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755,088 | snapShotContainer.inline.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/x86/sse4/snapShotContainer.inline.hpp | /*!
* \file snapshotContainer.inline.hpp
* \brief This file is used to add up using size every class.
* This source is optimized for SSE4 instruction set.
* Copyright (C) 2014 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General ... | 1,691 | C++ | .h | 43 | 36.093023 | 82 | 0.709854 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,089 | jvmInfo.inline.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/x86/avx/jvmInfo.inline.hpp | /*!
* \file jvmInfo.inline.hpp
* \brief Getting JVM performance information.
* This source is optimized for AVX instruction set.
* Copyright (C) 2014 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as publi... | 2,024 | C++ | .h | 60 | 30.766667 | 82 | 0.669388 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,090 | snapShotContainer.inline.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/x86/avx/snapShotContainer.inline.hpp | /*!
* \file snapShotContainer.inline.hpp
* \brief This file is used to add up using size every class.
* This source is optimized for AVX instruction set.
* Copyright (C) 2014 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General P... | 3,142 | C++ | .h | 100 | 27.73 | 82 | 0.601977 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,091 | avxBitMapMarker.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/x86/avx/avxBitMapMarker.hpp | /*!
* \file avxBitMapMarker.hpp
* \brief Storeing and Controlling G1 marking bitmap.
* This source is optimized for AVX instruction set.
* Copyright (C) 2014-2016 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public Licens... | 1,632 | C++ | .h | 46 | 32.934783 | 82 | 0.738608 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,092 | util.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/x86/avx/util.hpp | /*!
* \file util.hpp
* \brief Optimized utility functions for AVX instruction set.
* Copyright (C) 2015 Nippon Telegraph and Telephone Corporation
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Fo... | 1,129 | C++ | .h | 32 | 32.84375 | 82 | 0.715722 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,093 | armBitMapMarker.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/arm/armBitMapMarker.hpp | /*!
* \file armBitMapMarker.hpp
* \brief This file is used to store and control of bit map.
* Copyright (C) 2015-2016 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; ei... | 1,830 | C++ | .h | 53 | 31.811321 | 82 | 0.726964 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,094 | snapShotContainer.inline.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/arm/snapShotContainer.inline.hpp | /*!
* \file snapShotContainer.inline.hpp
* \brief This file is used to add up using size every class.
* Copyright (C) 2015 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundatio... | 2,964 | C++ | .h | 105 | 24.371429 | 82 | 0.516468 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,095 | lock.inline.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/arm/lock.inline.hpp | /*!
* \file lock.inline.hpp
* \brief This file defines spinlock functions.
* Copyright (C) 2015 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of t... | 1,624 | C++ | .h | 57 | 25.631579 | 82 | 0.638924 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,096 | jvmInfo.inline.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/arm/neon/jvmInfo.inline.hpp | /*!
* \file jvmInfo.inline.hpp
* \brief This file is used to get JVM performance information.
* This source is optimized for NEON instruction set.
* Copyright (C) 2015 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public L... | 1,840 | C++ | .h | 58 | 28.724138 | 82 | 0.625422 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,097 | snapShotContainer.inline.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/arm/neon/snapShotContainer.inline.hpp | /*!
* \file snapShotContainer.inline.hpp
* \brief This file is used to add up using size every class.
* This source is optimized for NEON instruction set.
* Copyright (C) 2015 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General ... | 2,531 | C++ | .h | 78 | 28.910256 | 82 | 0.625 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,098 | neonBitMapMarker.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/arm/neon/neonBitMapMarker.hpp | /*!
* \file neonBitMapMarker.hpp
* \brief Storeing and Controlling G1 marking bitmap.
* This source is optimized for NEON instruction set.
* Copyright (C) 2015-2016 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public Lice... | 1,635 | C++ | .h | 46 | 33 | 82 | 0.739735 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,099 | util.hpp | HeapStats_heapstats/agent/src/heapstats-engines/arch/arm/neon/util.hpp | /*!
* \file util.hpp
* \brief Optimized utility functions for NEON instruction set.
* Copyright (C) 2015 Nippon Telegraph and Telephone Corporation
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software F... | 1,188 | C++ | .h | 34 | 32.352941 | 82 | 0.692441 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,100 | heapstats_md_x86.hpp | HeapStats_heapstats/agent/src/arch/x86/heapstats_md_x86.hpp | /*!
* \file heapstats_md_x86.hpp
* \brief Proxy library for HeapStats backend.
* This file implements x86 specific code for loading backend library.
