
+    // SuperBB::reportCounters();
+
+    return 0;
+}

model/CombinatorialAssembler/Makefile

@@ -0,0 +1,42 @@
+BOOST_INCLUDE = /opt/homebrew/include
+BOOST_LIB = /opt/homebrew/lib/
+
+CC=g++
+# use -Wno-deprecated-declarations to suppress warnings from boost
+# CFLAGS=-c -Wall -I./libs_gamb -I./libs_DockingLib -I$(BOOST_INCLUDE) -O2 --std=c++11 # -fexpensive-optimizations -ffast-math
+CFLAGS=-c -Wall -Wno-deprecated-declarations -I./libs_gamb -I./libs_DockingLib -I$(BOOST_INCLUDE) -g -O2 --std=c++17 # -fexpensive-optimizations -ffast-math
+# CFLAGS=-c -Wall -I./libs_gamb -I./libs_DockingLib -I$(BOOST_INCLUDE) -O0 -g --std=c++11 # -fexpensive-optimizations -ffast-math
+
+SOURCES_MAIN = $(wildcard *.cc)
+SOURCES_GAMB = $(wildcard libs_gamb/*.cc)
+SOURCES_DOCKLIB = $(wildcard libs_DockingLib/*.cc)
+SOURCES_AF2TRANS = $(wildcard AF2trans/*.cc)
+
+OBJECTS_MAIN = $(SOURCES_MAIN:.cc=.o)
+OBJECTS_GAMB = $(SOURCES_GAMB:.cc=.o)
+OBJECTS_DOCKLIB = $(SOURCES_DOCKLIB:.cc=.o)
+OBJECTS_AF2TRANS = $(SOURCES_AF2TRANS:.cc=.o)
+
+all: MainCombAssemble MainAf2trans
+
+MainCombAssemble: libgamb.a libdocklib.a $(OBJECTS_MAIN)
+	$(CC) $(OBJECTS_MAIN) -L. -L$(BOOST_LIB) -lgamb -ldocklib -lboost_program_options -lpthread -o CombinatorialAssembler.out 
+
+MainAf2trans: libgamb.a libdocklib.a $(OBJECTS_AF2TRANS)
+	$(CC) $(OBJECTS_AF2TRANS) -L. -L$(BOOST_LIB) -lgamb -ldocklib -lboost_program_options -lpthread -o AF2trans.out 
+
+%.o: %.cc
+	$(CC) $(CFLAGS) $< -o $@
+
+libgamb.a: $(OBJECTS_GAMB)
+	ar rcs libgamb.a $(OBJECTS_GAMB)
+
+libdocklib.a: $(OBJECTS_DOCKLIB) libgamb.a
+	ar rcs libdocklib.a $(OBJECTS_DOCKLIB) $(OBJECTS_GAMB)
+
+clean_all:
+	rm -f *.o *.a AF2trans.out CombinatorialAssembler.out AF2trans/*.o libs_gamb/*.o libs_DockingLib/*.o
+
+clean:
+	rm -f *.o AF2trans/*.o AF2trans.out CombinatorialAssembler.out
+

model/CombinatorialAssembler/SuperBB.cc

@@ -0,0 +1,315 @@
+#include "SuperBB.h"
+#include "HierarchicalFold.h"
+
+
+SuperBB::SuperBB(std::shared_ptr<const BB> bb)
+    : backBonePen_(0), transScore_(0), weightedTransScore_(100) {
+    bbs_.push_back(bb);
+    Vector3 v(0, 0, 0);
+    Matrix3 M(1);
+    RigidTrans3 T(M, v);
+    trans_.push_back(T);
+    size_ = 1;
+    bitIDS_ = bb->bitId();
+}
+
+float getWeightedTransScore(std::vector<FoldStep> steps, std::vector<std::shared_ptr<const BB>> bbs) {
+    unsigned int totalCa = 0;
+    float totalScore = 0;
+    std::map<unsigned int, unsigned int> bbIdToCaLength;
+    for (std::shared_ptr<const BB> bb : bbs) {
+        bbIdToCaLength[bb->getID()] = bb->getNumOfAtoms();
+    }
+
+    for (FoldStep step : steps) {
+        std::vector<unsigned int> right;
+        std::vector<unsigned int> left;
+
+        right.push_back(step.i_);
+        left.push_back(step.j_);
+
+        std::vector<FoldStep> notUsedSteps(steps);
+
+        while (!notUsedSteps.empty()) {
+            FoldStep step2 = notUsedSteps.back();
+            notUsedSteps.pop_back();
+            if (step2.i_ == step.i_ && step2.j_ == step.j_)
+                continue;
+            if (std::find(right.begin(), right.end(), step2.i_) != right.end() &&
+                std::find(right.begin(), right.end(), step2.j_) == right.end()) {
+                right.push_back(step2.j_);
+            } else if (std::find(right.begin(), right.end(), step2.j_) != right.end() &&
+                       std::find(right.begin(), right.end(), step2.i_) == right.end()) {
+                right.push_back(step2.i_);
+            } else if (std::find(left.begin(), left.end(), step2.i_) != left.end() &&
+                       std::find(left.begin(), left.end(), step2.j_) == left.end()) {
+                left.push_back(step2.j_);
+            } else if (std::find(left.begin(), left.end(), step2.j_) != left.end() &&
+                       std::find(left.begin(), left.end(), step2.i_) == left.end()) {
+                left.push_back(step2.i_);
+            } else {
+                notUsedSteps.insert(notUsedSteps.begin(), step2);
+            }
+        }
+
+        unsigned int rightSize = 0;
+        unsigned int leftSize = 0;
+
+        for (unsigned int elem : right)
+            rightSize += bbIdToCaLength[elem];
+
+        for (unsigned int elem : left)
+            leftSize += bbIdToCaLength[elem];
+
+        unsigned int usedSize = rightSize;
+        if (rightSize > leftSize)
+            usedSize = leftSize;
+
+        totalScore += usedSize * step.tScore_;
+        totalCa += usedSize;
+    }
+    return totalScore / totalCa;
+}
+
+void SuperBB::join(const RigidTrans3 &trans, const SuperBB &other, int bbPen, FoldStep &step, float transScore) {
+    // now joining is simple
+    for (unsigned int j = 0; j < other.size_; j++) {
+        bbs_.push_back(other.bbs_[j]);
+        trans_.push_back(trans * other.trans_[j]);
+    }
+    size_ += other.size_;
+    bitIDS_ |= other.bitIDS_;
+    backBonePen_ = bbPen;
+
+    transScore_ += other.transScore_ + transScore;
+
+    if (!other.foldSteps_.empty()) {
+        foldSteps_.insert(foldSteps_.end(), other.foldSteps_.begin(), other.foldSteps_.end());
+    }
+    foldSteps_.push_back(step);
+
+    weightedTransScore_ = getWeightedTransScore(foldSteps_, bbs_);
+}
+
+void SuperBB::replaceIdentBB(BitId oldBBBitId, std::shared_ptr<const BB> bb) {
+    if((bb->bitId() & bitIDS_) != 0)
+        throw std::runtime_error("Tried to replace BB with BB that already exists in SuperBB");
+
+    std::shared_ptr<const BB> oldBB;
+    unsigned int bbIndex = -1;
+    for (unsigned int i = 0; i < size_; i++) {
+        if (bbs_[i]->bitId() == oldBBBitId) {
+            oldBB = bbs_[i];
+            bbIndex = i;
+            break;
+        }
+    }
+    if(bbIndex == -1)
+        throw std::runtime_error("SuperBB::replaceIdentBB: oldBBBitId not found in SuperBB");
+
+    bbs_[bbIndex] = bb;
+    // bitIDS_ -= oldBB->bitId();
+    // bitIDS_ += bb->bitId();
+    bitIDS_[oldBB->getID()] = false;
+    bitIDS_[bb->getID()] = true;
+
+    for(FoldStep &step : foldSteps_) {
+        if(step.i_ == oldBB->getID())
+            step.i_ = bb->getID();
+        if(step.j_ == oldBB->getID())
+            step.j_ = bb->getID();
+    }
+}
+
+bool SuperBB::isPenetrating(const RigidTrans3 &trans, const SuperBB &other, float threshold) const {
+    for (unsigned int i = 0; i < size_; i++) {
+        RigidTrans3 t = (!trans_[i]) * trans;
+        for (unsigned int j = 0; j < other.size_; j++) {
+            if (bbs_[i]->isPenetrating(t * other.trans_[j], *other.bbs_[j], threshold))
+                return true;
+        }
+    }
+    return false;
+}
+
+// RMSD between two SBBs (assuming same BBs in each SBB)
+double SuperBB::calcRmsd(const SuperBB &other, std::vector<std::vector<unsigned int>> &identGroups) const {
+    std::vector<std::vector<unsigned int>> presentIdentGroups;
+
+    for (std::vector<unsigned int> identGroup : identGroups) {
+        std::vector<unsigned int> possiblyRelevantIdentGroup;
+        for (unsigned int i : identGroup) {
+            if (bitIDS_.test(i))
+                possiblyRelevantIdentGroup.push_back(i);
+        }
+        if (possiblyRelevantIdentGroup.size() >= 2)
+            presentIdentGroups.push_back(possiblyRelevantIdentGroup);
+    }
+
+    std::map<unsigned int, unsigned int> bbIdToThisBBIndex;
+    std::map<unsigned int, unsigned int> bbIdToOtherBBIndex;
+    std::vector<unsigned int> bbIdsInThis;
+    for (unsigned int i = 0; i < bbs_.size(); i++) {
+        bbIdsInThis.push_back(bbs_[i]->getID());
+        bbIdToThisBBIndex[bbs_[i]->getID()] = i;
+        for (unsigned int j = 0; j < size_; j++) {
+            if (bbs_[i]->getID() == other.bbs_[j]->getID()) { // same BB
+                bbIdToOtherBBIndex[bbs_[i]->getID()] = j;
+                break;
+            }
+        }
+    }
+
+    // base rmsd find
+    Match cmMatch;
+    Molecule<Vector3> cmA, cmB;
+
+    for (unsigned int bbId : bbIdsInThis) {
+        Vector3 a = trans_[bbIdToThisBBIndex[bbId]] * bbs_[bbIdToThisBBIndex[bbId]]->cm_;
+        cmA.add(a);
+        Vector3 b = other.trans_[bbIdToOtherBBIndex[bbId]] * other.bbs_[bbIdToOtherBBIndex[bbId]]->cm_;
+        cmB.add(b);
+    }
+    for (unsigned int i = 0; i < size_; i++) {
+        cmMatch.add(i, i);
+    }
+    cmMatch.calculateBestFit(cmA, cmB);
+    float foundRMSD = cmMatch.rmsd();
+
+    int MAX_ITER = 10;
+    // try replacing chains with each other
+    for (int i = 0; i < MAX_ITER; i++) {
+        // std::cout << "iter " << i << std::endl;
+        bool somethingChanged = false;
+        for (std::vector<unsigned int> identGroup : presentIdentGroups) {
+            for (unsigned int i = 0; i < identGroup.size(); i++) {
+                for (unsigned int j = i + 1; j < identGroup.size(); j++) {
+                    Match cmMatch;
+                    Molecule<Vector3> cmA, cmB;
+
+                    for (unsigned int bbId : bbIdsInThis) {
+                        Vector3 a;
+                        if (bbId == identGroup[i]) {
+                            unsigned int replacedbbId = identGroup[j];
+                            a = trans_[bbIdToThisBBIndex[replacedbbId]] * bbs_[bbIdToThisBBIndex[replacedbbId]]->cm_;
+                        } else if (bbId == identGroup[j]) {
+                            unsigned int replacedbbId = identGroup[i];
+                            a = trans_[bbIdToThisBBIndex[replacedbbId]] * bbs_[bbIdToThisBBIndex[replacedbbId]]->cm_;
+                        } else {
+                            a = trans_[bbIdToThisBBIndex[bbId]] * bbs_[bbIdToThisBBIndex[bbId]]->cm_;
+                        }
+                        cmA.add(a);
+                        Vector3 b =
+                            other.trans_[bbIdToOtherBBIndex[bbId]] * other.bbs_[bbIdToOtherBBIndex[bbId]]->cm_;
+                        cmB.add(b);
+                    }
+                    for (unsigned int i = 0; i < size_; i++) {
+                        cmMatch.add(i, i);
+                    }
+                    cmMatch.calculateBestFit(cmA, cmB);
+                    float newRMSD = cmMatch.rmsd();
+                    if (newRMSD < foundRMSD) {
+                        // std::cout << "replacing chains in calcRMSD " << newRMSD << " " << foundRMSD << " " <<
+                        // identGroup[i] << " " << identGroup[j] << " " << bbIdToThisBBIndex[identGroup[i]] << " " <<
+                        // bbIdToThisBBIndex[identGroup[j]] << std::endl;
+                        unsigned int tmp = bbIdToThisBBIndex[identGroup[i]];
+                        bbIdToThisBBIndex[identGroup[i]] = bbIdToThisBBIndex[identGroup[j]];
+                        bbIdToThisBBIndex[identGroup[j]] = tmp;
+                        foundRMSD = newRMSD;
+                        somethingChanged = true;
+                    } else {
+                        // std::cout << "not replacing chains in calcRMSD " << newRMSD << " " << foundRMSD << " " <<
+                        // identGroup[i] << " " << identGroup[j] << std::endl;
+                    }
+                }
+            }
+        }
+        if (!somethingChanged)
+            break;
+        if (i == MAX_ITER - 1)
+            std::cout << "stops clustering because max iteration " << bitIDS_ << std::endl;
+    }
+
+    if (foundRMSD > 1.5)
+        return foundRMSD;
+
+    Match match;
+    Molecule<Atom> A, B;
+    for (unsigned int bbId : bbIdsInThis) {
+        Molecule<Atom> molA = bbs_[bbIdToThisBBIndex[bbId]]->caAtoms_;
+        molA.rigidTrans(trans_[bbIdToThisBBIndex[bbId]]);
+        A.concat(molA);
+
+        Molecule<Atom> molB = other.bbs_[bbIdToOtherBBIndex[bbId]]->caAtoms_;
+        molB.rigidTrans(other.trans_[bbIdToOtherBBIndex[bbId]]);
+        B.concat(molB);
+    }
+
+    for (unsigned int i = 0; i < A.size(); i++) {
+        match.add(i, i);
+    }
+    match.calculateBestFit(A, B);
+    return match.rmsd();
+}
+
+double SuperBB::calcRmsd(const SuperBB &other) const {
+    std::vector<std::vector<unsigned int>> emptyIdentGroups;
+    return calcRmsd(other, emptyIdentGroups);
+}
+
+void SuperBB::fullReport(std::ostream &s) {
+    HierarchicalFold::countResults_++;
+    RigidTrans3 tr;
+    s << "size_ " << size_ << " transScore_ " << transScore_ << " multPen_ " << multPen_ << " singlePen_ " 
+      << singlePen_ << " diffPen " << singlePen_ - multPen_ << " backBonePen_ " << backBonePen_ << " maxPen_ " 
+      << maxPen_ << " restraintsRatio_ " << restraintsRatio_ << " weightedTransScore " << weightedTransScore_;
+    s << " [";
+    int i = 0;
+    for (auto it = bbs_.begin(); it != bbs_.end(); it++, i++) {
+        s << (*it)->id_ << "(" << trans_[i] << ")";
+        if (it + 1 != bbs_.end())
+            s << ",";
+    }
+    s << "]  " << tr;
+    FoldStep::outputFoldSteps(s, foldSteps_);
+    s << std::endl;
+}
+
+std::ostream &operator<<(std::ostream &s, const SuperBB &sbb) {
+    // scores
+    s << "size_ " << sbb.size_ << " backBonePen_ " << sbb.backBonePen_ << " restraintsRatio_ " << sbb.restraintsRatio_;
+
+    // transformations
+    s << " [";
+    int i = 0;
+    for (auto it = sbb.bbs_.begin(); it != sbb.bbs_.end(); it++, i++) {
+        s << (*it)->getID() << "(" << sbb.trans_[i] << ")";
+        if (it + 1 != sbb.bbs_.end())
+            s << ",";
+    }
+    s << "]  ";
+
+    FoldStep::outputFoldSteps(s, sbb.foldSteps_);
+    s << std::endl;
+    return s;
+}
+
+TransIterator2::TransIterator2(const SuperBB &bb1, const SuperBB &bb2, int pbb1, int pbb2)
+    : bb1_(bb1), bb2_(bb2), index1_(0), index2_(0) {
+
+    std::shared_ptr<const BB> b1 = bb1_.bbs_[index1_];
+    while (b1->getID() != pbb1) {
+        b1 = bb1_.bbs_[++index1_];
+    }
+    std::shared_ptr<const BB> b2 = bb2_.bbs_[index2_];
+    while (b2->getID() != pbb2) {
+        b2 = bb2_.bbs_[++index2_];
+    }
+
+    mediatorTrans_ = !bb2_.trans_[index2_];
+    trans_ = &(b1->getTransformations(b2->getID())); // BB::trans(*b1, *b2);
+    it_ = trans_->begin();
+    if (!isAtEnd()) {
+        generateTransformation();
+    }
+}

