O3AAlignMolecules.h

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//
//  Copyright (C) 2013-2014 Paolo Tosco
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_O3AALIGNMOLECULES_H_
#define _RD_O3AALIGNMOLECULES_H_
 
#include <RDGeneral/Invariant.h>
#include <Geometry/Transform3D.h>
#include <Geometry/point.h>
#include <Numerics/Vector.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <GraphMol/MolAlign/AlignMolecules.h>
#include <vector>
#include <cmath>
#include <boost/shared_ptr.hpp>
#include <boost/multi_array.hpp>
#include <boost/dynamic_bitset.hpp>
 
namespace RDKit {
namespace MolAlign {
struct RDKIT_MOLALIGN_EXPORT O3AFuncData {
  const Conformer *prbConf;
  const Conformer *refConf;
  void *prbProp;
  void *refProp;
  int coeff;
  int weight;
  bool useMMFFSim;
};
inline bool isDoubleZero(const double x) {
  return ((x < 1.0e-10) && (x > -1.0e-10));
};
 
class O3AConstraintVect;
 
//! A class to define alignment constraints. Each constraint
//! is defined by a pair of atom indexes (one for the probe,
//! one for the reference) and a weight. Constraints can
//! can be added via the O3AConstraintVect class.
class RDKIT_MOLALIGN_EXPORT O3AConstraint {
  friend class O3AConstraintVect;
 
 public:
  double getPrbIdx() { return d_prbIdx; }
  double getRefIdx() { return d_refIdx; }
  double getWeight() { return d_weight; }
 
 private:
  unsigned int d_idx;
  unsigned int d_prbIdx;
  unsigned int d_refIdx;
  double d_weight;
};
 
//! A class to store a vector of alignment constraints. Each constraint
//! is defined by an O3AConstraint object. Each time the append()
//! method is invoked, the vector is sorted to make lookup faster.
//! Hence, constraints are not necessarily stored in the same order
//! they were appended.
class RDKIT_MOLALIGN_EXPORT O3AConstraintVect {
 public:
  O3AConstraintVect() {}
  ~O3AConstraintVect() = default;
  void append(unsigned int prbIdx, unsigned int refIdx, double weight) {
    O3AConstraint *o3aConstraint = new O3AConstraint();
    o3aConstraint->d_idx = d_count;
    o3aConstraint->d_prbIdx = prbIdx;
    o3aConstraint->d_refIdx = refIdx;
    o3aConstraint->d_weight = weight;
    d_o3aConstraintVect.emplace_back(o3aConstraint);
    std::sort(d_o3aConstraintVect.begin(), d_o3aConstraintVect.end(),
              d_compareO3AConstraint);
    ++d_count;
  }
  std::vector<boost::shared_ptr<O3AConstraint>>::size_type size() {
    return d_o3aConstraintVect.size();
  }
  O3AConstraint *operator[](unsigned int i) {
    return d_o3aConstraintVect[i].get();
  }
 
 private:
  unsigned int d_count{0};
  std::vector<boost::shared_ptr<O3AConstraint>> d_o3aConstraintVect;
  static bool d_compareO3AConstraint(boost::shared_ptr<O3AConstraint> a,
                                     boost::shared_ptr<O3AConstraint> b) {
    return (
        (a->d_prbIdx != b->d_prbIdx)
            ? (a->d_prbIdx < b->d_prbIdx)
            : ((a->d_refIdx != b->d_refIdx)
                   ? (a->d_refIdx < b->d_refIdx)
                   : ((a->d_weight != b->d_weight) ? (a->d_weight > b->d_weight)
                                                   : (a->d_idx < b->d_idx))));
  }
};
 
const int O3_DUMMY_COST = 100000;
const int O3_LARGE_NEGATIVE_WEIGHT = -1e9;
const int O3_DEFAULT_CONSTRAINT_WEIGHT = 100.0;
const unsigned int O3_MAX_H_BINS = 20;
const unsigned int O3_MAX_SDM_ITERATIONS = 100;
const unsigned int O3_MAX_SDM_THRESHOLD_ITER = 3;
const double O3_RANDOM_TRANS_COEFF = 5.0;
const double O3_THRESHOLD_DIFF_DISTANCE = 0.1;
const double O3_SDM_THRESHOLD_START = 0.7;
const double O3_SDM_THRESHOLD_STEP = 0.3;
const double O3_CHARGE_WEIGHT = 10.0;
const double O3_CRIPPEN_WEIGHT = 10.0;
const double O3_RMSD_THRESHOLD = 1.0e-04;
const double O3_SCORE_THRESHOLD = 0.01;
const double O3_SCORING_FUNCTION_ALPHA = 5.0;
const double O3_SCORING_FUNCTION_BETA = 0.5;
const double O3_CHARGE_COEFF = 5.0;
const double O3_CRIPPEN_COEFF = 1.0;
const int O3_MAX_WEIGHT_COEFF = 5;
enum {
  O3_USE_MMFF_WEIGHTS = (1 << 0),
  O3_ACCURACY_MASK = (1 << 0 | 1 << 1),
  O3_LOCAL_ONLY = (1 << 2)
};
 
class RDKIT_MOLALIGN_EXPORT MolHistogram {
 public:
  MolHistogram(const ROMol &mol, const double *dmat, bool cleanupDmat = false);
  ~MolHistogram() = default;
  inline int get(const unsigned int y, const unsigned int x) const {
    PRECONDITION(y < d_h.shape()[0], "Invalid index on MolHistogram");
    PRECONDITION(x < d_h.shape()[1], "Invalid index on MolHistogram");
    return d_h[y][x];
  }
 
 private:
  boost::multi_array<int, 2> d_h;
};
 