* Copyright (C) 2014-2016 Yasumasa Suenaga
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General P... | 1,201 | C++ | .h | 30 | 38.233333 | 82 | 0.761782 | HeapStats/heapstats | 128 | 18 | 1 | GPL-2.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,101 | test_mmcif.cpp | GrossfieldLab_loos/Packages/User/test_mmcif.cpp |
#include <loos.hpp>
#include <gemmi/mmread.hpp>
#include <gemmi/cif.hpp>
#include <gemmi/mmcif.hpp> // cif::Document -> Structure
#include <gemmi/gz.hpp>
namespace cif = gemmi::cif;
int main(int argc, char *argv[]) {
std::string filename = std::string(argv[1]);
loos::AtomicGroup ag;
auto s... | 2,761 | C++ | .cpp | 62 | 31.467742 | 94 | 0.505404 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | false | false | false |
755,102 | traj_calc.cpp | GrossfieldLab_loos/Packages/User/traj_calc.cpp | /*
traj_calc.cpp
(c) 2011 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
C++ template for writing a tool that performs a calculation on a trajectory
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented St... | 4,728 | C++ | .cpp | 111 | 39.234234 | 84 | 0.710624 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,103 | model_calc.cpp | GrossfieldLab_loos/Packages/User/model_calc.cpp | /*
model_calc.cpp
(c) 2011 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
C++ template for writing a tool that performs a calculation on a model
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Struct... | 4,371 | C++ | .cpp | 101 | 39.980198 | 84 | 0.710601 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,104 | traj_transform.cpp | GrossfieldLab_loos/Packages/User/traj_transform.cpp | /*
traj_transform.cpp
(c) 2011 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
C++ template for writing a tool that transforms a subset of a trajectory
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented ... | 5,853 | C++ | .cpp | 137 | 38.686131 | 84 | 0.698604 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,105 | simple_model_transform.cpp | GrossfieldLab_loos/Packages/User/simple_model_transform.cpp | /*
simple_model_transform.cpp
(c) 2011 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
C++ template for writing a tool that transforms a model, writing it
out as a PDB to stdout
*/
/*
This file is part of LOOS.
LOOS (L... | 2,227 | C++ | .cpp | 56 | 36.160714 | 83 | 0.732493 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,106 | test_mmcif_2.cpp | GrossfieldLab_loos/Packages/User/test_mmcif_2.cpp |
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2023 Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify
it under the ... | 1,530 | C++ | .cpp | 32 | 43.9375 | 84 | 0.695914 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | false | false | false |
755,107 | simple_model_calc.cpp | GrossfieldLab_loos/Packages/User/simple_model_calc.cpp | /*
simple_model_calc.cpp
(c) 2011 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
C++ template for writing a tool that performs a calculation on a model with minimal
command-line options
*/
/*
This file is part of LOOS.
... | 1,975 | C++ | .cpp | 50 | 35.84 | 85 | 0.730242 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,108 | hcontacts.cpp | GrossfieldLab_loos/Packages/HydrogenBonds/hcontacts.cpp | /*
hcontacts.cpp
Constructs a matrix representing time series for multiple for inter and/or intra-molecular hbonds
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentis... | 11,281 | C++ | .cpp | 262 | 38.038168 | 120 | 0.661065 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,109 | hbonds.cpp | GrossfieldLab_loos/Packages/HydrogenBonds/hbonds.cpp | /*
hbonds
Find putative hydrogen-bonds based on user-specified criteria (angle and distance)
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of R... | 9,501 | C++ | .cpp | 245 | 34.163265 | 150 | 0.648637 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,110 | hmatrix.cpp | GrossfieldLab_loos/Packages/HydrogenBonds/hmatrix.cpp | /*
hmatrix.cpp
Writes out a matrix representing hbonds over time
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOO... | 5,391 | C++ | .cpp | 133 | 36.586466 | 107 | 0.696463 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,111 | hcorrelation.cpp | GrossfieldLab_loos/Packages/HydrogenBonds/hcorrelation.cpp | /*
hcorrelation.cpp
Computes time-correlation for hydrogen bonds...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (... | 10,465 | C++ | .cpp | 258 | 34.813953 | 154 | 0.636554 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,112 | hcore.cpp | GrossfieldLab_loos/Packages/HydrogenBonds/hcore.cpp | /*
Core code for hbonds tools
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistrib... | 5,625 | C++ | .cpp | 146 | 34.582192 | 154 | 0.695967 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,113 | eigenflucc.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/eigenflucc.cpp | /*
eigenflucc
Predict isotropic B-factors from a set of eigenpairs...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010 Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (... | 7,320 | C++ | .cpp | 185 | 34.978378 | 144 | 0.645763 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,114 | side-nodes.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/side-nodes.cpp | /*
side-nodes
(c) 2010 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
Usage:
side-nodes selection model >output.pdb
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010 ... | 3,309 | C++ | .cpp | 91 | 31.593407 | 89 | 0.647114 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,115 | anm.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/anm.cpp | /*
anm
(c) 2008 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
Computes the anisotropic network model for a structure. It does
this by building a hessian for the structure, then computing the SVD
of it and the corresponding pseudo-... | 9,271 | C++ | .cpp | 217 | 36.912442 | 114 | 0.662465 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | true | false | false |
755,116 | enmovie.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/enmovie.cpp | /*
enmovie
Elastic Network MOde VIsualizEr
Usage:
enmovie [options] model-name eigenvector-matrix output-name
Notes:
use the "--help" option for more information about how to run...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008 Tod... | 19,178 | C++ | .cpp | 459 | 36.647059 | 206 | 0.649704 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,117 | vsa-lib.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/vsa-lib.cpp | /*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010 Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify
it under the ter... | 6,740 | C++ | .cpp | 172 | 33.761628 | 170 | 0.61593 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,118 | psf-masses.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/psf-masses.cpp | /*
psf-masses
Takes masses from a PSF file and places them into the occupancy field of a PDB.