model/CombinatorialAssembler/SuperBB.h

@@ -0,0 +1,91 @@
+/**
+ * This class represents a SuperBB - A subcomplex composed by multiple subunits (saved in bbs_) and in certain
+ * transformations (saved in trans_)
+ */
+#ifndef SUPERBB_H
+#define SUPERBB_H
+
+#include "BB.h"
+#include "FoldStep.h"
+
+class SuperBB {
+  public:
+    friend class BestK;
+    friend class HierarchicalFold;
+    friend class TransIterator2;
+
+    SuperBB(std::shared_ptr<const BB> bb);
+
+    BitId bitIds() const { return bitIDS_; }
+    unsigned int size() const { return size_; }
+    float getRestraintsRatio() const { return restraintsRatio_; }
+    void setRestraintsRatio(float r) { restraintsRatio_ = r; }
+
+    // This function takes Two super BBs and joins them using a transformation between to BBs
+    void join(const RigidTrans3 &trans, const SuperBB &other, int bbPen, FoldStep &step, float transScore);
+    void replaceIdentBB(BitId oldBBBitId, std::shared_ptr<const BB> bb);
+
+    // This function checks for collissions - Receives transformation and a second super BB and decides if
+    // they collide
+    bool isPenetrating(const RigidTrans3 &trans, const SuperBB &other, float threshold) const;
+    double calcRmsd(const SuperBB &other, std::vector<std::vector<unsigned int>> &identGroups) const;
+    double calcRmsd(const SuperBB &other) const;
+
+    void fullReport(std::ostream &s);
+    friend std::ostream &operator<<(std::ostream &s, const SuperBB &sbb);
+
+  private:
+    // members
+    unsigned int size_;
+    std::vector<FoldStep> foldSteps_; // FoldStep is a transformation between two SUs
+    BitId bitIDS_;
+    float restraintsRatio_;
+
+  public: // TODO: Make private
+    // BBs that make up the SuperBB
+    std::vector<std::shared_ptr<const BB>> bbs_;
+    // Holds the transformations of the BBs
+    std::vector<RigidTrans3> trans_;
+
+    int backBonePen_;
+    float maxPen_;
+    float transScore_;
+    float weightedTransScore_;
+    int multPen_;
+    int singlePen_;
+};
+
+class TransIterator2 {
+  public:
+    TransIterator2(const SuperBB &sbb1, const SuperBB &sbb2, int pbb1, int pbb2);
+
+    RigidTrans3 &transformation() { return transformation_; }
+
+    float getScore() { return (*it_)->score_.totalScore_; }
+
+    void generateTransformation() { transformation_ = bb1_.trans_[index1_] * (*it_)->refFrame_ * mediatorTrans_; }
+
+    TransIterator2 &operator++(int) {
+        while (!isAtEnd()) {
+            it_++;
+            if (it_ == trans_->end()) {
+                return *this;
+            }
+            generateTransformation();
+            return *this;
+        }
+        return *this;
+    }
+
+    bool isAtEnd() { return it_ == trans_->end(); }
+
+  private:
+    const SuperBB &bb1_, &bb2_;
+    unsigned int index1_, index2_;
+    const std::vector<std::shared_ptr<TransformationAndScore>> *trans_;
+    std::vector<std::shared_ptr<TransformationAndScore>>::const_iterator it_;
+    RigidTrans3 mediatorTrans_;
+    RigidTrans3 transformation_;
+};
+
+#endif /* SUPERBB_H */

model/CombinatorialAssembler/TransformationAndScore.cc

@@ -0,0 +1,11 @@
+#include "TransformationAndScore.h"
+
+template <>
+void TransformationAndScore_T<Score>::outputTrans(std::vector<TransformationAndScore_T<Score> *> &transformations) {
+    int count = 0;
+    for (std::vector<TransformationAndScore *>::iterator it = transformations.begin(); it != transformations.end();
+         it++) {
+        count++;
+        std::cout << count << ": " << **it << std::endl;
+    }
+}

model/CombinatorialAssembler/TransformationAndScore.h

@@ -0,0 +1,64 @@
+#ifndef TRANSFORMATIONANDSCORE_H
+#define TRANSFORMATIONANDSCORE_H
+
+#include <RigidTrans3.h>
+#include <vector>
+
+#define NO_OF_RANGES 8
+typedef struct pointsAndSurface_t {
+    int count_;
+    float surface_;
+} pointsAndSurface;
+
+template <class SCORE_T> class TransformationAndScore_T {
+  public:
+    const RigidTrans3 &trans() { return refFrame_; }
+    float score() { return score_.totalScore_; }
+
+    RigidTrans3 refFrame_;
+    SCORE_T score_;
+    float dist_; // for debug
+    static void outputTrans(std::vector<TransformationAndScore_T *> &transformations);
+};
+
+template <class SCORE_T> std::ostream &operator<<(std::ostream &s, const TransformationAndScore_T<SCORE_T> &ts) {
+    return s << ts.refFrame_ << " " << ts.score_ << " , " << ts.dist_ << " , " << ((ts.dist_ == 0) ? 1 : 0);
+}
+
+template <class SCORE_T> std::istream &operator>>(std::istream &s, TransformationAndScore_T<SCORE_T> &ts) {
+    char c;
+    return s >> c >> ts.score_ >> c >> c >> ts.refFrame_ >> c >> c >> ts.dist_;
+}
+
+class Score {
+  public:
+    Score() { init(); }
+
+    void init() {
+        totalScore_ = 0;
+        resCount1_ = resCount2_ = 0;
+        interfaceSurface_ = maxPenetrate_ = s_ = c_ = e_ = 0.0;
+        for (int i = 0; i < NO_OF_RANGES; i++) {
+            ps_[i].count_ = 0;
+            ps_[i].surface_ = 0;
+        }
+    }
+
+    float totalScore_;
+    pointsAndSurface ps_[NO_OF_RANGES];
+    int resCount1_;
+    int resCount2_;
+    float interfaceSurface_;
+    float maxPenetrate_;
+    float s_, c_, e_;
+    Score *referenceScore_;
+
+    friend std::ostream &operator<<(std::ostream &s, const Score &score) { return s << score.totalScore_; }
+
+    friend std::istream &operator>>(std::istream &s, Score &ts);
+};
+
+// #define CLUSTER_DEBUG
+typedef TransformationAndScore_T<Score> TransformationAndScore;
+
+#endif

model/CombinatorialAssembler/chem_params.txt

@@ -0,0 +1,412 @@
+ALA  N    1.83  -0.15  1
+ALA  CA   2.265  0.10  2
+ALA  CB   2.165  0.00  6
+ALA  C    1.87   0.60  3
+ALA  O    1.55  -0.55  4
+ALA  OXT  1.48  -0.57  9
+ALA  OT2  1.48  -0.57  9
+ARG  N    1.83  -0.15  1
+ARG  CA   2.265  0.10  2
+ARG  CB   2.235  0.00  6
+ARG  CG   2.235  0.00 16
+ARG  CD   2.235  0.10 12
+ARG  NE   1.83  -0.10 12
+ARG  CZ   1.87   0.50 10
+ARG  NH1  1.83   0.25 10
+ARG  NH2  1.83   0.25 10
+ARG  C    1.87   0.60  3
+ARG  O    1.55  -0.55  4
+ARG  OXT  1.48  -0.57  9
+ARG  OT2  1.48  -0.57  9
+ARGN N    1.83  -0.15  1
+ARGN CA   2.265  0.10  2
+ARGN CB   2.235  0.00  6
+ARGN CG   2.235  0.00 16
+ARGN CD   2.235  0.10 12
+ARGN NE   1.83  -0.10 12
+ARGN CZ   1.87  -0.20 11
+ARGN NH1  1.83   0.10 11
+ARGN NH2  1.83   0.10 11
+ARGN C    1.87   0.60  3
+ARGN O    1.55  -0.55  4
+ARGN OXT  1.48  -0.57  9
+ARGN OT2  1.48  -0.57  9
+ASN  N    1.83  -0.15  1
+ASN  CA   2.265  0.10  2
+ASN  CB   2.265  0.00  6
+ASN  CG   1.87   0.55 11
+ASN  OD1  1.55  -0.55 11
+ASN  ND2  1.83   0.00 11
+ASN  C    1.87   0.60  3
+ASN  O    1.55  -0.55  4
+ASN  OXT  1.48  -0.57  9
+ASN  OT2  1.48  -0.57  9
+ASP  N    1.83  -0.15  1
+ASP  CA   2.265  0.10  2
+ASP  CB   2.235  0.00  6
+ASP  CG   1.87   0.14  9
+ASP  OD1  1.66  -0.57  9
+ASP  OD2  1.66  -0.57  9
+ASP  C    1.87   0.60  3
+ASP  O    1.55  -0.55  4
+ASP  OXT  1.48  -0.57  9
+ASP  OT2  1.48  -0.57  9
+ASPH N    1.83  -0.15  1
+ASPH CA   2.265  0.10  2
+ASPH CB   2.235  0.00  6
+ASPH CG   1.87   0.70 11
+ASPH OD1  1.36  -0.35 11
+ASPH OD2  1.55  -0.35 11
+ASPH C    1.87   0.60  3
+ASPH O    1.55  -0.55  4
+ASPH OXT  1.48  -0.57  9
+ASPH OT2  1.48  -0.57  9
+CYS  N    1.83  -0.15  1
+CYS  CA   2.265  0.10  2
+CYS  CB   2.235  0.19  6
+CYS  SG   1.89  -0.19 18
+CYS  C    1.87   0.60  3
+CYS  O    1.55  -0.55  4
+CYS  OXT  1.48  -0.57  9
+CYS  OT2  1.48  -0.57  9
+GLN  N    1.83  -0.15  1
+GLN  CA   2.265  0.10  2
+GLN  CB   2.235  0.00  6
+GLN  CG   2.235  0.00 16
+GLN  CD   1.87   0.55 11
+GLN  OE1  1.55  -0.55 11
+GLN  NE2  1.83   0.00 11
+GLN  C    1.87   0.60  3
+GLN  O    1.55  -0.55  4
+GLN  OXT  1.48  -0.57  9
+GLN  OT2  1.48  -0.57  9
+GLU  N    1.83  -0.15  1
+GLU  CA   2.265  0.10  2
+GLU  CB   2.235  0.00  6
+GLU  CG   2.235  0.00 16
+GLU  CD   1.87   0.14  9
+GLU  OE1  1.66  -0.57  9
+GLU  OE2  1.66  -0.57  9
+GLU  C    1.87   0.60  3
+GLU  O    1.55  -0.55  4
+GLU  OXT  1.48  -0.57  9
+GLU  OT2  1.48  -0.57  9
+GLUH N    1.83  -0.15  1
+GLUH CA   2.265  0.10  2
+GLUH CB   2.235  0.00  6
+GLUH CG   2.235  0.00 16
+GLUH CD   1.87   0.70 11
+GLUH OE1  1.36  -0.35 11
+GLUH OE2  1.55  -0.35 11
+GLUH C    1.87   0.60  3
+GLUH O    1.55  -0.55  4
+GLUH OXT  1.48  -0.57  9
+GLUH OT2  1.48  -0.57  9
+GLY  N    1.83  -0.15  1
+GLY  CA   2.235  0.10  5
+GLY  C    1.87   0.60  3
+GLY  O    1.55  -0.55  4
+GLY  OXT  1.48  -0.57  9
+GLY  OT2  1.48  -0.57  9
+HIS  N    1.83  -0.15  1
+HIS  CA   2.265  0.10  2
+HIS  CB   2.235  0.00  6
+HIS  CG   2.04   0.10 14
+HIS  ND1  1.72  -0.10 14
+HIS  CD2  2.10   0.10 14
+HIS  NE2  1.72  -0.40 14
+HIS  CE1  2.10   0.30 14
+HIS  C    1.87   0.60  3
+HIS  O    1.55  -0.55  4
+HIS  OXT  1.48  -0.57  9
+HIS  OT2  1.48  -0.57  9
+ILE  N    1.83  -0.15  1
+ILE  CA   2.265  0.10  2
+ILE  CB   2.265  0.00  6
+ILE  CG2  2.165  0.00 17
+ILE  CG1  2.235  0.00 16
+ILE  CD   2.165  0.00 17
+ILE  CD1  2.165  0.00 17
+ILE  C    1.87   0.60  3
+ILE  O    1.55  -0.55  4
+ILE  OXT  1.48  -0.57  9
+ILE  OT2  1.48  -0.57  9
+LEU  N    1.83  -0.15  1
+LEU  CA   2.265  0.10  2
+LEU  CB   2.235  0.00  6
+LEU  CG   2.265  0.00 16
+LEU  CD1  2.165  0.00 17
+LEU  CD2  2.165  0.00 17
+LEU  C    1.87   0.60  3
+LEU  O    1.55  -0.55  4
+LEU  OXT  1.48  -0.57  9
+LEU  OT1  1.48  -0.57  9
+LEU  OT2  1.48  -0.57  9
+LYS  N    1.83  -0.15  1
+LYS  CA   2.265  0.10  2
+LYS  CB   2.235  0.00  6
+LYS  CG   2.235  0.00 16
+LYS  CD   2.235  0.00  8
+LYS  CE   2.235  0.25  7
+LYS  NZ   1.65   0.75  7
+LYS  C    1.87   0.60  3
+LYS  O    1.55  -0.55  4
+LYS  OXT  1.48  -0.57  9
+LYS  OT2  1.48  -0.57  9
+LYSN N    1.83  -0.15  1
+LYSN CA   2.265  0.10  2
+LYSN CB   2.235  0.00  6
+LYSN CG   2.235  0.00 16
+LYSN CD   2.235  0.00  8
+LYSN CE   2.235  0.00 11
+LYSN NZ   1.65   0.00  7
+LYSN C    1.87   0.60  3
+LYSN O    1.55  -0.55  4
+LYSN OXT  1.48  -0.57  9
+LYSN OT2  1.48  -0.57  9
+MET  N    1.83  -0.15  1
+MET  CA   2.265  0.10  2
+MET  CB   2.235  0.00  6
+MET  CG   2.235  0.06 16
+MET  SD   1.97  -0.12 16
+MET  CE   2.165  0.06 17
+MET  C    1.87   0.60  3
+MET  O    1.55  -0.55  4
+MET  OXT  1.48  -0.57  9
+MET  OT2  1.48  -0.57  9
+PHE  N    1.83  -0.15  1
+PHE  CA   2.265  0.10  2
+PHE  CB   2.235  0.00  6
+PHE  CG   2.04   0.00 16
+PHE  CD1  1.99   0.00 16
+PHE  CD2  1.99   0.00 16
+PHE  CE1  1.99   0.00 16
+PHE  CE2  1.99   0.00 16
+PHE  CZ   1.99   0.00 16
+PHE  C    1.87   0.60  3
+PHE  O    1.55  -0.55  4
+PHE  OXT  1.48  -0.57  9
+PHE  OT2  1.48  -0.57  9
+PRO  N    1.83  -0.25  1
+PRO  CD   2.235  0.10  6
+PRO  CA   2.265  0.10  2
+PRO  CB   2.235  0.00  6
+PRO  CG   2.235  0.00  6
+PRO  C    1.87   0.60  3
+PRO  O    1.55  -0.55  4
+PRO  OXT  1.48  -0.57  9
+PRO  OT2  1.48  -0.57  9
+PRO  OD   1.55  -0.25 13
+5HP  N    1.83  -0.25  1
+5HP  CD   2.235  0.10  6
+5HP  CA   2.265  0.10  2
+5HP  CB   2.235  0.00  6
+5HP  CG   2.235  0.00  6
+5HP  C    1.87   0.60  3
+5HP  O    1.55  -0.55  4
+5HP  OD   1.55  -0.25 13
+5HP  OXT  1.48  -0.57  9
+5HP  OT2  1.48  -0.57  9
+SER  N    1.83  -0.15  1
+SER  CA   2.265  0.10  2
+SER  CB   2.235  0.25 13
+SER  OG   1.55  -0.25 13
+SER  C    1.87   0.60  3
+SER  O    1.55  -0.55  4
+SER  OXT  1.48  -0.57  9
+SER  OT2  1.48  -0.57  9
+THR  N    1.83  -0.15  1
+THR  CA   2.265  0.10  2
+THR  CB   2.265  0.25  6
+THR  OG1  1.55  -0.25 13
+THR  CG2  2.165  0.00 16
+THR  C    1.87   0.60  3
+THR  O    1.55  -0.55  4
+THR  OXT  1.48  -0.57  9
+THR  OT2  1.48  -0.57  9
+TRP  N    1.83  -0.15  1
+TRP  CA   2.265  0.10  2
+TRP  CB   2.235  0.00  6
+TRP  CG   2.04  -0.03 16
+TRP  CD2  2.04   0.10 16
+TRP  CE2  2.04  -0.04 16
+TRP  CE3  1.99  -0.03 16
+TRP  CD1  2.10   0.06 16
+TRP  NE1  1.72  -0.06 14
+TRP  CZ2  1.99   0.00 16
+TRP  CZ3  1.99   0.00 16
+TRP  CH2  1.99   0.00 16
+TRP  C    1.87   0.60  3
+TRP  O    1.55  -0.55  4
+TRP  OXT  1.48  -0.57  9
+TRP  OT2  1.48  -0.57  9
+TYR  N    1.83  -0.15  1
+TYR  CA   2.265  0.10  2
+TYR  CB   2.235  0.00  6
+TYR  CG   2.04   0.00 16
+TYR  CD1  1.99   0.00 16
+TYR  CE1  1.99   0.00 15
+TYR  CD2  1.99   0.00 16
+TYR  CE2  1.99   0.00 15
+TYR  CZ   2.04   0.25 15
+TYR  OH   1.55  -0.25 13
+TYR  C    1.87   0.60  3
+TYR  O    1.55  -0.55  4
+TYR  OXT  1.48  -0.57  9
+TYR  OT2  1.48  -0.57  9
+VAL  N    1.83  -0.15  1
+VAL  CA   2.265  0.10  2
+VAL  CB   2.265  0.00  6
+VAL  CG1  2.165  0.00 17
+VAL  CG2  2.165  0.00 17
+VAL  C    1.87   0.60  3
+VAL  O    1.55  -0.55  4
+VAL  OXT  1.48  -0.57  9
+VAL  OT2  1.48  -0.57  9
+HSC  N    1.83  -0.15  1
+HSC  CA   2.265  0.10  2
+HSC  CB   2.235  0.10  6
+HSC  CG   2.04   0.15 14
+HSC  CD2  1.87   0.20 14
+HSC  ND1  1.54   0.05 10
+HSC  CE1  1.87   0.45 14
+HSC  NE2  1.54   0.05 10
+HSC  C    1.87   0.60  3
+HSC  O    1.55  -0.55  4
+HSC  OXT  1.48  -0.57  9
+HSC  OT2  1.48  -0.57  9
+HSD  N    1.83  -0.15  1
+HSD  CA   2.265  0.10  2
+HSD  CB   2.235  0.00  6
+HSD  CG   2.04   0.10 14
+HSD  ND1  1.54  -0.40 14
+HSD  CE1  1.87   0.30 14
+HSD  CD2  1.87   0.10 14
+HSD  NE2  1.54  -0.10 14
+HSD  C    1.87   0.60  3
+HSD  O    1.55  -0.55  4
+HSD  OXT  1.48  -0.57  9
+HSD  OT2  1.48  -0.57  9
+HEM  FE   2.13   0.24 10
+HEM  E    2.13   0.24 10
+HEM  NA   1.54  -0.18 14
+HEM  NB   1.54  -0.18 14
+HEM  NC   1.54  -0.18 14
+HEM  ND   1.54  -0.18 14
+HEM  C1A  1.87   0.03  3
+HEM  CHA  2.265  0.04  2
+HEM  C4D  1.87   0.02  3
+HEM  C1B  1.87   0.03  3
+HEM  CHB  2.265  0.04  2
+HEM  C4A  1.87   0.02  3
+HEM  C1C  1.87   0.03  3
+HEM  CHC  2.265  0.04  2
+HEM  C4B  1.87   0.02  3
+HEM  C1D  1.87   0.03  3
+HEM  CHD  2.265  0.04  2
+HEM  C4C  1.87   0.02  3
+HEM  C2A  1.87  -0.02  3
+HEM  CAA  2.235  0.04  6
+HEM  C3A  1.87   0.02  3
+HEM  CMA  2.235 -0.04 17
+HEM  CBA  2.235 -0.10  6
+HEM  CGA  1.87   0.30  9
+HEM  O1A  1.48  -0.50  9
+HEM  O2A  1.48  -0.50  9
+HEM  C2B  1.87   0.02  3
+HEM  CMB  2.235 -0.04 17
+HEM  C3B  1.87  -0.05  3
+HEM  CAB  2.265  0.03  2
+HEM  CBB  2.235 -0.10  6
+HEM  C2C  1.87   0.02  3
+HEM  CMC  2.235 -0.04 17
+HEM  C3C  1.87  -0.05  3
+HEM  CAC  2.265  0.03  2
+HEM  CBC  2.235 -0.10  6
+HEM  C2D  1.87   0.02  3
+HEM  CMD  2.235 -0.04 17
+HEM  C3D  1.87  -0.02  3
+HEM  CAD  2.235  0.04  6
+HEM  CBD  2.235 -0.10  6
+HEM  CGD  1.87   0.30  9
+HEM  O1D  1.48  -0.50  9
+HEM  O2D  1.48  -0.50  9
+TML  CH1  2.235  0.00 17
+TML  CH2  2.235  0.00 17
+TML  CH3  2.235  0.00 17
+SO4  S    1.76   0.53  9
+SO4  O1   1.48  -0.62  9
+SO4  O2   1.48  -0.62  9
+SO4  O3   1.48  -0.62  9
+SO4  O4   1.48  -0.62  9
+GDP  C2   2.04   0.88 14
+GDP  N3   1.54  -0.71 14
+GDP  C4   2.04   0.39 14
+GDP  C5   2.04  -0.06 14
+GDP  C6   1.87   0.69 14
+GDP  N1   1.54  -0.25 14
+GDP  N9   1.54  -0.11 14
+GDP  C8   1.88   0.33 14
+GDP  N7   1.54  -0.54 14
+GDP  C2*  2.02   0.33  6
+GDP  C3*  2.02   0.26  6
+GDP  C4*  2.02   0.11  6
+GDP  O4*  1.43  -0.37  4
+GDP  C1*  2.02   0.21  6
+GDP  C5*  2.00   0.01  6
+GDP  O5*  1.43  -0.46  4
+GDP  PA   1.70   0.90  3
+GDP  O1A  1.48  -0.72  4
+GDP  O2A  1.48  -0.72  4
+GDP  O3A  1.43  -0.67  4
+GDP  PB   1.70   0.53  9
+GDP  O1B  1.48  -0.62  9
+GDP  O2B  1.48  -0.62  9
+GDP  O3B  1.48  -0.62  9
+GDP  O6   1.55  -0.55  4
+GDP  N2   1.83  -0.12  7
+GDP  O2   1.55  -0.25 13
+GDP  O3   1.55  -0.25 13
+GNP  N1   1.54  -0.25 14
+GNP  C2   2.04   0.88 14
+GNP  N2   1.83  -0.12  7
+GNP  N3   1.54  -0.71 14
+GNP  C4   2.04   0.39 14
+GNP  C5   2.04  -0.06 14
+GNP  C6   1.87   0.69 14
+GNP  O6   1.55  -0.55  4
+GNP  N7   1.54  -0.54 14
+GNP  C8   1.88   0.33 14
+GNP  N9   1.54  -0.11 14
+GNP  C1*  2.02   0.21  6
+GNP  C2*  2.02   0.33  6
+GNP  O2*  1.55  -0.25 13
+GNP  C3*  2.02   0.26  6
+GNP  O3*  1.55  -0.25 13
+GNP  C4*  2.02   0.11  6
+GNP  O4*  1.43  -0.37  4
+GNP  C5*  2.00   0.01  6
+GNP  O5*  1.43  -0.46  4
+GNP  PA   1.70   0.90  3
+GNP  O1A  1.48  -0.72  4
+GNP  O2A  1.48  -0.72  4
+GNP  O3A  1.43  -0.67  4
+GNP  PB   1.70   1.11  3
+GNP  O1B  1.48  -0.72  4
+GNP  O2B  1.48  -0.72  4
+GNP  N3B  1.83  -0.15  1
+GNP  PG   1.70   0.53  9
+GNP  O1G  1.48  -0.62  9
+GNP  O2G  1.48  -0.62  9
+GNP  O3G  1.48  -0.62  9
+UNK  CAL  1.97   2.00 10
+XXX  XXX  1.83   0.00  0
+XXX  C??  2.23   0.00  3
+XXX  N??  1.83   0.00  1
+XXX  O??  1.55  -0.55  4
+XXX  S??  1.97  -0.19 18
+XXX  P??  1.87   0.53  9
+XXX  FE?  2.13   0.24 10
+XXX  MG?  2.13   0.24 10
+XXX  F??  2.13   0.24 10
+XXX  BR?  2.13   0.24 10

