File size: 3,642 Bytes
8efb4bd | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 | #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 */
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