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009 Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, Universit... | 3,264 | C++ | .cpp | 91 | 31.472527 | 81 | 0.661033 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,119 | heavy-ca.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/heavy-ca.cpp | /*
heavy-ca
Given a PDB where masses are stored in the occupancy field, reduce
the structure to CA's only where the mass of the CA is the sum of
the mass of all atoms in the corresponding residue...
Usage- heavy-ca selection model >output
*/
/*
This file is part of LOOS.
LOOS (Lightweight Obje... | 3,415 | C++ | .cpp | 94 | 32.042553 | 86 | 0.677832 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,120 | spring_functions.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/spring_functions.cpp | /*
Spring Functions from Elastic Network Tools in LOOS
(c) 2010 Tod D. Romo, Grossfield Lab, URMC
*/
#include "spring_functions.hpp"
namespace ENM {
std::vector<std::string> splitCommaSeparatedList(const std::string& s){
std::vector<std::string> holder;
std::string::size_type prev =s.find_first_not_of... | 2,332 | C++ | .cpp | 64 | 31.140625 | 73 | 0.642857 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,121 | vsa.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/vsa.cpp | /*
vsa
Usage:
vsa [options] subset environment model output_prefix
See:
Woodcock et al, J Chem Phys (2008) 129:214109
Haffner & Zheng, J Chem Phys (2009) 130:194111
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009 Tod D. Romo
Depart... | 8,979 | C++ | .cpp | 212 | 38.29717 | 138 | 0.691256 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,122 | gnm.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/gnm.cpp | /*
gnm
Computes the gaussian normal mode (elastic network model)
decomposition for a structure. Does this by building the Kirchoff
matrix given a PDB and a selection, then computes the SVD of the
matrix and finally the pseudo-inverse.
Usage:
gnm [selection-string] radius model-name output-prefix
... | 7,202 | C++ | .cpp | 189 | 33.740741 | 121 | 0.665804 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,123 | enm-lib.cpp | GrossfieldLab_loos/Packages/ElasticNetworks/enm-lib.cpp | /*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010 Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify
it under the ter... | 3,068 | C++ | .cpp | 85 | 30.270588 | 112 | 0.596396 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,124 | gridscale.cpp | GrossfieldLab_loos/Packages/DensityTools/gridscale.cpp | /*
gridscale.cpp
Applies a constant scaling to a grid...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This packa... | 1,515 | C++ | .cpp | 40 | 34.85 | 80 | 0.745205 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,125 | contained.cpp | GrossfieldLab_loos/Packages/DensityTools/contained.cpp | /*
contained.cpp
Tracks the number of atoms within a blob over time...
usage:
contained model trajectory selection grid
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
... | 3,796 | C++ | .cpp | 98 | 34.969388 | 96 | 0.702592 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,126 | water-count.cpp | GrossfieldLab_loos/Packages/DensityTools/water-count.cpp | /*
water-count.cpp
usage:
water-count prefix >output.asc
Description:
Counts the number of waters that are inside the protein at each
timepoint and writes this out as a vector. In other words, it
just sums the rows for each column of the water matrix.