model/CombinatorialAssembler/libs_DockingLib/ChemAtom.cc

@@ -0,0 +1,69 @@
+#include "ChemAtom.h"
+
+const float ChemAtom::maxRadius = 3.5;
+ChemAtom::ChemAtom(){}
+
+ChemAtom::ChemAtom(const Vector3& p, const char ch, const unsigned int aid,
+		   const unsigned int resid, const char* const t, const char resTp,
+		   const int chemType, const float radius, const float charge):
+  Atom(p, ch, aid, resid, t, resTp),
+  chemType_(chemType), radius_(radius), charge_(charge), epsilon_(-0.01),
+  hbType_(NONE), hbDirection_(Vector3(0,0,0)), ASA_(0) {
+  setPolarity();
+}
+
+ChemAtom::ChemAtom(const std::string& PDBrec, bool cif) :
+  Atom(PDBrec, cif),
+  chemType_(0), radius_(1.5), charge_(0), epsilon_(-0.01), hbType_(NONE), hbDirection_(Vector3(0,0,0)), ASA_(0) {
+  setPolarity();
+}
+
+void ChemAtom::setHBData(const HB_TYPE hbType, const Vector3& hbDirection) {
+  // set type
+  if(hbType_ == NONE) hbType_ = hbType;
+  if((hbType_ == DONOR && hbType == ACCEPTOR) || (hbType_ == ACCEPTOR && hbType == DONOR)) hbType_ = HB_BOTH;
+
+  // set direction
+  if(hbDirection_.isZero()) {
+    hbDirection_ = hbDirection;
+  }
+}
+
+void ChemAtom::setPolarity() {
+  const char res = residueType();
+  const char* atomT = type();
+
+  bool nonPolar = true;
+
+  if (atomT[1] == 'S') nonPolar = true;
+
+  if (atomT[1] != 'C') nonPolar = false;
+  if ((atomT[2] == 'A' || atomT[2] == 'B' ) && atomT[3] == ' ') nonPolar = true;
+  if ( atomT[2] == 'H') nonPolar = true;
+  if ( atomT[2] == 'G') {
+    if (res == 'N') nonPolar = false;
+    nonPolar = true;
+  }
+  if ( atomT[2] == 'D') {
+    if (res == 'Q') nonPolar = false;
+    nonPolar = true;
+  }
+  if ( atomT[2] == 'E') {
+    if (res == 'H') nonPolar = false;
+    nonPolar = true;
+  }
+  if ( atomT[2] == 'Z') {
+    if (res == 'R') nonPolar = false;
+    nonPolar = true;
+  }
+  if ( atomT[2] == 'Z') {
+    if (res == 'R') nonPolar = false;
+    nonPolar = true;
+  }
+
+
+  if(fabs(charge_) > 0.4 && nonPolar) {
+    //Logger::warningMessage() << "Non Polar atom " << *this << " charge = " << charge_ << endl;
+  }
+  isNonPolar_ = nonPolar;
+}

model/CombinatorialAssembler/libs_DockingLib/ChemAtom.h

@@ -0,0 +1,156 @@
+#ifndef CHEM_ATOM_H
+#define CHEM_ATOM_H
+
+#include "Atom.h"
+
+enum HB_TYPE {DONOR = 0, ACCEPTOR = 1, HB_BOTH = 2, NONE = 3};
+enum MOL2_TYPE {C2 = 0, C3 =1 , Car = 2, Ccat = 3, N2 = 4, N4 = 5, Nam = 6,
+                Nar = 7, Npl3 = 8, O2 = 9, O3 = 10, Oco2 = 11, P3 = 12, S3 = 13, UNK_MOL2_TYPE = 14 };
+
+/*
+CLASS
+  ChemAtom
+
+  This is a class that addes additional atrributes to Atom
+
+KEYWORD
+  ChemAtom, radius, charge, type, ASA, solvation
+
+AUTHORS
+  Dina Schneidman (duhovka@tau.ac.il)
+
+  copyright: GAMBA Group , Tel-Aviv Univ. Israel, 2004.
+
+GOALS
+  ChemAtom extends Atom and has 4 additional attributes: chemical
+  type, radius, charge and probability of the atom of being steady.
+
+CHANGES LOG
+<UL>
+</UL>
+
+USAGE
+*/
+
+class ChemAtom : public Atom { //, public EnergyAtom {
+ public:
+  // GROUP: Constructors
+
+  //// empty atom
+  ChemAtom();
+
+  //// construction with atom data
+  ChemAtom(const Vector3& p, const char ch, const unsigned int aid,
+	   const unsigned int resid, const char* const t, const char resTp,
+	   const int chem_type=0, const float rad=1.5, const float charge=0);
+
+  ChemAtom(const std::string& PDBrec, bool cif = false);
+
+
+  // GROUP: modifiers
+
+  //// set chemical type
+  void setChemType(const int chem_type) {
+    if(chem_type <= 0 || chem_type > 18) {
+      std::cerr << "Error in ChemType for atom " << *this << std::endl;
+    } else {
+      chemType_ = chem_type;
+    }
+  }
+
+  //// set radius
+  void setRadius(const float r) { radius_ = r; }
+
+  //// set epsilon
+  void setEpsilon(const float e) { epsilon_ = e; }
+
+  //// set charge
+  void setCharge(const float c) { charge_ = c; }
+
+  //// set HB data
+  void setHBData(const HB_TYPE hbType, const Vector3& hbDirection);
+
+  //// set probability of being steady
+  void setSteadyProb(const float p) { steadyProb_ = p; }
+
+  //// set ASA
+  void setASA(const float ASA) { ASA_ = ASA; }
+
+  //// set atom position
+  void setPosition(const Vector3& v) { update(v); }
+
+  //// set mol2 type
+  void setMol2Type(const MOL2_TYPE t) { mol2Type_ = t; }
+
+  // GROUP: Inspectors
+
+  //// get atom chemical type for ACE computation
+  int getChemType() const {
+    if(chemType_ <= 0 || chemType_ > 18) return 0;
+    return chemType_;
+  }
+
+  //// get atom radius
+  float getRadius() const { return radius_; }
+
+  //// get epsilon value
+  float getEpsilon() const { return epsilon_; }
+
+  ////
+  bool isHydrogen() const { return isH(); }
+
+  //// get atom charge
+  float getCharge() const { return charge_; }
+
+  ////
+  bool isDonor() const { return (hbType_ == HB_BOTH || hbType_ == DONOR); }
+
+  ////
+  bool isAcceptor() const { return (hbType_ == HB_BOTH || hbType_ == ACCEPTOR); }
+
+  //// returns direction of h-donor/acceptor, in case of undefined direction zero vector is returned
+  const Vector3& getHBDirection() const { return hbDirection_; }
+
+  //// get probability of being steady
+  float getSteadyProb() const { return steadyProb_; }
+
+  //// get ASA
+  float getASA() const { return ASA_; }
+
+  ////
+  bool isNonPolar() const { return isNonPolar_; }
+
+  ////
+  MOL2_TYPE getMol2Type() const { return mol2Type_; }
+
+  Vector3 position() const {return (Atom(*this)).position(); }
+
+  friend Vector3& operator*=(ChemAtom &v,const RigidTrans3 &rt) {
+    //cout << "ChemAtom *= RigidTrans3" << endl;
+    v += (rt.rotation() * v) + rt.translation() - v;
+    if (!v.hbDirection_.isZero())
+      v.hbDirection_ = rt.rotation() * v.hbDirection_;
+    return v;
+  }
+
+
+  //// maximal atom radius
+  static const float maxRadius;
+
+
+private:
+  void setPolarity();
+
+ private:
+  int chemType_; // type required for ACE computation
+  float radius_;
+  float charge_;
+  float epsilon_; // for vdw computation
+  HB_TYPE hbType_;
+  Vector3 hbDirection_;
+  bool isNonPolar_;
+  float steadyProb_;
+  float ASA_;
+  MOL2_TYPE mol2Type_;
+};
+#endif /* IMP_CHEMATOM_H */

model/CombinatorialAssembler/libs_DockingLib/ChemLib.cc

@@ -0,0 +1,121 @@
+#include "ChemLib.h"
+
+#include <boost/algorithm/string.hpp>
+
+bool ChemEntry::isSameEntry(const std::string residueName, const std::string atomName) const {
+  if(residueName == residueName_ && atomName == atomName_)
+    return true;
+  return false;
+}
+
+ChemLib::ChemLib(const std::string libFileName) {
+  loadLibrary(libFileName);
+}
+
+void ChemLib::loadLibrary(const std::string libFileName) {
+  std::ifstream libFile(libFileName);
+  if(!libFile) {
+    std::cerr << "Can't find library file: " << libFileName << std::endl;
+    exit(1);
+  }
+
+  std::string line;
+  while (!libFile.eof()) {
+    getline(libFile, line);
+    boost::trim(line); // remove all spaces
+    // skip comments
+    if (line[0] == '#' || line[0] == '\0') continue;
+    std::vector < std::string > splitResults;
+    boost::split(splitResults, line, boost::is_any_of(" "), boost::token_compress_on);
+    for(unsigned int i=0; i<splitResults.size(); i++) boost::trim(splitResults[i]);
+
+    ChemEntry entry;
+
+    entry.residueName_ = splitResults[0];
+    entry.atomName_  = splitResults[1];
+    entry.radius_ = atof(splitResults[2].c_str());
+    entry.charge_ = atof(splitResults[3].c_str());
+    entry.chemType_ = atoi(splitResults[4].c_str());
+    libVector.push_back(entry);
+
+  }
+}
+
+const ChemEntry* ChemLib::getLibEntry(const char* residueName, const char* atomPDBType) const {
+  std::string resName(residueName);
+  std::string atomName(atomPDBType);
+
+  if(resName.length() != 3) {
+    std::cerr << "Error in resName: " << resName << " length " << resName.length() << std::endl;
+    //    exit(1);
+  }
+
+  if(atomName.length() != 4) {
+    std::cerr << "Error in atomName: " << atomName << " length " << atomName.length() << std::endl;
+    //    exit(1);
+  }
+
+  std::string atomTrimmedName = atomName;
+  boost::trim(atomTrimmedName);
+
+  const ChemEntry* libEntry = searchLibEntry(resName, atomTrimmedName);
+  if(libEntry == NULL) {
+    libEntry = searchLibEntry("XXX", atomTrimmedName);
+    if(libEntry == NULL) {
+      switch(atomTrimmedName.length()) {
+      case 1: atomTrimmedName.append("??"); break;
+      case 2: atomTrimmedName.append("?"); break;
+      case 3: atomTrimmedName[2] = '?'; break;
+      default: atomTrimmedName = "???"; break;
+      }
+      libEntry = searchLibEntry("XXX", atomTrimmedName);
+
+      if(libEntry == NULL) {
+	atomTrimmedName[1] = '?';
+	libEntry = searchLibEntry("XXX", atomTrimmedName);
+	if(libEntry == NULL)
+          std::cerr << "Unidentified atom " << atomName << " using default values!!!" << std::endl;
+      }
+    }
+  }
+  return libEntry;
+}
+
+const ChemEntry* ChemLib::searchLibEntry(const std::string residueName, const std::string atomName) const {
+  const ChemEntry* libEntry = NULL;
+  for(std::vector<ChemEntry>::const_iterator iter = libVector.begin();
+      iter != libVector.end(); iter++)
+    if((*iter).isSameEntry(residueName, atomName)) {
+      libEntry = &(*iter);
+      break;
+    }
+  return libEntry;
+}
+
+float ChemLib::getAtomRadius(const char* residueName, const char* atomPDBType) const {
+  const ChemEntry* libEntry = getLibEntry(residueName, atomPDBType);
+  if(libEntry!=NULL)
+    return libEntry->getEntryRadius();
+  return 1.5;
+}
+
+float ChemLib::getAtomCharge(const char* residueName, const char* atomPDBType) const {
+  const ChemEntry* libEntry = getLibEntry(residueName, atomPDBType);
+  if(libEntry!=NULL)
+    return libEntry->getEntryCharge();
+  return 0.0;
+}
+
+int ChemLib::getAtomChemType(const char* residueName, const char* atomPDBType) const {
+  const ChemEntry* libEntry = getLibEntry(residueName, atomPDBType);
+  if(libEntry!=NULL)
+    return libEntry->getEntryChemType();
+  return 0;
+}
+
+void ChemLib::printLibrary(std::ostream& outFile) const {
+  for(std::vector<ChemEntry>::const_iterator iter = libVector.begin();
+      iter != libVector.end(); iter++) {
+    outFile << *iter << std::endl;
+  }
+}

model/CombinatorialAssembler/libs_DockingLib/ChemLib.h

@@ -0,0 +1,127 @@
+#ifndef CHEM_LIB
+#define CHEM_LIB
+
+#include <vector>
+#include <string>
+#include <iostream>
+#include <fstream>
+
+/*
+CLASS
+  ChemEntry
+
+  This is a class that keeps protein atom attributes: type, radius and charge
+
+KEYWORD
+  ChemEntry, ChemAtom radius, charge, type
+
+AUTHORS
+  Dina Schneidman (duhovka@tau.ac.il)
+
+  copyright: GAMBA Group , Tel-Aviv Univ. Israel, 2004.
+
+GOALS
+  ChemEntry keeps atom attribures that are not given in PDB file.
+
+CHANGES LOG
+<UL>
+</UL>
+
+USAGE
+*/
+class ChemEntry {
+ public:
+  // GROUP: Inspectors
+  ////
+  bool isSameEntry(const std::string residueName, const std::string atomName) const;
+
+  //// returns radius
+  float getEntryRadius() const { return radius_; }
+
+  //// returns charge
+  float getEntryCharge() const { return charge_; }
+
+  //// returns atom type
+  int getEntryChemType() const { return chemType_; }
+
+  //// read entry
+  friend std::istream& operator>>(std::istream& s, ChemEntry &entry) {
+    return s >> entry.residueName_ >> entry.atomName_ >> entry.radius_ >> entry.charge_ >> entry.chemType_;
+  }
+
+  //// output entry
+  friend std::ostream& operator<<(std::ostream& s, const ChemEntry &entry) {
+    s << entry.residueName_ << ' ' << entry.atomName_  << ' '
+      << entry.radius_ << ' ' << entry.charge_ << ' ' <<  entry.chemType_;
+    return s;
+  }
+
+ public:
+  std::string residueName_;
+  std::string atomName_;
+  float radius_;
+  float charge_;
+  int chemType_;
+};
+
+
+/*
+CLASS
+  ChemLib
+
+  This is a class that serves as a library for protein attributes:
+  type, radius and charge.
+
+KEYWORD
+  ChemEntry, ChemAtom, ChemLib radius, charge, type
+
+AUTHORS
+  Dina Schneidman (duhovka@tau.ac.il)
+
+  copyright: GAMBA Group , Tel-Aviv Univ. Israel, 2004.
+
+GOALS
+  ChemLib keeps attribures for each of the 20 amino acids atoms. These
+  attribures are not given in PDB file.
+
+CHANGES LOG
+<UL>
+</UL>
+
+USAGE
+ The ChemLib is initialized with the special library file (mol/lib/gamb++/chem.lib).
+
+*/
+class ChemLib {
+ public:
+  // GROUP: Constructors
+
+  //// Init and load library
+  ChemLib(const std::string libFileName);
+  void loadLibrary(const std::string libFileName);
+
+  // GROUP: Inspectors
+
+  //// get radius
+  float getAtomRadius(const char* residueName, const char* atomPDBType) const;
+
+  //// get charge
+  float getAtomCharge(const char* residueName, const char* atomPDBType) const;
+
+  //// get chemical type
+  int getAtomChemType(const char* residueName, const char* atomPDBType) const;
+
+  //// print function
+  void printLibrary(std::ostream& outFile) const;
+
+  //// get the whole lib entry
+  const ChemEntry* getLibEntry(const char* residueName, const char* atomPDBType) const;
+
+ private:
+  const ChemEntry* searchLibEntry(const std::string residueName, const std::string atomName) const;
+
+ private:
+  std::vector<ChemEntry> libVector;
+};
+
+#endif

model/CombinatorialAssembler/libs_DockingLib/ChemMolecule.cc

@@ -0,0 +1,309 @@
+#include "ChemMolecule.h"
+#include "SASurface.h"
+
+/* ARG,LYS,GLU,GLN,ASP,
+   ASN,PRO,GLY,SER,THR,
+   HIS,ALA,ILE,LEU,VAL,
+   PHE,CYS,MET,TYR,TRP */
+const float ChemMolecule::flexProbs[MAX_AA]={0.24, 0.38, 0.14, 0.23, 0.06,
+					     0.11, 0.05, 0.05, 0.06, 0.07,
+					     0.05, 0.00, 0.13, 0.13, 0.08,
+					     0.015,0.02, 0.24, 0.07, 0.02,
+					     0.0//OTHER
+};
+
+const float ChemMolecule::maxCaDist[MAX_AA]={8.0, 6.3, 5.5, 5.3, 4.2,
+					     4.2, 3.0, 2.0, 3.0, 3.0,
+					     5.4, 3.0, 4.5, 4.4, 3.1,
+					     5.7, 3.5, 5.7, 7.0, 6.6,
+					     0.0//OTHER
+};
+
+bool compareFragment(ChemMolecule::Fragment f1, ChemMolecule::Fragment f2) {
+  if(f1.first != f2.first) { //different chains
+    return f1.first < f2.first;
+  }
+  // same chain
+  return f1.second.first < f2.second.first;
+}
+
+void ChemMolecule::loadMolecule(std::istream &molFile, const ChemLib& chemLib, const PDB::Selector& selector) {
+  Molecule<ChemAtom>::readAllPDBfile(molFile, selector);
+  for(Molecule<ChemAtom>::iterator molIter = begin(); molIter != end(); molIter++) {
+    if(!molIter->isHydrogen()) {
+      const ChemEntry* entry=chemLib.getLibEntry(molIter->residueName(), molIter->type());
+      if(entry != NULL) {
+	molIter->setRadius(entry->getEntryRadius());
+	molIter->setCharge(entry->getEntryCharge());
+	molIter->setChemType(entry->getEntryChemType());
+      }
+    }
+  }
+
+  centroid_ = centroid();
+  setIsProtein();
+}
+
+void ChemMolecule::readAllPDBfile(std::istream &molFile, const PDB::Selector& selector) {
+  Molecule<ChemAtom>::readAllPDBfile(molFile, selector);
+  computeASAperAtom();
+  centroid_ = centroid();
+  setIsProtein();
+}
+
+float ChemMolecule::computeASAperAtom() {
+  SASurface sas(*this, 1.8, 10); //probe radius = 1.8, density = 10
+  float asa = sas.computeASAForAtoms();
+  Logger::infoMessage() << "ASA of the molecule = " << asa << std::endl;
+  return asa;
+}
+
+void ChemMolecule::computeSteadyProbs() {
+  Vector3 caAtom;
+  for(Molecule<ChemAtom>::iterator molIter = begin(); molIter != end(); molIter++) {
+    RESIDUE_INDEX resIndex = RESIDUE_INDEX(*molIter);
+    if(molIter->isBackbone()) {
+      // glycine backbone can be flexible, since it has no side-chain
+      if(resIndex == GLY)
+	molIter->setSteadyProb(1-flexProbs[resIndex]);
+      else {
+	molIter->setSteadyProb(1-flexProbs[OTHER]);
+	if(molIter->isCA())
+	  caAtom = molIter->position();
+      }
+    } else {
+      float distanceFromCa = caAtom.dist(molIter->position());
+      float normFactor= distanceFromCa/maxCaDist[resIndex];
+      molIter->setSteadyProb(1-flexProbs[resIndex]*normFactor);
+    }
+  }
+}
+
+void ChemMolecule::setIsProtein() {
+  for(Molecule<ChemAtom>::iterator molIter = begin(); molIter != end(); molIter++) {
+    if(molIter->isCA()) {
+      isProtein_ = true;
+      return;
+    }
+  }
+  isProtein_ = false;
+}
+
+unsigned int ChemMolecule::readBindingSite(const std::string fileName) {
+  bindingSites_.push_back(std::set<unsigned int>());
+  return readSiteFile(fileName, bindingSites_.back());
+}
+
+unsigned int ChemMolecule::readBlockingSite(const std::string fileName) {
+  blockingSites_.push_back(std::set<unsigned int>());
+  return readSiteFile(fileName, blockingSites_.back());
+}
+
+unsigned int ChemMolecule::readSiteFile(const std::string fileName, std::set<unsigned int>& site) {
+  std::ifstream file(fileName.c_str());
+  if(!file) {
+    std::cerr << "Can't open file " << fileName << std::endl;
+    Logger::errorMessage() << "Can't open file " << fileName << std::endl;
+    exit(1);
+  }
+
+  char chainId;
+  std::string residueSequenceID;
+
+  while(!file.eof()) {
+    std::string line;
+    getline(file, line);
+    boost::trim(line);
+    if(line.length() == 0) continue;
+    int entry = -1;
+
+    char record[line.size()+1];
+    strcpy(record, line.c_str());
+
+    char* splittedRecord = strtok(record, " ");
+    residueSequenceID = std::string(splittedRecord);
+
+    splittedRecord = strtok (NULL, " ");
+    if(splittedRecord != NULL) {
+      chainId = splittedRecord[0];
+    } else {
+      chainId = ' ';
+    }
+    //cerr << residueSequenceID << ";" << chainId << ";" << endl;
+    entry = residueEntry(chainId, residueSequenceID);
+
+    if(entry != -1) {
+      site.insert(entry);
+    } else {
+      Logger::errorMessage() << "Invalid line in site file: " << line << std::endl;
+      std::cerr << "Invalid line in site file: " << line << std::endl;
+      exit(1);
+    }
+  }
+
+  Logger::infoMessage() << site.size() << " residues were read from site file: " << fileName << std::endl;
+  file.close();
+  return site.size();
+}
+
+
+const std::set<unsigned int>& ChemMolecule::getBindingSite(unsigned int siteNumber) const {
+  const static std::set<unsigned int> emptySet;
+  if(bindingSites_.size() > siteNumber) {
+    return bindingSites_[siteNumber];
+  }
+  return emptySet;
+}
+
+const std::set<unsigned int>& ChemMolecule::getBlockingSite(unsigned int siteNumber) const {
+  const static std::set<unsigned int> emptySet;
+  if(blockingSites_.size() > siteNumber) {
+    return blockingSites_[siteNumber];
+  }
+  return emptySet;
+}
+
+const ChemAtom& ChemMolecule::getChemAtom(int atomIndex) const {
+  for(Molecule<ChemAtom>::const_iterator molIter = begin(); molIter != end(); molIter++) {
+    if((int)molIter->atomIndex() == atomIndex) {
+      return *molIter;
+    }
+  }
+  Logger::errorMessage() << "Input Error: Can't find atom with atom index " << atomIndex << "!" << std::endl;
+  std::cerr << "Input Error: Can't find atom with atom index " << atomIndex << "!" << std::endl;
+  exit(1);
+}
+
+double ChemMolecule::getVolume() const {
+  double volume = 0.0;
+  double c = (4.0/3.0)*M_PI;
+  for(Molecule<ChemAtom>::const_iterator molIter = begin(); molIter != end(); molIter++) {
+    double r = molIter->getRadius();
+    volume += c * r * r * r;
+  }
+  return volume;
+}
+
+const std::vector<ChemMolecule::Fragment>& ChemMolecule::getFragments() const {
+  if(fragments_.size() == 0) {
+    ChemMolecule* nonConstThis = const_cast<ChemMolecule*>(this);
+    nonConstThis->computeFragments();
+  }
+  return fragments_;
+}
+
+void ChemMolecule::computeFragments() {
+  // calculate endpoints
+  char currChain;
+  int firstResIndex, prevResIndex;
+  bool currChainSet = false;
+  for(auto i = begin(); i != end(); i++) {
+    if(!i->isCA() || i->getAtomEntryType() == HETATM) continue;
+    char chain = i->chainId();
+    int resIndex = i->residueIndex();
+    //if(i->getAtomEntryType() == HETATM) continue;
+    // one more residue of the same chain - advance
+    if(currChainSet && currChain == chain &&
+       resIndex > prevResIndex) {
+      prevResIndex = resIndex;
+    } else { // new chain
+      if(currChainSet) { // save currChain
+        ResidueRange range(firstResIndex, prevResIndex);
+        Fragment fragment(std::make_pair(currChain, range));
+        fragments_.push_back(fragment);
+      }
+      // update
+      currChain = chain;
+      firstResIndex = prevResIndex = resIndex;
+      currChainSet = true;
+    }
+  }
+  // save last fragment
+  if(currChainSet) { // save currChain
+    ResidueRange range(firstResIndex, prevResIndex);
+    Fragment fragment(std::make_pair(currChain, range));
+    fragments_.push_back(fragment);
+  }
+
+  std::sort(fragments_.begin(), fragments_.end(), compareFragment);
+
+  for(int i=0; i<(int)fragments_.size(); i++) {
+    std::cout << "Fragment " << i << " chainId "
+              << fragments_[i].first << " range "
+              << fragments_[i].second.first << ":"
+              << fragments_[i].second.second << std::endl;
+  }
+}
+
+void ChemMolecule::addMol2Type() {
+
+
+  for(auto i = begin(); i != end(); i++) {
+    const char* type = i->type();
+    char res = i->residueType();
+    i->setMol2Type(UNK_MOL2_TYPE);
+    if(i->isN()) i->setMol2Type(N2);
+    if(i->isC()) i->setMol2Type(C2);
+    if(i->isCA()) i->setMol2Type(C3);
+    if(i->isO()) i->setMol2Type(O2); // TODO: the last residue should be O.co2
+    if(i->isCB()) i->setMol2Type(C3);
+
+    // carbon
+    if(i->isCD() && (res == 'K' || res == 'P' || res == 'R')) i->setMol2Type(C3);
+    if(i->isCD() && (res == 'Q' || res == 'E' )) i->setMol2Type(C2);
+
+    if(i->isCG() && (res == 'K' || res == 'P' || res == 'R' || res == 'M' || res == 'L' || res == 'Q' || res == 'E' )) i->setMol2Type(C3);
+    if(i->isCG() && (res == 'D' || res == 'N')) i->setMol2Type(C2);
+    if(i->isCG() && (res == 'H' || res == 'F' || res == 'W' || res == 'Y')) i->setMol2Type(Car);
+    if(i->isCZ() && (res == 'F' || res == 'Y')) i->setMol2Type(Car);
+    if(i->isCZ() && res == 'R') i->setMol2Type(Ccat);
+    if((i->isCD1() || i->isCD2()) && (res == 'F' || res == 'W' || res == 'Y' || res == 'H')) i->setMol2Type(Car);
+    if((i->isCD1() || i->isCD2()) && (res == 'L'  || res == 'I')) i->setMol2Type(C3);
+    if(i->isCE() || i->isCG1() || i->isCG2()) i->setMol2Type(C3);
+    if(i->isCE1() || i->isCE2() || i->isCE3() || i->isCZ2() || i->isCZ3() || i->isCH2() ) i->setMol2Type(Car);
+
+    // for RNA
+    if (i->isSugarCarbon())
+      i->setMol2Type(C3);
+
+    // oxygen
+    if((i->isOD1() || i->isOE1()) && ((res == 'N' || res == 'Q'))) i->setMol2Type(O2);
+    if((i->isOD1() || i->isOE1()|| i->isOD2()|| i->isOE2()) && (res == 'D' || res == 'E')) i->setMol2Type(Oco2);
+    if(i->isOH() || i->isOG()|| i->isOG1()) i->setMol2Type(O3);
+
+    // for RNA
+    if (i->isSugarOxygen())
+      i->setMol2Type(O3);
+    if (i->isPhosphateOxygen())
+      i->setMol2Type(Oco2);
+
+    // nitrogen
+    if(i->isNH1() || i->isNH2() || i->isNE()) i->setMol2Type(Npl3);
+    if((i->isND2() && res == 'N') || (i->isNE2() && res == 'Q')) i->setMol2Type(Nam);
+    if(((i->isND1() || i->isNE2()) && res == 'H') ||  (i->isNE1() && res == 'W')) i->setMol2Type(Nar);
+    if(i->isNZ()) i->setMol2Type(N4);
+
+    // for RNA
+    if (i->isNitrogenousBaseAtom()) {
+      if (type[1] == 'N') {
+        if ((type[2] == '4' && res == 'C') || (type[2] == '6' && res == 'A') || (type[2] == '2' && res == 'G'))
+          i->setMol2Type(Npl3);
+        else
+          i->setMol2Type(Nar);
+      }
+      else if (type[1] == 'O')
+        i->setMol2Type(O2);
+      else if (type[1] == 'C')
+        i->setMol2Type(Car);
+    }
+
+    // sulfur
+    if(i->isSD() || i->isSG()) i->setMol2Type(S3);
+
+    // phosphate
+    if(i->isP()) i->setMol2Type(P3);
+
+    if(i->getMol2Type() == UNK_MOL2_TYPE)
+      std::cout << "Can't assign mol2 type:" << type[0] << type[1] << type[2] << type[3] << ":" << std::endl;
+  }
+}