*/
/*
This file is part of LOOS.... | 2,234 | C++ | .cpp | 60 | 33.383333 | 77 | 0.68345 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,127 | water-hist.cpp | GrossfieldLab_loos/Packages/DensityTools/water-hist.cpp | /*
water-hist.cpp
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redis... | 12,393 | C++ | .cpp | 279 | 39.422939 | 135 | 0.669322 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,128 | grid2xplor.cpp | GrossfieldLab_loos/Packages/DensityTools/grid2xplor.cpp | /*
grid2xplor.cpp
Converts a grid (with a number of types) into an Xplor map...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of... | 4,717 | C++ | .cpp | 136 | 30.875 | 113 | 0.684977 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,129 | water-autocorrel.cpp | GrossfieldLab_loos/Packages/DensityTools/water-autocorrel.cpp | /*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2014, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify
... | 2,244 | C++ | .cpp | 66 | 30.121212 | 96 | 0.637332 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,130 | blob_stats.cpp | GrossfieldLab_loos/Packages/DensityTools/blob_stats.cpp | /*
blob_stats.cpp
Gather statistics on blobs...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS)... | 3,509 | C++ | .cpp | 103 | 30.514563 | 97 | 0.64069 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,131 | gridstat.cpp | GrossfieldLab_loos/Packages/DensityTools/gridstat.cpp | /*
gridstat.cpp
Simple grid statistics...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is fr... | 5,755 | C++ | .cpp | 173 | 29.369942 | 118 | 0.613583 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,132 | grid2ascii.cpp | GrossfieldLab_loos/Packages/DensityTools/grid2ascii.cpp | /*
grid2ascii
Convert a grid into a serialized ascii representation
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
... | 1,800 | C++ | .cpp | 46 | 35.586957 | 87 | 0.703405 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,133 | blobid.cpp | GrossfieldLab_loos/Packages/DensityTools/blobid.cpp | /*
blobid.cpp
Flood-fills a grid to identify blobs...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This packa... | 5,262 | C++ | .cpp | 133 | 35.669173 | 152 | 0.681102 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,134 | water-extract.cpp | GrossfieldLab_loos/Packages/DensityTools/water-extract.cpp | /*
water-extract.cpp
usage:
water-extract [options] model trajectory >output.pdb
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2011, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, Univers... | 2,453 | C++ | .cpp | 64 | 34.59375 | 82 | 0.72989 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,135 | gridautoscale.cpp | GrossfieldLab_loos/Packages/DensityTools/gridautoscale.cpp | /*
gridautoscale.cpp
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2012, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can re... | 3,276 | C++ | .cpp | 94 | 30.819149 | 87 | 0.658188 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,136 | gridmask.cpp | GrossfieldLab_loos/Packages/DensityTools/gridmask.cpp | /*
gridmask.cpp
Given an int grid that represents picked blobs, use this as a mask
against a double grid...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medi... | 3,606 | C++ | .cpp | 90 | 36.188889 | 93 | 0.702524 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,137 | internal-water-filter.cpp | GrossfieldLab_loos/Packages/DensityTools/internal-water-filter.cpp | /*
Internal water filter library
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software... | 12,847 | C++ | .cpp | 352 | 28.857955 | 116 | 0.530028 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,138 | gridgauss.cpp | GrossfieldLab_loos/Packages/DensityTools/gridgauss.cpp | /*
Gridgauss
Apply a gaussian kernel to a grid
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS)... | 2,732 | C++ | .cpp | 70 | 35.2 | 81 | 0.690087 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,139 | water-hist-lib.cpp | GrossfieldLab_loos/Packages/DensityTools/water-hist-lib.cpp | // -------------------------------------------------
// Water Histogram Library
// -------------------------------------------------
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009 Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
Sc... | 6,191 | C++ | .cpp | 159 | 30.289308 | 126 | 0.533087 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,140 | near_blobs.cpp | GrossfieldLab_loos/Packages/DensityTools/near_blobs.cpp | /*
near_blobs.cpp
Find residues within a given distance of a blob
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2012, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
... | 3,381 | C++ | .cpp | 95 | 31.115789 | 105 | 0.651235 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,141 | GridUtils.cpp | GrossfieldLab_loos/Packages/DensityTools/GridUtils.cpp | /*
Utility functions/classes for LOOS grids
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is fre... | 1,355 | C++ | .cpp | 35 | 33.942857 | 77 | 0.714509 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,142 | gridavg.cpp | GrossfieldLab_loos/Packages/DensityTools/gridavg.cpp | /*
gridavg
Average grids together. Requires that grids have the same dimensions.