model/CombinatorialAssembler/libs_DockingLib/ChemMolecule.h

@@ -0,0 +1,132 @@
+#ifndef CHEM_MOL_H
+#define CHEM_MOL_H
+
+#include "ChemAtom.h"
+#include "ResidueIndexedMolecule.h"
+#include "ChemLib.h"
+#include "PDB.h"
+#include "Logger.h"
+#include "EnergyAtom.h"
+
+#include <iostream>
+#include <fstream>
+#include <set>
+
+/*
+CLASS
+  ChemMolecule
+
+  This is a class that is a container of ChemAtoms
+
+KEYWORD
+  ChemAtom, radius, charge, type
+
+AUTHORS
+  Dina Schneidman (duhovka@tau.ac.il)
+
+  copyright: GAMBA Group , Tel-Aviv Univ. Israel, 2004.
+
+GOALS
+  ChemMolecule is a molecule of ChemAtoms. ChemAtom extends Atom and has 4
+  additional attributes: chemical type, radius, charge and probability of
+  the atom of being steady. The type, radius and charge are taken from
+  ChemLib. This library is initiated with chem.lib file.
+  The chemical types are from:
+  Zhang,C., Cornette,J.L. and DeLisi,C. (1997) Determination of atomic
+  desolvation energies from the structures of crystallized
+  proteins. J. Mol. Biol., 267, 707 726.
+  This types are only for protein atoms!
+  The radii are taken from CHARMM, however they are slightly bigger
+  to account for missing hydrogens. The charges are from CHARMM too.
+  The probabilities of being steady were computed based on the maximal
+  distance between C-alpha and side-chain atoms of that residue. The
+  lower the distance the higher is the prob. of being steady.
+CHANGES LOG
+<UL>
+</UL>
+
+USAGE
+  ChemMolecule chemMolecule;
+  ifstream pdbFile("mol.pdb");
+  ChemLib chemLib("chem.lib");
+  chemMolecule.loadMolecule(pdbFile, chemLib);
+*/
+class ChemMolecule : public ResidueIndexedMolecule<ChemAtom> {
+private:
+  static const float flexProbs[];
+  static const float maxCaDist[];
+
+public:
+  //// load molecule from PDB file, using chemLib for attributes.
+  void loadMolecule(std::istream &molFile, const ChemLib& chemLib, const PDB::Selector& selector = PDB::WaterHydrogenUnSelector());
+
+  //// reads and assigns default values for radius, charge and chemType
+  void readAllPDBfile(std::istream &molFile, const PDB::Selector& selector = PDB::WaterHydrogenUnSelector());
+
+  //// compute probabilities of being steady
+  void computeSteadyProbs();
+
+  //// read and save binding site, returns number of residues in site
+  unsigned int readBindingSite(const std::string fileName);
+
+  //// read and save blocking site, returns number of residues in site
+  unsigned int readBlockingSite(const std::string fileName);
+
+  ////
+  const std::set<unsigned int>& getBindingSite(unsigned int siteNumber = 0) const;
+
+  ////
+  const std::set<unsigned int>& getBlockingSite(unsigned int siteNumber = 0) const;
+
+  ////
+  const ChemAtom& getChemAtom(int atomIndex) const;
+
+  ////
+  const Vector3& getCentroid() const { return centroid_; }
+
+  bool isProtein() const { return isProtein_; }
+
+  //// get the volume by summing the volume of all atoms
+  double getVolume() const;
+
+  typedef std::pair<int, int> ResidueRange;
+  typedef std::pair<char, ResidueRange> Fragment;
+
+  //// get the fragments
+  const std::vector<Fragment>& getFragments() const;
+
+  //// add mol2 atom type
+  void addMol2Type();
+
+  //// compute accessible surface area
+  float computeASAperAtom();
+private:
+  //// read site file and return number of reasidues that were read
+  unsigned int readSiteFile(const std::string fileName, std::set<unsigned int>& site);
+
+  //// checks if the molecule is protein (if there is at least one Ca atom)
+  void setIsProtein();
+
+  //// compute fragments of the same chain
+  void computeFragments();
+
+protected:
+  //// entries of binding site residues according to ResidueIndexedMolecule
+  std::vector<std::set<unsigned int> > bindingSites_;
+
+  //// entries of blocking site residues according to ResidueIndexedMolecule
+  std::vector<std::set<unsigned int> > blockingSites_;
+
+  ////
+  Vector3 centroid_;
+
+  ////
+  bool isProtein_;
+
+  //// fragments of the same chain in the molecule
+  std::vector<Fragment> fragments_;
+};
+
+bool compareFragment(ChemMolecule::Fragment f1, ChemMolecule::Fragment f2);
+
+#endif

model/CombinatorialAssembler/libs_DockingLib/Common.cc

@@ -0,0 +1,41 @@
+#include "Common.h"
+
+void Common::checkFile(const char* fileName, std::ifstream& file) {
+  if(!file) {
+    std::cerr << "Can't open file: " << fileName << std::endl;
+    Logger::errorMessage() << "Can't open file: " << fileName << std::endl;
+    exit(1);
+  }
+}
+
+void Common::readChemMolecule(const std::string fileName, ChemMolecule& mol, const ChemLib& protLib) {
+  std::ifstream molFile(fileName.c_str());
+  checkFile(fileName.c_str(), molFile);
+  mol.loadMolecule(molFile, protLib);
+  molFile.close();
+  Logger::infoMessage() << "Chem molecule: " << mol.size() << " atoms were read" << std::endl;
+}
+
+void Common::readChemMolecule(const std::string fileName, ChemMolecule& mol) {
+  std::ifstream molFile(fileName.c_str());
+  checkFile(fileName.c_str(), molFile);
+  mol.readPDBfile(molFile, PDB::WaterHydrogenUnSelector());
+  molFile.close();
+  Logger::infoMessage() << "Chem molecule: " << mol.size() << " atoms were read" << std::endl;
+}
+
+void Common::readHydrogenMolecule(const std::string fileName, Molecule<Atom>& mol) {
+  std::ifstream molFile(fileName.c_str());
+  checkFile(fileName.c_str(), molFile);
+  mol.readAllPDBfile(molFile, PDB::WaterUnSelector());
+  molFile.close();
+  Logger::infoMessage() << "Hydrogen molecule: " << mol.size() << " atoms were read" << std::endl;
+}
+
+void Common::readSurface(const std::string fileName, Surface& surface) {
+  std::ifstream surfFile(fileName.c_str());
+  checkFile(fileName.c_str(), surfFile);
+  surface.readShouFile(surfFile);
+  surfFile.close();
+  Logger::infoMessage() << "Surface: " << surface.size() << " surface points were read" << std::endl;
+}

model/CombinatorialAssembler/libs_DockingLib/Common.h

@@ -0,0 +1,21 @@
+#ifndef COMMON_H
+#define COMMON_H
+
+#include <Surface.h>
+#include <Logger.h>
+
+#include "ChemMolecule.h"
+
+#include <fstream>
+
+class Common {
+public:
+
+  static void checkFile(const char* fileName, std::ifstream& file);
+  static void readChemMolecule(const std::string fileName, ChemMolecule& mol, const ChemLib& protLib);
+  static void readChemMolecule(const std::string fileName, ChemMolecule& mol);
+  static void readHydrogenMolecule(const std::string fileName, Molecule<Atom>& mol);
+  static void readSurface(const std::string fileName, Surface& surface);
+};
+
+#endif //COMMON_H

model/CombinatorialAssembler/libs_DockingLib/CrossLink.cc

@@ -0,0 +1,140 @@
+#include "CrossLink.h"
+
+#include <boost/algorithm/string.hpp>
+
+#include <iostream>
+
+int readCrossLinkFile(const std::string& fileName,
+                      std::vector<CrossLink>& crossLinks,
+                      bool addReverse) {
+  std::ifstream s(fileName);
+  if (!s) {
+    std::cerr << "Can't find cross links file " << fileName << std::endl;
+    exit(0);
+  }
+  CrossLink cl;
+  while (s >> cl) {
+    if(! cl.isInList(crossLinks)) { // check for duplicates
+
+      if(!addReverse) {
+        // check reversed for duplicates
+        CrossLink clReversed = cl.getReversed();
+        if(! clReversed.isInList(crossLinks)) {
+          crossLinks.push_back(cl);
+        }
+      } else {
+        crossLinks.push_back(cl);
+      }
+
+    } else {
+      // TODO: check if shorter distance restraint and replace if needed
+      std::cerr << "Duplicate cross link " << cl << std::endl;
+    }
+
+    // add reverse
+    if(addReverse) {
+      CrossLink clReversed = cl.getReversed();
+      if(! clReversed.isInList(crossLinks)) {
+        crossLinks.push_back(clReversed);
+      }
+    }
+  }
+  return crossLinks.size();
+}
+
+void writeCrossLinkFile(const std::string& fileName,
+                        const std::vector<CrossLink>& crossLinks) {
+  std::ofstream ofile(fileName);
+  for (unsigned int i = 0; i < crossLinks.size(); i++) {
+    ofile << crossLinks[i];
+    ofile << std::endl;
+  }
+  ofile.close();
+}
+
+void writeXLAnalizerFile(const std::string& fileName,
+                         const std::vector<CrossLink>& crossLinks) {
+  std::ofstream ofile(fileName);
+  ofile << "id,Protein1,Protein2,AbsPos1,AbsPos2,score" << std::endl;
+  for (unsigned int i = 0; i < crossLinks.size(); i++) {
+    ofile << i+1 << "," << crossLinks[i].getChain1() << "," << crossLinks[i].getChain2() <<  ","
+          << crossLinks[i].getResidue1() << "," << crossLinks[i].getResidue2()
+          << ",100" << std::endl;
+    ofile << std::endl;
+  }
+  ofile.close();
+}
+
+std::ostream& operator<<(std::ostream& s, const CrossLink& cl) {
+  s << cl.residueNumber1_ << " ";
+  if (cl.chainId1_ == " ")
+    s << "-";
+  else
+    s << cl.chainId1_;
+
+  s << " " << cl.residueNumber2_ << " ";
+  if (cl.chainId2_ == " ")
+    s << "-";
+  else
+    s << cl.chainId2_;
+  s << " " << cl.minDistance_ << " " << cl.maxDistance_;
+  return s;
+}
+
+std::istream& operator>>(std::istream& s, CrossLink& cl) {
+
+  std::string line;
+  std::getline(s, line);
+  boost::trim(line); // remove spaces at the beginning/end of the line
+  if(line.length()==0) return s;
+  // skip comments
+  if (line[0] == '#' || line[0] == '\0' || !isdigit(line[0])) return s;
+
+  std::vector<std::string> split_results;
+  boost::split(split_results, line, boost::is_any_of("\t "),
+               boost::token_compress_on);
+
+  if (split_results.size() >= 5 && split_results.size() <= 7) {
+    cl.residueSequenceID1_ = split_results[0];
+    cl.chainId1_ = split_results[1];
+    cl.residueSequenceID2_ = split_results[2];
+    cl.chainId2_ = split_results[3];
+    cl.residueNumber1_ = std::stoi(cl.residueSequenceID1_);
+    cl.residueNumber2_ = std::stoi(cl.residueSequenceID2_);
+    cl.maxDistance_ = std::stof(split_results[4]);
+
+    if(split_results.size() >= 6) {
+      cl.minDistance_ = std::stof(split_results[4]);
+      cl.maxDistance_ = std::stof(split_results[5]);
+    }
+
+    if(split_results.size() == 7) {
+      cl.weight_ = std::stof(split_results[6]);
+    }
+  }
+
+  if (cl.chainId1_ == "-") cl.chainId1_ = " ";
+  if (cl.chainId2_ == "-") cl.chainId2_ = " ";
+  //  std::cerr << cl << std::endl;
+  return s;
+}
+
+bool CrossLink::operator==(const CrossLink& cl) const {
+  return (residueNumber1_ == cl.residueNumber1_ && residueNumber2_ == cl.residueNumber2_ &&
+          residueSequenceID1_ == cl.residueSequenceID1_ && residueSequenceID2_ == cl.residueSequenceID2_ &&
+          chainId1_ == cl.chainId1_ && chainId2_ == cl.chainId2_);
+}
+
+bool CrossLink::isInList(const std::vector<CrossLink>& crossLinks) const {
+  for(unsigned int i = 0; i<crossLinks.size(); i++)
+    if(*this == crossLinks[i])
+      return true;
+  return false;
+}
+
+CrossLink CrossLink::getReversed() const {
+  CrossLink reversed(residueNumber2_, chainId2_,
+                     residueNumber1_, chainId1_,
+                     minDistance_, maxDistance_, weight_);
+  return reversed;
+}

model/CombinatorialAssembler/libs_DockingLib/CrossLink.h

@@ -0,0 +1,69 @@
+#ifndef CROSS_LINK_H
+#define CROSS_LINK_H
+
+#include <fstream>
+#include <iostream>
+#include <vector>
+
+class CrossLink {
+ public:
+  CrossLink()
+      : residueNumber1_(0), chainId1_(" "),
+        residueNumber2_(0), chainId2_(" "),
+        minDistance_(0.0), maxDistance_(0.0), weight_(1.0) {}
+
+  CrossLink(int residueNumber1, std::string chainId1,
+            int residueNumber2, std::string chainId2,
+            float minDistance, float maxDistance, float weight=1.0)
+    : residueNumber1_(residueNumber1), residueSequenceID1_(std::to_string(residueNumber1)), chainId1_(chainId1),
+      residueNumber2_(residueNumber2), residueSequenceID2_(std::to_string(residueNumber2)), chainId2_(chainId2),
+        minDistance_(minDistance), maxDistance_(maxDistance), weight_(weight) {}
+
+
+  int getResidue1() const { return residueNumber1_; }
+  int getResidue2() const { return residueNumber2_; }
+
+  std::string getResidueSequenceID1() const { return residueSequenceID1_; }
+  std::string getResidueSequenceID2() const { return residueSequenceID2_; }
+
+  std::string getChain1() const { return chainId1_; }
+  std::string getChain2() const { return chainId2_; }
+
+  float getMinDistance() const { return minDistance_; }
+  float getMaxDistance() const { return maxDistance_; }
+  float getWeight() const { return weight_; }
+
+  bool operator==(const CrossLink& cl) const;
+
+  bool isInList(const std::vector<CrossLink>& crossLinks) const;
+
+  CrossLink getReversed() const;
+
+  friend std::ostream& operator<<(std::ostream& q, const CrossLink& cl);
+  friend std::istream& operator>>(std::istream& s, CrossLink& cl);
+
+ protected:
+  int residueNumber1_;
+  std::string residueSequenceID1_; // to support numbering of type 99A
+  std::string chainId1_;
+  int residueNumber2_;
+  std::string residueSequenceID2_;
+  std::string chainId2_;
+  float minDistance_;
+  float maxDistance_;
+  float weight_;
+};
+
+
+int readCrossLinkFile(const std::string& fileName,
+                      std::vector<CrossLink>& crossLinks,
+                      bool addReverse = false);
+
+
+void writeCrossLinkFile(const std::string& fileName,
+                        const std::vector<CrossLink>& crossLinks);
+
+void writeXLAnalizerFile(const std::string& fileName,
+                         const std::vector<CrossLink>& crossLinks);
+
+#endif

model/CombinatorialAssembler/libs_DockingLib/DistanceRestraint.cc

@@ -0,0 +1,40 @@
+#include "DistanceRestraint.h"
+#include <boost/algorithm/string/trim.hpp>
+
+float DistanceRestraint::minDistanceIndices(unsigned int& index1, unsigned int& index2) const {
+  float bestdist = std::numeric_limits<float>::max();
+  for(unsigned int i = 0; i < p1_.size(); i++) {
+    for(unsigned int j = 0; j < p2_.size(); j++) {
+      float dist = p1_[i].dist(p2_[j]);
+      if(dist < bestdist) {
+        bestdist = dist;
+        index1 = i;
+        index2 = j;
+      }
+    }
+  }
+  return bestdist;
+}
+
+std::string DistanceRestraint::getChimeraXPseudoBond() const {
+  unsigned int best_i = 0, best_j = 0;
+  float bestdist = minDistanceIndices(best_i, best_j);
+
+  if(p1Info_.size() == p1_.size() && p2Info_.size() == p2_.size()) {
+    // /E:157@ca /B:58@ca  red
+    std::string res1 = p1Info_[best_i].first;
+    boost::algorithm::trim(res1);
+    std::string res2 = p2Info_[best_j].first;
+    boost::algorithm::trim(res2);
+
+    // skip self cross link
+    if(res1 == res2 && p1Info_[best_i].second == p2Info_[best_j].second)
+      return std::string();
+
+    std::string ret = "/" + p1Info_[best_i].second + ":" + res1 + "@ca /" +
+      p2Info_[best_j].second + ":" + res2 + "@ca";
+    if(bestdist > maxdist_) ret += " red";
+    return ret;
+  }
+  return std::string();
+}

model/CombinatorialAssembler/libs_DockingLib/DistanceRestraint.h

@@ -0,0 +1,189 @@
+#ifndef DISTANCE_RESTRAINT_H
+#define DISTANCE_RESTRAINT_H
+
+#include <Vector3.h>
+#include <RigidTrans3.h>
+
+#include <vector>
+#include <limits>
+
+class DistanceRestraint {
+public:
+  DistanceRestraint(const std::vector<Vector3>& p1,
+                    const std::vector<Vector3>& p2,
+                    float maxdist, float mindist = 0.0, float weight=1.0)
+    : p1_(p1), p2_(p2), mindist_(mindist), maxdist_(maxdist),
+      mindist2_(mindist*mindist), maxdist2_(maxdist*maxdist),
+      weight_(weight) {}
+
+  DistanceRestraint(const std::vector<Vector3>& p1,
+                    const std::vector<Vector3>& p2,
+                    const std::vector<std::pair<std::string, std::string>>& p1Info,
+                    const std::vector<std::pair<std::string, std::string>>& p2Info,
+                    float maxdist, float mindist = 0.0, float weight=1.0)
+    : DistanceRestraint(p1, p2, maxdist, mindist, weight) {
+    p1Info_ = p1Info;
+    p2Info_ = p2Info;
+  }
+
+  DistanceRestraint(const Vector3& p1, const Vector3& p2,
+                    float maxdist, float mindist = 0.0, float weight=1.0)
+    :  mindist_(mindist), maxdist_(maxdist),
+      mindist2_(mindist*mindist), maxdist2_(maxdist*maxdist),
+      weight_(weight)
+  {
+    p1_.push_back(p1);
+    p2_.push_back(p2);
+  }
+
+  DistanceRestraint() = default;
+
+  float getWeight() const { return weight_; }
+  float getMinDistance() const { return mindist_; }
+  float getMaxDistance() const { return maxdist_; }
+  const std::vector<Vector3>& getPoints1() const { return p1_; }
+  const std::vector<Vector3>& getPoints2() const { return p2_; }
+
+  bool isViolated() const {
+    // calculate the distance and compare to mindist_ and maxdist_
+    for(unsigned int i = 0; i < p1_.size(); i++) {
+      for(unsigned int j = 0; j < p2_.size(); j++) {
+        float dist2 = p1_[i].dist2(p2_[j]);
+        if(dist2 <= maxdist2_) return false; // found one in range
+      }
+    }
+    return true;
+  }
+
+  bool isViolated(const std::vector<RigidTrans3>& trans) const {
+    // calculate the distance and compare to mindist_ and maxdist_
+    for(unsigned int i = 0; i < p1_.size(); i++) {
+      for(unsigned int j = 0; j < p2_.size(); j++) {
+        float dist2 = p1_[i].dist2(trans[j]*p2_[j]);
+        if(dist2 <= maxdist2_) return false; // found one in range
+      }
+    }
+    return true;
+  }
+
+  bool isViolated(const std::vector<RigidTrans3>& trans1,
+                  const std::vector<RigidTrans3>& trans2) const {
+    // calculate the distance and compare to mindist_ and maxdist_
+    for(unsigned int i = 0; i < p1_.size(); i++) {
+      Vector3 transP1 = trans1[i]*p1_[i];
+      for(unsigned int j = 0; j < p2_.size(); j++) {
+        float dist2 = transP1.dist2(trans2[j]*p2_[j]);
+        if(dist2 <= maxdist2_) return false; // found one in range
+      }
+    }
+    return true;
+  }
+
+  // backward compatability
+  bool isSatisfied() const { return !isViolated(); }
+  bool isSatisfied(const RigidTrans3& trans) const {
+    std::vector<RigidTrans3> t(p2_.size(), trans);
+    return !isViolated(t);
+  }
+  bool isSatisfied(const RigidTrans3& trans1,
+                   const RigidTrans3& trans2) const {
+    std::vector<RigidTrans3> t1(p1_.size(), trans1);
+    std::vector<RigidTrans3> t2(p2_.size(), trans2);
+    return !isViolated(t1, t2);
+  }
+
+  //calculate violationDistance
+  float violationDistance() const {
+    float bestdist = distance();
+    if(bestdist > maxdist_) return bestdist - maxdist_;
+    return 0.0;
+  }
+
+  float violationDistance(const std::vector<RigidTrans3>& trans) const {
+    float bestdist = distance(trans);
+    if(bestdist > maxdist_) return bestdist - maxdist_;
+    return 0.0;
+  }
+
+  float violationDistance(const std::vector<RigidTrans3>& trans1,
+                          const std::vector<RigidTrans3>& trans2) const {
+    float bestdist = distance(trans1, trans2);
+    if(bestdist > maxdist_) return bestdist - maxdist_;
+    return 0.0;
+  }
+
+  float distance2() const {
+    float bestdist2 = std::numeric_limits<float>::max();
+    for(unsigned int i = 0; i < p1_.size(); i++) {
+      for(unsigned int j = 0; j < p2_.size(); j++) {
+        float dist2 = p1_[i].dist2(p2_[j]);
+        if(dist2 < bestdist2) bestdist2 = dist2;
+      }
+    }
+    return bestdist2;
+  }
+
+  float distance() const { return sqrt(distance2()); }
+
+  float distance2(const std::vector<RigidTrans3>& trans) const {
+    float bestdist2 = std::numeric_limits<float>::max();
+    for(unsigned int i = 0; i < p1_.size(); i++) {
+      for(unsigned int j = 0; j < p2_.size(); j++) {
+        float dist2 = p1_[i].dist2(trans[j]*p2_[j]);
+        if(dist2 < bestdist2) bestdist2 = dist2;
+      }
+    }
+    return bestdist2;
+  }
+
+  float distance(const std::vector<RigidTrans3>& trans) const {
+    return sqrt(distance2(trans));
+  }
+
+  float distance(const RigidTrans3& trans) const {
+    std::vector<RigidTrans3> t(1, trans);
+    return distance(t);
+  }
+
+  float distance2(const std::vector<RigidTrans3>& trans1,
+                  const std::vector<RigidTrans3>& trans2) const {
+    float bestdist2 = std::numeric_limits<float>::max();
+    for(unsigned int i = 0; i < p1_.size(); i++) {
+      Vector3 transP1 = trans1[i]*p1_[i];
+      for(unsigned int j = 0; j < p2_.size(); j++) {
+        float dist2 = transP1.dist2(trans2[j]*p2_[j]);
+        if(dist2 < bestdist2) bestdist2 = dist2;
+      }
+    }
+    return bestdist2;
+  }
+
+  float distance(const std::vector<RigidTrans3>& trans1,
+                 const std::vector<RigidTrans3>& trans2) const {
+    return sqrt(distance2(trans1, trans2));
+  }
+
+  // TODO: add trans versions
+  float minDistanceIndices(unsigned int& index1, unsigned int& index2) const;
+
+  std::string getChimeraXPseudoBond() const;
+
+  bool operator < (const DistanceRestraint& d) const { return (maxdist_ < d.maxdist_); }
+
+  friend std::ostream& operator<<(std::ostream& s, const DistanceRestraint& d) {
+    // TODO
+    return s << d.p1_[0] << ' ' << d.p2_[0] << ' ' << d.mindist_ <<' ' << d.maxdist_;
+  }
+
+private:
+  std::vector<Vector3> p1_; // end point1, vector for ambiguity
+  std::vector<Vector3> p2_; // end point2, vector for ambiguity
+  std::vector<std::pair<std::string, std::string>> p1Info_, p2Info_; // residueSequenceID and chain for p1 and p2 endpoints
+  float mindist_; // minimal distance threshold
+  float maxdist_; // maximal distance threshold
+  float mindist2_; // minimal distance threshold (squared)
+  float maxdist2_; // maximal distance threshold (squared)
+  float weight_;
+};
+
+#endif /* DISTANCE_RESTRAINT_H */

model/CombinatorialAssembler/libs_DockingLib/DotSphere.cc

@@ -0,0 +1,22 @@
+#include "DotSphere.h"
+#include <numerics.h>
+
+int DotSphere::createSphereDots(float radius, float density) {
+
+  float num_equat = 2*pi*radius*sqrt(density);
+  float vert_count = 0.5*num_equat;
+  
+  for(int i=0; i<vert_count; i++) {
+    float phi = (pi*i)/vert_count;
+    float z = cos(phi);
+    float xy = sin(phi);
+    float horz_count = xy*num_equat;
+    for(int j=0; j<horz_count-1; j++) {
+      float teta = (2*pi*j)/horz_count;
+      float x = xy*cos(teta);
+      float y = xy*sin(teta);
+      push_back(Vector3(radius*x,radius*y,radius*z));
+    }
+  }
+  return size();
+}

model/CombinatorialAssembler/libs_DockingLib/DotSphere.h

@@ -0,0 +1,18 @@
+#ifndef DOT_SPHERE_H
+#define DOT_SPHERE_H
+
+#include <Vector3.h>
+
+#include <vector>
+
+class DotSphere : public std::vector<Vector3> {
+ public:
+  // Constructors
+  DotSphere(float radius, float density) {
+    createSphereDots(radius, density);
+  }
+
+  int createSphereDots(float radius, float density);
+};
+
+#endif

model/CombinatorialAssembler/libs_DockingLib/EnergyAtom.h

@@ -0,0 +1,21 @@
+
+#ifndef ENERGY_ATOM_H
+#define ENERGY_ATOM_H
+
+class EnergyAtom{
+ public:
+
+    virtual float getRadius() const = 0;
+    virtual float getEpsilon() const = 0;
+    virtual bool isHydrogen() const = 0;
+    virtual float getCharge() const = 0;
+    virtual bool isDonor() const = 0;
+    virtual bool isAcceptor() const = 0;
+    virtual const Vector3& getHBDirection() const = 0;
+    virtual Vector3 position() const = 0;
+
+    virtual ~EnergyAtom() {}
+};
+
+#endif
+