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2013, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University ... | 2,581 | C++ | .cpp | 74 | 30.540541 | 111 | 0.65749 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,143 | gridinfo.cpp | GrossfieldLab_loos/Packages/DensityTools/gridinfo.cpp | /*
gridinfo.cpp
Just dump the grid header info...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOO... | 2,072 | C++ | .cpp | 57 | 32.77193 | 89 | 0.673347 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,144 | peakify.cpp | GrossfieldLab_loos/Packages/DensityTools/peakify.cpp | /*
Peakify.cpp
Creates a PDB representing peaks in the grid...
Usage: peakify threshold <input.grid >output.pdb
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of... | 2,375 | C++ | .cpp | 59 | 36.474576 | 90 | 0.70993 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,145 | water-survival.cpp | GrossfieldLab_loos/Packages/DensityTools/water-survival.cpp | // (c) 2014 Tod D. Romo, Grossfield Lab, URMC
#include <loos.hpp>
using namespace loos;
using namespace std;
typedef Math::Matrix<int> WaterClassMatrix;
int main(int argc, char *argv[]) {
string hdr = invocationHeader(argc, argv);
if (argc == 1) {
cerr << "Usage- " << argv[0] << " water_matrix [max-t] ... | 1,357 | C++ | .cpp | 49 | 23.265306 | 92 | 0.551779 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,146 | blob_contact.cpp | GrossfieldLab_loos/Packages/DensityTools/blob_contact.cpp | /*
blob_contact.cpp
Find residues within a given distance of a blob
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2012, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
... | 5,434 | C++ | .cpp | 150 | 31.546667 | 123 | 0.635544 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,147 | gridslice.cpp | GrossfieldLab_loos/Packages/DensityTools/gridslice.cpp | /*
gridslice.cpp
Takes a double grid and extracts a plane from it as a matrix...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of... | 3,015 | C++ | .cpp | 82 | 32.463415 | 104 | 0.65093 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,148 | griddiff.cpp | GrossfieldLab_loos/Packages/DensityTools/griddiff.cpp | /*
griddiff.cpp
Subtract one grid from another (required grids to match)
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2012, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Roches... | 1,895 | C++ | .cpp | 55 | 31.145455 | 77 | 0.717666 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,149 | water-sides.cpp | GrossfieldLab_loos/Packages/DensityTools/water-sides.cpp | /*
water-sides.cpp
Desc:
Classifies a water as being on one side of the membrane or the
other or inside the membrane (1 = upper, 0 = inside, -1 = lower).
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Departm... | 4,744 | C++ | .cpp | 128 | 33.15625 | 97 | 0.682991 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,150 | water-inside.cpp | GrossfieldLab_loos/Packages/DensityTools/water-inside.cpp | /*
water-inside.cpp
(c) 2008 Tod D. Romo,
Grossfield Lab,
University of Rochester Medical and Dental School
Applies a given set of criteria to determine whether or not a water
is inside a protein. A matrix is then built up where each column
represents a timepoint in the trajectory and each ro... | 4,853 | C++ | .cpp | 116 | 37.793103 | 102 | 0.678313 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,151 | pick_blob.cpp | GrossfieldLab_loos/Packages/DensityTools/pick_blob.cpp | /*
pick_blob.cpp
Given an grid-mask, a PDB, and a selection, finds the blob closest
to ANY atom in the selection...
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School ... | 8,999 | C++ | .cpp | 252 | 31.404762 | 132 | 0.652661 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,152 | water-lib.cpp | GrossfieldLab_loos/Packages/DensityTools/water-lib.cpp | // -------------------------------------------------
// Water (density) Library
// -------------------------------------------------
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009 Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
Sc... | 1,786 | C++ | .cpp | 44 | 34.863636 | 98 | 0.623248 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,153 | AverageLinkage.cpp | GrossfieldLab_loos/Packages/Clustering/AverageLinkage.cpp | #include "AverageLinkage.hpp"
namespace Clustering
{
Eigen::Matrix<dtype, 1, Eigen::Dynamic> AverageLinkage::dist(idxT idxA, idxT idxB)
{
idxT sizeA = currStg[idxA]->size();
idxT sizeB = currStg[idxB]->size();
return (sizeA * clusterDists.row(idxA) + sizeB * clusterDists.row(idxB)) / (sizeA + sizeB);
... | 325 | C++ | .cpp | 10 | 29.6 | 95 | 0.692063 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,154 | ClusteringOptions.cpp | GrossfieldLab_loos/Packages/Clustering/ClusteringOptions.cpp | #include "ClusteringOptions.hpp"
#include "ClusteringUtils.hpp"
#include <iostream>
#include <string>
namespace Clustering{
void ClusteringOptions::addGeneric(po::options_description & opts){
opts.add_options()
("score-file,f", po::value<std::string>(&similarity_filename), "File containing whitespace-delimit... | 1,372 | C++ | .cpp | 40 | 28.525 | 152 | 0.645675 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | true | false | false |
755,155 | KGS.cpp | GrossfieldLab_loos/Packages/Clustering/KGS.cpp | #include "KGS.hpp"
#include "ClusteringUtils.hpp"
#include <iostream>
using std::cout;
using std::endl;
using std::vector;
using namespace Eigen;
namespace Clustering
{
// call this to search for a cutoff stage in clustering.
idxT KGS::cutoff()
{
dtype min = avgSpread.minCoeff();
dtype max = avgSpread.maxCoeff();... | 3,585 | C++ | .cpp | 102 | 31.480392 | 100 | 0.653835 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,156 | cluster-kgs.cpp | GrossfieldLab_loos/Packages/Clustering/cluster-kgs.cpp | // cluster-kgs.cpp
// Kelly, Gardner, and Sutcliffe, Prot. Eng. 9 11 1063-1065 (1996)
// hereafter KGS
// To perform exactly the analysis specified there, one must first apply
// one of the all-to-all rmsd tolls (such as rmsds or multi-rmsds) before
// running this tool. Those tools write their RMSD matricies to cout, ... | 7,476 | C++ | .cpp | 139 | 52.172662 | 85 | 0.720797 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | true | false | false |
755,157 | ClusteringUtils.cpp | GrossfieldLab_loos/Packages/Clustering/ClusteringUtils.cpp | #include "ClusteringUtils.hpp"
#include "ClusteringTypedefs.hpp"
#include <iostream>
#include <algorithm>
#include <fstream>
using std::cout;
using std::endl;
using std::istream;
using std::ostream;
using std::sort;
using std::string;
using std::stringstream;
using std::vector;
using namespace Eigen;
namespace Cluste... | 3,394 | C++ | .cpp | 97 | 33.927835 | 87 | 0.639319 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,158 | HAC.cpp | GrossfieldLab_loos/Packages/Clustering/HAC.cpp | #include "HAC.hpp"
#include "ClusteringUtils.hpp"
#include <iostream>
using std::cout;
using std::endl;
using std::unique_ptr;
using std::vector;
using namespace Eigen;
// Merge two clusters into whichever is larger.
// Return true if new composite cluster is minRow, else return false
// In the case where clusters ar... | 4,233 | C++ | .cpp | 113 | 31.769912 | 101 | 0.663667 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | true | false | false |
755,159 | ufidpick.cpp | GrossfieldLab_loos/Packages/Convergence/ufidpick.cpp | /*
ufidpick
Picks uniform fiducial structures for a structural histogram, a la Lyman &
Zuckerman, J Phys Chem B (2007) 111:12876-12882
Usage- ufidpick model trajectory selection output-name probability [seed]
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
... | 3,912 | C++ | .cpp | 96 | 36.927083 | 105 | 0.692084 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,160 | expfit.cpp | GrossfieldLab_loos/Packages/Convergence/expfit.cpp | /*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2011, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify
it under the t... | 4,355 | C++ | .cpp | 126 | 30.214286 | 107 | 0.652403 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,161 | block_average.cpp | GrossfieldLab_loos/Packages/Convergence/block_average.cpp | /*
Compute block-averaged standard error for a time series
using the Flyvbjerg & Petersen approach. Outputs the block averaged
standard error as a function of block size -- you'll need to plot it
and estimate the plateau value.
References:
Flyvbjerg, H. & Petersen, H. G. Error estimates on averages ... | 8,500 | C++ | .cpp | 209 | 37.856459 | 162 | 0.682049 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,162 | fidpick.cpp | GrossfieldLab_loos/Packages/Convergence/fidpick.cpp | /*
Picks fiducial structures for a structural histogram, a la Lyman &
Zuckerman, Biophys J (2006) 91:164-172
Usage- fidpick model trajectory selection output-name cutoff [seed]
Note: This is the older method of partitioning based on a distance
cutoff only, rather than only taking the closest N structures ... | 4,992 | C++ | .cpp | 129 | 34.325581 | 107 | 0.687188 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,163 | decorr_time.cpp | GrossfieldLab_loos/Packages/Convergence/decorr_time.cpp | /*
Structural Histogram IID analysis a la Lyman & Zuckerman J Phys Chem
B (2007) 111:12876-12882
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of... | 10,658 | C++ | .cpp | 260 | 36.596154 | 102 | 0.655924 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,164 | coscon.cpp | GrossfieldLab_loos/Packages/Convergence/coscon.cpp | /*
Cosine content for varying windows of a trajectory,
based on:
Hess, B. "Convergence of sampling in protein simulations."