model/CombinatorialAssembler/libs_DockingLib/GeomScore.cc

@@ -0,0 +1,423 @@
+#include "GeomScore.h"
+#include "Logger.h"
+
+RangeParams::RangeParams(const std::vector<int>& wts) {
+  ranges.push_back(-3.6);
+  ranges.push_back(-2.2);
+  ranges.push_back(-1.0);
+  ranges.push_back(1.0);
+  weights.insert(weights.begin(), wts.begin(), wts.end());
+}
+
+//-------------------------------- GeomScore class -----------------------------
+
+GeomScore::GeomScore(const Surface& lowLevel, MoleculeGrid* grid,
+		     const std::vector<int>& wts, float penetration_thr, float ns_thr, float d, float gridMargins) :
+  grid_(grid), rangeParams(wts),
+  penetrationThr_(penetration_thr), divNsThr(1.0/ns_thr),
+  density(d), tree(lowLevel, density, gridMargins)
+{}
+
+GeomScore::GeomScore(const Surface& lowLevel,
+		     const std::vector<int>& wts, float penetration_thr, float ns_thr, float d, float gridMargins) :
+  grid_(NULL), rangeParams(wts),
+  penetrationThr_(penetration_thr), divNsThr(1.0/ns_thr),
+  density(d), tree(lowLevel, density, gridMargins)
+{}
+
+GeomScore::GeomScore(MoleculeGrid* grid,
+		     const std::vector<int>& wts, float penetration_thr, float ns_thr, float d, float gridMargins) :
+  grid_(grid), rangeParams(wts),
+  penetrationThr_(penetration_thr), divNsThr(1.0/ns_thr),
+  density(d)
+{}
+
+void GeomScore::buildTree() {
+  tree.buildTree();
+}
+
+void GeomScore::buildTree(const std::vector<bool>& as) {
+  tree.buildTree(as);
+  //  countActiveSitePoints(as);
+}
+
+float GeomScore::maxPenetration(const RigidTrans3& trans) {
+  float maxPenetration=MAX_FLOAT;
+  Level& highLevel = tree.getLevel(tree.size()-1);
+  std::stack<const Node *> st;
+  for (unsigned int i=0; i< highLevel.size(); i++)
+    st.push(&highLevel[i]);
+  while (!st.empty()) {
+    const Node *node = st.top();
+    st.pop();
+    float dist = grid_->getDist(trans*(node->position()));
+    if (dist != MAX_FLOAT) {
+      if (node->getLevel() == 0) {
+	if (dist < maxPenetration)
+	  maxPenetration = dist;
+	continue;
+      }
+      if (dist - node->getRadius() <= maxPenetration) {
+	const std::vector<const Node *>& lowLevelPointers = node->getChildren();
+	for (unsigned int i=0; i<lowLevelPointers.size(); i++)
+	  st.push(lowLevelPointers[i]);
+      }
+    }
+  }
+  return maxPenetration;
+}
+
+bool GeomScore::isPenetrating(const RigidTrans3& trans) {
+  Level& highLevel = tree.getLevel(tree.size()-1);
+  std::stack<const Node *> st;
+  for(unsigned int i=0; i< highLevel.size(); i++) {
+    float dist = grid_->getDist(trans*(highLevel[i].position()));
+    if(dist < penetrationThr_) {
+      return true;
+    } else {
+      st.push(&highLevel[i]);
+    }
+  }
+  while(!st.empty()) {
+    const Node *node = st.top();
+    st.pop();
+    float dist = grid_->getDist(trans*(node->position()));
+    if(dist < penetrationThr_)
+      return true;
+    if(node->getLevel() != 0) {
+      // check if dist - pointRadius is more then thr
+      if(dist - node->getRadius() <= penetrationThr_) {
+	const std::vector<const Node *>& lowLevelPointers = node->getChildren();
+	for(unsigned int i=0; i< lowLevelPointers.size(); i++)
+	  st.push(lowLevelPointers[i]);
+      }
+    }
+  }
+  return false;
+}
+
+bool GeomScore::fastIsPenetrating(const RigidTrans3& trans) {
+  Level& highLevel = tree.getLevel(tree.size()-1);
+  std::stack<const Node *> st;
+  for(unsigned int i=0; i< highLevel.size(); i++) {
+    float dist = grid_->getDist(trans*(highLevel[i].position()));
+    if(dist < penetrationThr_) {
+      return true;
+    }
+  }
+  return false;
+}
+
+
+void GeomScore::getInterface(const RigidTrans3& trans, float low_thr, float high_thr,
+                             std::vector<const SurfacePoint*>& interface) {
+  Level& highLevel = tree.getLevel(tree.size()-1);
+  std::stack<const Node *> st;
+  for (unsigned int i=0; i< highLevel.size(); i++)
+    st.push(&highLevel[i]);
+  while (!st.empty()) {
+    const Node *node = st.top();
+    st.pop();
+    float dist = grid_->getDist(trans*(node->position()));
+    if (dist == MAX_FLOAT) continue;
+    if (node->getLevel() == 0) {
+      if (dist > low_thr && dist < high_thr)
+	interface.push_back(node->getPoint());
+      continue;
+    }
+    if (dist - node->getRadius() > low_thr && dist + node->getRadius() < high_thr) {
+      node2interface(node, interface);
+      continue;
+    }
+    const std::vector<const Node *>& lowLevelPointers = node->getChildren();
+    for (unsigned int i=0; i<lowLevelPointers.size(); i++)
+      st.push(lowLevelPointers[i]);
+  }
+}
+
+void GeomScore::node2interface(const Node* node, std::vector<const SurfacePoint*>& interface) {
+  std::stack<const Node *> st;
+  st.push(node);
+  while (!st.empty()) {
+    const Node *node = st.top();
+    st.pop();
+    if (node->getLevel() == 0) {
+      interface.push_back(node->getPoint());
+      continue;
+    }
+    const std::vector<const Node *>& lowLevelPointers = node->getChildren();
+    for (unsigned int i=0; i<lowLevelPointers.size(); i++)
+      st.push(lowLevelPointers[i]);
+  }
+}
+
+int GeomScore::score(const RigidTrans3& trans) {
+  std::vector<unsigned int> pointsInRanges(rangeParams.weights.size(),0);
+  scoreRanges(trans, pointsInRanges);
+  //calculate total, based on weights
+  int score=0;
+  for(unsigned int i=0; i<rangeParams.weights.size(); i++)
+    score+= (pointsInRanges[i]*rangeParams.weights[i]);
+
+  if(score <= 0)
+    return -1;
+
+  if(((float)pointsInRanges[pointsInRanges.size()-2])/score > divNsThr) {
+    return -1;
+  }
+  return score;
+}
+
+int GeomScore::score(const RigidTrans3& trans, const Surface& surface, float& penetration) {
+  std::vector<unsigned int> pointsInRanges(rangeParams.weights.size(),0);
+  penetration = MAX_FLOAT;
+  // count number of points
+  for(unsigned int i=0; i<surface.size(); i++) {
+    float dist = grid_->getDist(trans * (surface[i].position()));
+    if(dist < penetrationThr_)
+      return -1;
+    if(dist < penetration)
+      penetration = dist;
+    unsigned int range = rangeParams.findRange(dist);
+    pointsInRanges[range]++;
+  }
+
+  //calculate total, based on weights
+  int score=0;
+  for(unsigned int i=0; i<rangeParams.weights.size(); i++)
+    score+= (pointsInRanges[i]*rangeParams.weights[i]);
+
+  if(score <= 0)
+    return -1;
+
+  if(((float)pointsInRanges[pointsInRanges.size()-2])/score > divNsThr) {
+    return -1;
+  }
+  return score;
+}
+
+int GeomScore::score(const RigidTrans3& trans, float& asRatio, int& asScore) {
+  std::vector<unsigned int> pointsInRanges(rangeParams.weights.size(),0);
+  std::vector<unsigned int> asInRanges(rangeParams.weights.size(),0);
+  scoreRanges(trans, pointsInRanges, asInRanges);
+  //calculate total, based on weights
+  int score=0;
+  int interfaceCount = 0;
+  int asInterfaceCount = 0;
+  asScore=0;
+  for(unsigned int i=0; i<rangeParams.weights.size(); i++) {
+    score+= (pointsInRanges[i]*rangeParams.weights[i]);
+    asScore+= (asInRanges[i]*rangeParams.weights[i]);
+    if(i < rangeParams.weights.size() -1 ) {
+      interfaceCount+= pointsInRanges[i];
+      asInterfaceCount+= asInRanges[i];
+    }
+  }
+
+  if(interfaceCount == 0) {
+    asRatio = 0;
+  } else {
+    asRatio = ((float)asInterfaceCount)/interfaceCount;
+  }
+
+  if(score <= 0)
+    return -1;
+
+  if(((float)pointsInRanges[pointsInRanges.size()-2])/score > divNsThr) {
+    return -1;
+  }
+
+  return score;
+}
+
+void GeomScore::scoreRanges(const RigidTrans3& trans, std::vector<unsigned int>& pointsInRanges) {
+  Level& highLevel = tree.getLevel(tree.size()-1);
+  std::stack<const Node *> st;
+  for (unsigned int i=0; i< highLevel.size(); i++)
+    st.push(&highLevel[i]);
+  while (!st.empty()) {
+    const Node *node = st.top();
+    st.pop();
+    float dist = grid_->getDist(trans*(node->position()));
+    if (dist == MAX_FLOAT) { //add to last range
+      pointsInRanges[pointsInRanges.size()-1]+=node->getSubtreeSize();
+      continue;
+    }
+    unsigned int range = rangeParams.findRange(dist);
+    if (node->getLevel() == 0) {
+      pointsInRanges[range]++;
+      continue;
+    }
+    unsigned int range1 = rangeParams.findRange(dist + node->getRadius());
+    unsigned int range2 = rangeParams.findRange(dist - node->getRadius());
+    if (range == range1 && range == range2) {
+      pointsInRanges[range] += node->getSubtreeSize();
+      continue;
+    }
+    const std::vector<const Node *>& lowLevelPointers = node->getChildren();
+    for (unsigned int i=0; i<lowLevelPointers.size(); i++)
+      st.push(lowLevelPointers[i]);
+  }
+}
+
+void GeomScore::scoreRanges(const RigidTrans3& trans, std::vector<unsigned int>& pointsInRanges,
+                            std::vector<unsigned int>& asInRanges) {
+  Level& highLevel = tree.getLevel(tree.size()-1);
+  std::stack<const Node *> st;
+  for (unsigned int i=0; i< highLevel.size(); i++)
+    st.push(&highLevel[i]);
+  while (!st.empty()) {
+    const Node *node = st.top();
+    st.pop();
+    Vector3 point = trans*(node->position());
+    float dist = grid_->getDist(point);
+    if (dist == MAX_FLOAT) { //add to last range
+      pointsInRanges[pointsInRanges.size()-1]+=node->getSubtreeSize();
+      asInRanges[asInRanges.size()-1]+=node->getAsNum();
+      continue;
+    }
+    unsigned int range = rangeParams.findRange(dist);
+    if (node->getLevel() == 0) {
+      pointsInRanges[range]++;
+      asInRanges[range]+=node->getAsNum();
+      continue;
+    }
+    unsigned int range1 = rangeParams.findRange(dist + node->getRadius());
+    unsigned int range2 = rangeParams.findRange(dist - node->getRadius());
+    if (range == range1 && range == range2) {
+      pointsInRanges[range]+=node->getSubtreeSize();
+      asInRanges[range]+=node->getAsNum();
+      continue;
+    }
+    const std::vector<const Node *>& lowLevelPointers = node->getChildren();
+    for (unsigned int i=0; i< lowLevelPointers.size(); i++)
+      st.push(lowLevelPointers[i]);
+  }
+}
+
+ScoreData GeomScore::fullScore(const RigidTrans3& trans, bool as) {
+  ScoreData scoreData;
+  std::vector<unsigned int> pointsInRanges(rangeParams.weights.size(),0);
+  if (as) {
+    std::vector<unsigned int> asInRanges(rangeParams.weights.size(),0);
+    scoreRanges(trans, pointsInRanges, asInRanges);
+    for (unsigned int i=0; i<rangeParams.weights.size()-1; i++) {
+      scoreData.score+= (pointsInRanges[i] * rangeParams.weights[i]);
+      scoreData.asScore+= (asInRanges[i] * rangeParams.weights[i]);
+      scoreData.interfaceArea+= pointsInRanges[i];
+    }
+    asInRanges.clear();
+  } else {
+    scoreRanges(trans, pointsInRanges);
+    for (unsigned int i=0; i<rangeParams.weights.size()-1; i++) {
+      scoreData.score+= (pointsInRanges[i] * rangeParams.weights[i]);
+      scoreData.interfaceArea+= pointsInRanges[i];
+    }
+  }
+  scoreData.interfaceArea/=density;
+  scoreData.maxPenetration = maxPenetration(trans);
+  pointsInRanges.clear();
+  return scoreData;
+}
+
+float GeomScore::computePropensity(const RigidTrans3& trans) {
+  std::vector<unsigned int> pointsInRanges(rangeParams.weights.size(),0);
+  std::vector<unsigned int> asInRanges(rangeParams.weights.size(),0);
+  scoreRanges(trans, pointsInRanges, asInRanges);
+  //calculate total, based on weights
+  int score=0;
+  int asScore=0;
+  for (unsigned int i=0; i<rangeParams.weights.size()-1; i++) {
+    score+= pointsInRanges[i];
+    asScore+= asInRanges[i];
+  }
+  float prop = ((float)asScore/score)/((float)tree.getAsPointsNumber()/tree.getLevel(0).size());
+  return prop;
+}
+
+int GeomScore::refineTrans(const RigidTrans3& trans, RigidTrans3& newTrans) {
+/*
+    float Tmag = 0.1;
+    float Rmag =  0.05;
+
+
+    // compute ligand interface points
+    std::vector<const SurfacePoint*> interface;
+    getInterface(trans, -2.0, 1.5, interface);  //add thr - which??
+
+    Logger::debugMessage() << "interface size: " << interface.size() << " trans " << trans << endl;
+
+    std::vector<Vector3> interfacePoints(interface.size());
+    std::vector<Vector3> virtualPoints(interface.size());
+    MyMatch matchList;
+
+    Vector3 centerOfRotation;
+    for (unsigned int i=0; i<interface.size(); i++) {
+        interfacePoints[i] = interface[i]->position();
+        centerOfRotation += interfacePoints[i];
+        matchList.add(i,i);
+    }
+    centerOfRotation /= interface.size();
+
+    RigidTrans3 bestTrans;
+    RigidTrans3 currTrans = trans;
+    int currScore=1000000;
+    int oldScore = score(trans);
+    MMonteCarlo::init(oldScore);
+    newTrans = trans;
+    int nums = 0;
+    while (nums < 1000) {
+
+        currTrans = newTrans;
+        nums++;
+        //Logger::debugMessage() << "oldScore: " << oldScore;
+        for (unsigned int i=0; i<interface.size(); i++) {
+            Vector3 point = newTrans * interfacePoints[i];
+            float dist = grid_->getDist(point);
+            virtualPoints[i] = point + dist*(interface[i]->normal());
+            if (dist == 0.00)
+                matchList.setScore(i,10.0);
+            else
+                matchList.setScore(i,1/fabs(dist));
+        }
+        matchList.calculateBestFit(virtualPoints, interfacePoints);
+        newTrans = matchList.rigidTrans();
+        //oldScore = currScore;
+        currScore = score(newTrans);
+        MMonteCarlo::MMC_acceptance mmc_accept = MMonteCarlo::step(currScore);
+
+        if (mmc_accept == MMonteCarlo::ACCEPT_LOWEST) {
+            bestTrans = newTrans;
+        }
+
+        if (mmc_accept == MMonteCarlo::REJECT) {
+
+
+            float delta_TR[6] = {0.0};
+            delta_TR[0] = MMonteCarlo::getGaussianRandomNumber() * Tmag;
+            delta_TR[1] = MMonteCarlo::getGaussianRandomNumber() * Tmag;
+            delta_TR[2] = MMonteCarlo::getGaussianRandomNumber() * Tmag;
+            delta_TR[3] = MMonteCarlo::getGaussianRandomNumber() * Rmag;
+            delta_TR[4] = MMonteCarlo::getGaussianRandomNumber() * Rmag;
+            delta_TR[5] = MMonteCarlo::getGaussianRandomNumber() * Rmag;
+
+            Vector3 rotVec(delta_TR[3],delta_TR[4],delta_TR[5]);
+            Vector3 transVec(delta_TR[0],delta_TR[1],delta_TR[2]);
+
+            RigidTrans3 delta_rt3(rotVec,transVec);
+
+            const Matrix3 &delta_mat3 = delta_rt3.rotation();
+            RigidTrans3 delta_rt3_COR(delta_mat3,centerOfRotation-delta_mat3*centerOfRotation+delta_rt3.translation());
+            newTrans = delta_rt3_COR*currTrans;
+
+        }
+
+        //Logger::debugMessage() << " RMSD: " << matchList.rmsd() << " newTrans " << newTrans << " newScore " << currScore << endl;
+    }
+
+    newTrans = bestTrans;
+
+    //Logger::debugMessage() << "oldScore: " << oldScore << "  newScore " << currScore << endl;
+    return currScore;*/
+return 0;
+}

model/CombinatorialAssembler/libs_DockingLib/GeomScore.h

@@ -0,0 +1,129 @@
+#ifndef GEOM_SCORE_H
+#define GEOM_SCORE_H
+
+#include <stack>
+#include <utility>
+#include <vector>
+
+#include <Surface.h>
+#include <MoleculeGrid.h>
+#include "MultiResolution.h"
+
+#include <Match.h>
+#include <Particle.h>
+//#include "MMonteCarlo.h"
+
+class MyMatch : public Match {
+ public:
+  void setScore(unsigned int pairIndex, float score) { pairs[pairIndex].score = score; }
+};
+
+class RangeParams {
+ public:
+  RangeParams(const std::vector<int>& wts);
+  unsigned int findRange(float dist) const {
+    for(unsigned int i=0; i< ranges.size(); i++)
+      if(dist <= ranges[i]) return i;
+    return ranges.size();
+  }
+ public:
+  std::vector<float> ranges;
+  std::vector<int> weights;
+};
+
+class ScoreData {
+ public:
+  ScoreData() { score=0; asScore=0; interfaceArea=0;}
+  int score;
+  int asScore;
+  float interfaceArea;
+  float maxPenetration;
+ public:
+  //  int getSurfaceRange() {return pointsInRanges[3];}
+  friend std::ostream& operator<<(std::ostream& s, const ScoreData& data) {
+    s.width(5); s << data.score << "|";
+    s.width(5); s << data.asScore << "|";
+    s.width(5); s << data.maxPenetration << "|";
+    s.width(5); s << data.interfaceArea << "|";
+    return s;
+  }
+};
+
+class ScorePair : public std::pair<ScoreData, ScoreData> {
+ public:
+  ScorePair(ScoreData f, ScoreData s, RigidTrans3 trans) : std::pair<ScoreData, ScoreData> (f,s) {
+    trans_ = trans;
+    score_ = f.score + s.score - abs(f.score - s.score);
+  }
+  int score() const { return score_; }
+  const RigidTrans3& rigidTrans() const { return trans_; }
+  friend std::ostream& operator<<(std::ostream& s, const ScorePair& p) {
+    s << p.first << "|";
+    s << std::endl << "           ";
+    s << p.second << "|";
+    return s;
+  }
+ protected:
+  RigidTrans3 trans_;
+  int score_;
+};
+
+class GeomScore {
+ public:
+  typedef MultiResolution<SurfacePoint>::Node Node;
+  typedef MultiResolution<SurfacePoint>::Level Level;
+
+  GeomScore(const Surface& lowLevel, MoleculeGrid* grid,
+	    const std::vector<int>& wts, float penetration_thr, float ns_thr, float density=10.0, float gridMargins=7.0);
+
+  GeomScore(const Surface& lowLevel,
+	    const std::vector<int>& wts, float penetration_thr, float ns_thr, float density=10.0, float gridMargins=7.0);
+
+  GeomScore(MoleculeGrid* grid,
+	    const std::vector<int>& wts, float penetration_thr, float ns_thr=0.5, float density=10.0, float gridMargins=7.0);
+
+  void setGrid(const MoleculeGrid* grid) { grid_ = grid; }
+
+  void setSurface(const Surface& lowLevel) {
+    tree.setPointSet(lowLevel);
+    buildTree();
+  }
+
+  void buildTree();
+  void buildTree(const std::vector<bool>& as);
+
+  //// Penetration checks
+  float maxPenetration(const RigidTrans3& trans);
+  bool isPenetrating(const RigidTrans3& trans);
+
+  //// fast check, but can return false for penetrating trans
+  bool fastIsPenetrating(const RigidTrans3& trans);
+
+  void getInterface(const RigidTrans3& trans, float low_thr, float high_thr, std::vector<const SurfacePoint*>& interface);
+
+  //// Scoring functions
+  int score(const RigidTrans3& trans);
+  int score(const RigidTrans3& trans, float& asRatio, int& asScore);
+  int score(const RigidTrans3& trans, const Surface& surface, float& penetration);
+  ScoreData fullScore(const RigidTrans3& trans, bool as=false);
+
+  int refineTrans(const RigidTrans3& trans, RigidTrans3& newTrans);
+
+  void printTree(std::ofstream& outFile);
+  float computePropensity(const RigidTrans3& trans);
+ private:
+  void scoreRanges(const RigidTrans3& trans, std::vector<unsigned int>& pointsInRanges);
+  void scoreRanges(const RigidTrans3& trans, std::vector<unsigned int>& pointsInRanges,
+		   std::vector<unsigned int>& asInRanges);
+  void node2interface(const Node* node, std::vector<const SurfacePoint*>& interface);
+  void countActiveSitePoints(const std::vector<bool>& as);
+ private:
+  const MoleculeGrid* grid_;
+  const RangeParams rangeParams;
+  float penetrationThr_;
+  float divNsThr; // 1/nsThr
+  float density;
+  MultiResolution<SurfacePoint> tree;
+};
+
+#endif