Phys Rev E (2002) 65(3):031910
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2011, Tod D. Romo
Department of B... | 8,126 | C++ | .cpp | 209 | 34.086124 | 119 | 0.673571 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,165 | block_avgconv.cpp | GrossfieldLab_loos/Packages/Convergence/block_avgconv.cpp | /*
block_avgconv.cpp
Convergence of average via block averaging
Usage- block_avgconv model traj selection range
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Den... | 5,248 | C++ | .cpp | 129 | 36.03876 | 101 | 0.667129 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | true | false | false |
755,166 | neff.cpp | GrossfieldLab_loos/Packages/Convergence/neff.cpp | /*
neff
Based on Zhang, Bhatt, and Zuckerman; JCTC, DOI: 10.1021/ct1002384
and code provided by the Zuckerman Lab
(http://www.ccbb.pitt.edu/Faculty/zuckerman/software.html)
Computes effective sample size given an assignment file and a state file
*/
/*
This file is part of LOOS.
LOOS (Lightweight ... | 5,518 | C++ | .cpp | 170 | 28.188235 | 93 | 0.63111 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,167 | avgconv.cpp | GrossfieldLab_loos/Packages/Convergence/avgconv.cpp | /*
avgconv
Usage- avgconv model traj selection range
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2011, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free ... | 4,790 | C++ | .cpp | 113 | 38.265487 | 144 | 0.691793 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | false | false | false | true | false | false |
755,168 | qcoscon.cpp | GrossfieldLab_loos/Packages/Convergence/qcoscon.cpp | /*
"Quick" Cosine content. Calculates the cosine content for the
entire trajectory for the first N modes.
based on:
Hess, B. "Convergence of sampling in protein simulations."
Phys Rev E (2002) 65(3):031910
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure libra... | 4,358 | C++ | .cpp | 116 | 33.706897 | 105 | 0.70231 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,169 | chist.cpp | GrossfieldLab_loos/Packages/Convergence/chist.cpp | // Histogram of a time series using an increasingly larger window
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2014, Tod D. Romo and Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This ... | 7,757 | C++ | .cpp | 198 | 33.813131 | 156 | 0.647414 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,170 | assign_frames.cpp | GrossfieldLab_loos/Packages/Convergence/assign_frames.cpp | /*
Assign frames of a trajectory to bins (determined by reference structures)
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2011, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This p... | 3,020 | C++ | .cpp | 79 | 34.43038 | 106 | 0.702749 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,171 | bcom.cpp | GrossfieldLab_loos/Packages/Convergence/bcom.cpp | /*
Perform a block-overlap in comparison to a full PCA
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is fr... | 10,746 | C++ | .cpp | 250 | 38.188 | 138 | 0.674808 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,172 | hierarchy.cpp | GrossfieldLab_loos/Packages/Convergence/hierarchy.cpp | /*
hierarchy
Based on Zhang, Bhatt, and Zuckerman; JCTC, DOI: 10.1021/ct1002384
and code provided by the Zuckerman Lab
(http://www.ccbb.pitt.edu/Faculty/zuckerman/software.html)
Given a trajectory whose structures have been binned into states via
reference structures, computes the MFPT between states and... | 10,278 | C++ | .cpp | 295 | 28.888136 | 105 | 0.588379 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,173 | fid-lib.cpp | GrossfieldLab_loos/Packages/Convergence/fid-lib.cpp | /*
fid-lib
Fiducial library
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2010, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redist... | 5,519 | C++ | .cpp | 142 | 34.246479 | 119 | 0.683833 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,174 | rsv-coscon.cpp | GrossfieldLab_loos/Packages/Convergence/rsv-coscon.cpp | /*
Matrix cosine content. Calculates the cosine content
of a matrix. Expected input is the RSVs of a PCA...
based on:
Hess, B. "Convergence of sampling in protein simulations."