model/CombinatorialAssembler/libs_DockingLib/MolIntersection.h

@@ -0,0 +1,116 @@
+#ifndef MOL_INTERSECTION_H
+#define MOL_INTERSECTION_H
+
+#include <Interface.h>
+#include <Vector3.h>
+
+/*
+  Class for checking sphere intersections with atoms of the molecule
+*/
+template<class MoleculeT>
+class MolIntersection {
+ public:
+  // GROUP: Constructors
+  MolIntersection();
+  MolIntersection(MoleculeT* mol, float probe_radius);
+
+  void setMolecule(MoleculeT* mol) { molecule = mol; }
+
+  // GROUP: neighbours related queries
+  bool isNeighbours(unsigned int atom1, unsigned int atom2) const;
+
+  const Interface::ParticleAdjacency& getNeighbours(unsigned int atom) const;
+
+  // GROUP: intersections queries
+  bool isIntersectingSpheres(const Vector3& sphereCenter1, const Vector3& sphereCenter2,
+			     const float radius1, const float radius2) const;
+
+  bool isIntersecting(const Vector3& probeCenter, unsigned int atomIndex) const;
+
+  bool isIntersecting(const Vector3& probeCenter, unsigned int atomIndex1, unsigned int atomIndex2) const;
+
+  bool isIntersecting(const Vector3& probeCenter,
+		      unsigned int atom1Index, unsigned int atom2Index, unsigned int atom3Index) const;
+ private:
+  void computeNeighbours();
+
+ private:
+  MoleculeT* molecule;
+  Interface neighbours;
+  float probeRadius;
+};
+
+template<class MoleculeT>
+MolIntersection<MoleculeT>::MolIntersection(MoleculeT* mol, float probe_radius) :
+  molecule(mol), probeRadius(probe_radius) {
+  computeNeighbours();
+}
+
+template<class MoleculeT>
+bool MolIntersection<MoleculeT>::isNeighbours(unsigned int atom1, unsigned int atom2) const {
+  if(neighbours.isAdjacent(atom1, atom2))
+    return true;
+  return false;
+}
+
+template<class MoleculeT>
+const Interface::ParticleAdjacency& MolIntersection<MoleculeT>::getNeighbours(unsigned int atom) const {
+  return neighbours.adjacencies(atom);
+}
+
+template<class MoleculeT>
+bool MolIntersection<MoleculeT>::isIntersectingSpheres(const Vector3& sphereCenter1, const Vector3& sphereCenter2,
+						       const float radius1, const float radius2) const {
+  float radiusSum2 = (radius1+radius2)*(radius1+radius2);
+  float dist2 = sphereCenter1.dist2(sphereCenter2);
+  if(fabs(radiusSum2-dist2) < 0.0001)
+    return false;
+  if(radiusSum2 > dist2)
+    return true;
+  return false;
+}
+
+template<class MoleculeT>
+bool MolIntersection<MoleculeT>::isIntersecting(const Vector3& probeCenter, unsigned int atomIndex) const {
+  const Interface::ParticleAdjacency& atomNeighbours = neighbours.adjacencies(atomIndex);
+  for(Interface::ParticleAdjacency::const_iterator it = atomNeighbours.begin(); it != atomNeighbours.end(); it++)
+    if(isIntersectingSpheres(probeCenter, (*molecule)(it->first), probeRadius, (*molecule)[it->first].getRadius()))
+      return true;
+  return false;
+}
+
+template<class MoleculeT>
+bool MolIntersection<MoleculeT>::isIntersecting(const Vector3& probeCenter,
+						unsigned int atom1Index, unsigned int atom2Index) const {
+  std::vector<unsigned int> nUnion;
+  neighbours.neighboursUnion(neighbours.adjacencies(atom1Index), neighbours.adjacencies(atom2Index), nUnion);
+  for(std::vector<unsigned int>::iterator it=nUnion.begin(); it!=nUnion.end(); it++)
+    if(isIntersectingSpheres(probeCenter, (*molecule)(*it), probeRadius, (*molecule)[*it].getRadius()))
+      return true;
+  return false;
+    //  return (isIntersecting(probeCenter, atom1Index) || isIntersecting(probeCenter, atom2Index));
+}
+
+template<class MoleculeT>
+bool MolIntersection<MoleculeT>::isIntersecting(const Vector3& probeCenter, unsigned int atom1Index,
+						unsigned int atom2Index, unsigned int atom3Index) const {
+  return (isIntersecting(probeCenter, atom1Index) ||
+	  isIntersecting(probeCenter, atom2Index) || isIntersecting(probeCenter, atom3Index));
+}
+
+template<class MoleculeT>
+void MolIntersection<MoleculeT>::computeNeighbours() {
+  for(unsigned int i=0; i<molecule->size(); i++) {
+    for(unsigned int j=i+1; j<molecule->size(); j++) {
+      float radiusSum = (*molecule)[i].getRadius() + (*molecule)[j].getRadius() + 2*probeRadius;
+      float dist2 = (*molecule)(i).dist2((*molecule)(j));
+      if(dist2 < radiusSum*radiusSum) {
+	float dist = sqrt(dist2);
+	neighbours.addAdjacency(i, j, dist);
+	neighbours.addAdjacency(j, i, dist);
+      }
+    }
+  }
+}
+
+#endif

model/CombinatorialAssembler/libs_DockingLib/MultiResolution.h

@@ -0,0 +1,279 @@
+#ifndef MULT_RES_H
+#define MULT_RES_H
+
+#include <Vector3.h>
+#include <Atom.h>
+#include <GeomHash.h>
+#include <numerics.h>
+
+template<class PointT>
+class MultiResolution {
+ public:
+
+  //// TreeNode
+  class Node {
+
+   public:
+    // GROUP: Constructors
+    Node(const PointT* point, short level=0, float lowLevelRadius=0.0,
+	 unsigned int subtreeSize=1, unsigned int asNum=0):
+      point_(point), level_(level), lowLevelRadius_(lowLevelRadius), subtreeSize_(subtreeSize), asNum_(asNum) {}
+
+    // GROUP: Modifiers
+    //// update asNum
+    void incrementAsNum(unsigned int num) { asNum_ += num; }
+
+    //// add children to node
+    void addChildren(const std::vector<const Node *>& children) {
+      lowLevelPointers_.insert(lowLevelPointers_.begin(), children.begin(), children.end());
+    }
+
+    // GROUP: Queries
+    //// return point pointer
+    const PointT* getPoint() const { return point_; }
+
+    //// return point position
+    Vector3 position() const { return point_->position(); }
+
+    //// get node level
+    short getLevel() const { return level_; }
+
+    //// get radius
+    float getRadius() const { return lowLevelRadius_; }
+
+    //// get subtree size
+    unsigned int getSubtreeSize() const { return subtreeSize_; }
+
+    //// get number of active nodes in the subtree
+    unsigned int getAsNum() const { return asNum_; }
+
+    //// get pointers to node children
+    const std::vector<const Node *>& getChildren() const { return lowLevelPointers_; }
+
+   protected:
+    // point
+    const PointT* point_;
+    // level
+    short level_;
+    // radius of lower level points
+    float lowLevelRadius_;
+    // number of subtree nodes
+    unsigned int subtreeSize_;
+    // number of active site nodes
+    unsigned int asNum_;
+    // pointers to lower level
+    std::vector<const Node *> lowLevelPointers_;
+
+  };
+
+  typedef std::vector<Node> Level;
+
+  // GROUP: Contructors
+  //// The initial bin size is computed based on density and number of tree
+  // levels is computed based on the size of the grid margins
+  MultiResolution(const std::vector<PointT>& pointSet, float density=10.0, float gridMargins=6.0);
+  MultiResolution(float density=10.0, float gridMargins=6.0);
+
+  // GROUP: Modifiers
+  void setPointSet(const std::vector<PointT>& pointSet) { pointSet_ = pointSet; }
+  void buildTree();
+  void buildTree(const std::vector<bool>& as);
+  void countActiveSitePoints(const std::vector<bool>& as);
+
+  // GROUP: Queries
+  Level& getLevel(unsigned int num) { return tree_[num]; }
+  unsigned int size() const { return tree_.size(); }
+  int getAsPointsNumber() const { return asPointsNumber_; }
+  void printTree(std::ofstream& outFile);
+
+ private:
+  void createHighLevel(const int lowLevelIndex, float radius);
+  void findMaxRadiusForPoint(const Vector3& point, const Node* currNode, float& currMaxRadius2);
+
+ private:
+  std::vector<PointT> pointSet_;
+  std::vector<Level> tree_;
+  int asPointsNumber_;
+  float binSize_;
+};
+
+template<class PointT>
+MultiResolution<PointT>::MultiResolution(const std::vector<PointT>& pointSet, float density, float gridMargins) :
+  pointSet_(pointSet) {
+  unsigned int POINTS_PER_CUBE = 5;
+  binSize_ = POINTS_PER_CUBE/density;
+  Level l;
+  for(float cs=binSize_; cs <= gridMargins*2; cs*=2) { //-1
+    tree_.push_back(l);
+  }
+  //  cout << "Tree size: " << tree_.size() << endl;
+}
+
+template<class PointT>
+MultiResolution<PointT>::MultiResolution(float density, float gridMargins) {
+  unsigned int POINTS_PER_CUBE = 5;
+  binSize_ = POINTS_PER_CUBE/density;
+  Level l;
+  for(float cs=binSize_; cs <= gridMargins*2; cs*=2) { //-1
+    tree_.push_back(l);
+  }
+  // cout << "Tree size: " << tree_.size() << endl;
+}
+
+
+template<class PointT>
+void MultiResolution<PointT>::createHighLevel(const int lowLevelIndex, float binSize) {
+  const Level& lowLevel = tree_[lowLevelIndex];
+  // insert to ghash
+  GeomHash<Vector3, const Node* > gHash(3, binSize);
+  for(unsigned int i=0; i< lowLevel.size(); i++)
+    gHash.insert(lowLevel[i].position(), &lowLevel[i]);
+
+  // init Level
+  short levelIndex = lowLevelIndex+1;
+  Level& highLevel = tree_[levelIndex];
+
+  // compute high resolution - iterate over each Bucket
+  typename GeomHash<Vector3, const Node*>::BucketsPointerList *bucketList = gHash.getBuckets();
+  typename GeomHash<Vector3, const Node*>::BucketsPointerList::const_iterator bIter, bEndIter = bucketList->end();
+  for(bIter = bucketList->begin(); bIter != bEndIter; bIter++) {
+    const std::vector<const Node*>& currBucket = **bIter;
+    // compute average bucket point
+    // compute subtree size
+    Vector3 average;
+    unsigned int subTreeSize=0;
+    typename std::vector<const Node*>::const_iterator currBucketIter, bucketEndIter = currBucket.end();
+    for(currBucketIter = currBucket.begin(); currBucketIter != bucketEndIter; currBucketIter++) {
+      average+= (*currBucketIter)->position();
+      subTreeSize+=(*currBucketIter)->getSubtreeSize();
+    }
+    average/=currBucket.size();
+
+    // find point closest to average
+    float minDist2 = MAX_FLOAT;
+    const Node* selectedNode=NULL;
+    for(currBucketIter = currBucket.begin(); currBucketIter != bucketEndIter; currBucketIter++) {
+      float currDist2 = average.dist2((*currBucketIter)->position());
+      if(currDist2 < minDist2) {
+	selectedNode = *currBucketIter;
+	minDist2 = currDist2;
+      }
+    }
+
+    // find radius of pts == maxDist from average
+    float maxDist2 = MIN_FLOAT;
+    for(currBucketIter = currBucket.begin(); currBucketIter != bucketEndIter; currBucketIter++)
+      findMaxRadiusForPoint(selectedNode->position(), *currBucketIter, maxDist2);
+
+    // create new node
+    Node newNode(selectedNode->getPoint(), levelIndex, sqrt(maxDist2), subTreeSize);
+    newNode.addChildren(currBucket);
+    highLevel.push_back(newNode);
+  }
+  delete bucketList;
+  // cout << ": " << highLevel.size() << "  ";
+}
+
+template<class PointT>
+void MultiResolution<PointT>::findMaxRadiusForPoint(const Vector3& point, const Node* currNode, float& currMaxRadius2) {
+  int levelIndex = currNode->getLevel();
+  float dist2 = currNode->position().dist2(point);
+  if(levelIndex==0) {
+    if(dist2 > currMaxRadius2)
+      currMaxRadius2=dist2;
+    return;
+  }
+  // check if distance to (point+radius)^2 < currMaxRadius2
+  float radius = currNode->getRadius();
+  float dist = sqrt(dist2);
+  if(sqr(radius+dist) < currMaxRadius2) return;
+  const std::vector<const Node*>& lowLevelPointersForPoint = currNode->getChildren();
+  typename std::vector<const Node*>::const_iterator iter, endIter=lowLevelPointersForPoint.end();
+  if(levelIndex==1) {
+    for(iter=lowLevelPointersForPoint.begin(); iter!=endIter; iter++) {
+      float dist2=point.dist2((*iter)->position());
+      if(dist2 > currMaxRadius2)
+	currMaxRadius2=dist2;
+    }
+    return;
+  }
+  if(levelIndex > 1) {
+    for(iter=lowLevelPointersForPoint.begin(); iter!=endIter; iter++) {
+      findMaxRadiusForPoint(point, *iter, currMaxRadius2);
+    }
+    return;
+  }
+  return;
+}
+
+template<class PointT>
+void MultiResolution<PointT>::buildTree() {
+  // initiate lowest level
+  Level& lowLevel = tree_[0];
+  for(unsigned int i=0; i<pointSet_.size(); i++) {
+    Node node(&pointSet_[i], 0, 0, 1);
+    lowLevel.push_back(node);
+  }
+
+  // create the rest of the tree
+  // cout << "start building levels ";
+  float radius = binSize_;
+  for(unsigned int i=0; i< tree_.size()-1; i++) {
+    // cout << i+1;
+    createHighLevel(i, radius);
+    radius*=2;
+  }
+  // cout << "done " << endl;
+}
+
+template<class PointT>
+void MultiResolution<PointT>::buildTree(const std::vector<bool>& as) {
+  buildTree();
+  countActiveSitePoints(as);
+}
+
+template<class PointT>
+void MultiResolution<PointT>::countActiveSitePoints(const std::vector<bool>& as) {
+  Level& lowLevel = tree_[0];
+  if(as.size() != lowLevel.size()) {
+    std::cerr << "Error in active site array" << std::endl;
+    return;
+  }
+  // mark low level leaves
+  asPointsNumber_=0;
+  for(unsigned int i=0; i<lowLevel.size(); i++) {
+    lowLevel[i].incrementAsNum(as[i]);
+    if(as[i]==1) asPointsNumber_++;
+  }
+  // go up the tree and mark nodes
+  for(unsigned int levelIndex=1; levelIndex<tree_.size(); levelIndex++) {
+    Level& currLevel = tree_[levelIndex];
+    for(unsigned int nodeIndex=0; nodeIndex<currLevel.size(); nodeIndex++) {
+      Node& currNode = currLevel[nodeIndex];
+      const std::vector<const Node *>& lowLevelPointers = currNode.getChildren();
+      for(unsigned int lowLevelIndex=0; lowLevelIndex<lowLevelPointers.size(); lowLevelIndex++)
+	currNode.incrementAsNum(lowLevelPointers[lowLevelIndex]->getAsNum());
+    }
+  }
+}
+
+template<class PointT>
+void MultiResolution<PointT>::printTree(std::ofstream& outFile)
+{
+  int count=0;
+  for(unsigned int levelIndex=0; levelIndex<tree_.size(); levelIndex++) {
+    Level& currLevel = tree_[levelIndex];
+    for(unsigned int nodeIndex=0; nodeIndex<currLevel.size(); nodeIndex++) {
+      Node& currNode = currLevel[nodeIndex];
+      if(currNode.asNum_ > 0) {
+	Atom atom(currNode.position(), 'A', count++, levelIndex, "INT", 'X');
+	outFile << atom << std::endl;
+      } else {
+	Atom atom(currNode.position(), 'A', count++, levelIndex, "PRB", 'X');
+	outFile << atom << std::endl;
+      }
+    }
+  }
+}
+
+#endif