Phys Rev E (2002) 65(3):031910
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure libr... | 4,407 | C++ | .cpp | 117 | 33.726496 | 105 | 0.691584 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,175 | sortfids.cpp | GrossfieldLab_loos/Packages/Convergence/sortfids.cpp | /*
sortfids
Structural histogram, a la Lyman &
Zuckerman, Biophys J (2006) 91:164-172
Usage- sortfids model selection fids hist newfidname
Sorts fiducials based on decreasing histogram bin population
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright... | 2,903 | C++ | .cpp | 84 | 31 | 84 | 0.709294 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,176 | boot_bcom.cpp | GrossfieldLab_loos/Packages/Convergence/boot_bcom.cpp |
/*
Perform a bootstrap analysis of a trajectory
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2009, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software... | 11,993 | C++ | .cpp | 274 | 39.051095 | 141 | 0.675911 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,177 | transition_contacts.cpp | GrossfieldLab_loos/Tools/transition_contacts.cpp | /*
transition_contacts: compute the fraction of native contacts in a trajectory,
based on an initial structure.
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2013, Nick Leioats, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine &... | 15,774 | C++ | .cpp | 359 | 38.130919 | 191 | 0.632269 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,178 | rmsds.cpp | GrossfieldLab_loos/Tools/rmsds.cpp | /*
rmsds.cpp
Pair-wise RMSD
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistri... | 15,477 | C++ | .cpp | 423 | 31.962175 | 185 | 0.638539 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,179 | fixdcd.cpp | GrossfieldLab_loos/Tools/fixdcd.cpp |
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2013, Tod D. Romo, Grossfield Lab
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify
... | 2,175 | C++ | .cpp | 61 | 29.967213 | 88 | 0.666175 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,180 | rad-gyr.cpp | GrossfieldLab_loos/Tools/rad-gyr.cpp | /*
Compute the distribution or timeseries of radii of gyration for a selection of
atoms.
Alan Grossfield
Grossfield Lab
Department of Biochemistry and Biophysics
University of Rochester Medical School
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 202... | 11,880 | C++ | .cpp | 252 | 42.43254 | 87 | 0.698318 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,181 | model-select.cpp | GrossfieldLab_loos/Tools/model-select.cpp | /*
model-select.cpp
Takes a model (PDB, PSF, etc) and a selection string. Parses the selection, then
applies it to the PDB and writes the output to stdout. This tool is
used maily for checking your selection strings to make sure you're
actually selecting what you intend to select...
*/
/*
This file is... | 6,235 | C++ | .cpp | 184 | 29.548913 | 107 | 0.666 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,182 | exposure.cpp | GrossfieldLab_loos/Tools/exposure.cpp | /*
exposure
(c) 2009 Tod D. Romo, Grossfield Lab
Department of Biochemistry
University of Rochster School of Medicine and Dentistry
Computes the degree of exposure of a set of selections over time.
The exposure is defined as the average density of a probe selection
within a spherical shell about each ... | 7,985 | C++ | .cpp | 190 | 37.742105 | 143 | 0.68276 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,183 | verap.cpp | GrossfieldLab_loos/Tools/verap.cpp | /*
Vertical (along Z) area profile using radius of gyration or max radius
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2016, Tod D. Romo, Grossfield Lab,
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
Th... | 6,863 | C++ | .cpp | 194 | 30.814433 | 106 | 0.652696 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,184 | rms-overlap.cpp | GrossfieldLab_loos/Tools/rms-overlap.cpp | /*
trans-rmsd.cpp
RMSDS between two sets of multiple trajectories
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008,2016 Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package... | 19,674 | C++ | .cpp | 491 | 36.069246 | 139 | 0.658878 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,185 | smooth-traj.cpp | GrossfieldLab_loos/Tools/smooth-traj.cpp | /*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2012, Tod D. Romo
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify
it under the t... | 7,249 | C++ | .cpp | 177 | 36.214689 | 127 | 0.669054 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,186 | rotamer.cpp | GrossfieldLab_loos/Tools/rotamer.cpp | /*
rotamer.cpp
Computes chi-1, chi-2 angles for selected side-chains. If the
requested angle doesn't exist, then -9999.99 is output as a marker.
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008 Tod D. Romo
Department of Biochemistry and Biophys... | 9,328 | C++ | .cpp | 245 | 34.465306 | 117 | 0.626195 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
755,187 | density-dist-windowed.cpp | GrossfieldLab_loos/Tools/density-dist-windowed.cpp | /*
density-dist-windowed.cpp
Compute the charge/mass/electron density along the z dimension of a system
*/
/*
This file is part of LOOS.
LOOS (Lightweight Object-Oriented Structure library)
Copyright (c) 2008, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, ... | 5,755 | C++ | .cpp | 148 | 29.763514 | 84 | 0.560382 | GrossfieldLab/loos | 121 | 26 | 11 | GPL-3.0 | 9/20/2024, 9:42:21 PM (Europe/Amsterdam) | false | false | true | false | false | true | false | false |
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