class RDKIT_MOLALIGN_EXPORT LAP {
 public:
  LAP(unsigned int dim)
      : d_rowSol(dim),
        d_colSol(dim),
        d_free(dim),
        d_colList(dim),
        d_matches(dim),
        d_d(dim),
        d_v(dim),
        d_pred(dim),
        d_cost(boost::extents[dim][dim]) {}
  ~LAP() = default;
  int getCost(const unsigned int i, const unsigned int j) {
    PRECONDITION(i < d_cost.shape()[0], "Invalid index on LAP.cost");
    PRECONDITION(j < d_cost.shape()[1], "Invalid index on LAP.cost");
    return d_cost[i][j];
  }
  int getRowSol(const unsigned int i) {
    PRECONDITION(i < d_rowSol.size(), "Invalid index on LAP.rowSol");
    return d_rowSol[i];
  }
  void computeMinCostPath(const int dim);
  void computeCostMatrix(const ROMol &prbMol, const MolHistogram &prbHist,
                         const ROMol &refMol, const MolHistogram &refHist,
                         O3AConstraintVect *o3aConstraintVect,
                         int (*costFunc)(const unsigned int, const unsigned int,
                                         double, void *),
                         void *data, const unsigned int n_bins = O3_MAX_H_BINS);
 
 private:
  std::vector<int> d_rowSol;
  std::vector<int> d_colSol;
  std::vector<int> d_free;
  std::vector<int> d_colList;
  std::vector<int> d_matches;
  std::vector<int> d_d;
  std::vector<int> d_v;
  std::vector<int> d_pred;
  boost::multi_array<int, 2> d_cost;
};
 
class RDKIT_MOLALIGN_EXPORT SDM {
 public:
  // constructor
  SDM(const Conformer *prbConf = nullptr, const Conformer *refConf = nullptr,
      O3AConstraintVect *o3aConstraintVect = nullptr)
      : d_prbConf(prbConf),
        d_refConf(refConf),
        d_o3aConstraintVect(o3aConstraintVect) {}
  // copy constructor
  SDM(const SDM &other)
      : d_prbConf(other.d_prbConf),
        d_refConf(other.d_refConf),
        d_o3aConstraintVect(other.d_o3aConstraintVect),
        d_SDMPtrVect(other.d_SDMPtrVect.size()) {
    for (unsigned int i = 0; i < d_SDMPtrVect.size(); ++i) {
      d_SDMPtrVect[i] = boost::shared_ptr<SDMElement>(new SDMElement());
      memcpy(d_SDMPtrVect[i].get(), other.d_SDMPtrVect[i].get(),
             sizeof(SDMElement));
    }
  }
  // assignment operator
  SDM &operator=(const SDM &other) {
    if (this == &other) {
      return *this;
    }
    d_prbConf = other.d_prbConf;
    d_refConf = other.d_refConf;
    d_o3aConstraintVect = other.d_o3aConstraintVect;
    d_SDMPtrVect.resize(other.d_SDMPtrVect.size());
    for (unsigned int i = 0; i < d_SDMPtrVect.size(); ++i) {
      d_SDMPtrVect[i] = boost::shared_ptr<SDMElement>(new SDMElement());
      memcpy(d_SDMPtrVect[i].get(), other.d_SDMPtrVect[i].get(),
             sizeof(SDMElement));
    }
 
    return *this;
  }
  // destructor
  ~SDM() = default;
  void fillFromDist(double threshold,
                    const boost::dynamic_bitset<> &refHvyAtoms,
                    const boost::dynamic_bitset<> &prbHvyAtoms);
  void fillFromLAP(LAP &lap);
  double scoreAlignment(double (*scoringFunc)(const unsigned int,
                                              const unsigned int, void *),
                        void *data);
  void prepareMatchWeightsVect(RDKit::MatchVectType &matchVect,
                               RDNumeric::DoubleVector &weights,
                               double (*weightFunc)(const unsigned int,
                                                    const unsigned int, void *),
                               void *data);
  unsigned int size() { return d_SDMPtrVect.size(); }
 
 private:
  typedef struct SDMElement {
    unsigned int idx[2];
    int score;
    int cost;
    double sqDist;
    O3AConstraint *o3aConstraint;
  } SDMElement;
  const Conformer *d_prbConf;
  const Conformer *d_refConf;
  O3AConstraintVect *d_o3aConstraintVect;
  std::vector<boost::shared_ptr<SDMElement>> d_SDMPtrVect;
  static bool compareSDMScore(boost::shared_ptr<SDMElement> a,
                              boost::shared_ptr<SDMElement> b) {
    return ((a->score != b->score)
                ? (a->score < b->score)
                : ((a->cost != b->cost)
                       ? (a->cost < b->cost)
                       : ((a->idx[0] != b->idx[0]) ? (a->idx[0] < b->idx[0])
                                                   : (a->idx[1] < b->idx[1]))));
  }
  static bool compareSDMDist(boost::shared_ptr<SDMElement> a,
                             boost::shared_ptr<SDMElement> b) {
    double aWeight = (a->o3aConstraint ? a->o3aConstraint->getWeight() : 0.0);
    double bWeight = (b->o3aConstraint ? b->o3aConstraint->getWeight() : 0.0);
    return ((aWeight != bWeight)
                ? (aWeight > bWeight)
                : ((a->sqDist != b->sqDist)
                       ? (a->sqDist < b->sqDist)
                       : ((a->idx[0] != b->idx[0]) ? (a->idx[0] < b->idx[0])
                                                   : (a->idx[1] < b->idx[1]))));
  }
};
 
class RDKIT_MOLALIGN_EXPORT O3A {
 public:
  //! pre-defined atom typing schemes
  typedef enum { MMFF94 = 0, CRIPPEN } AtomTypeScheme;
  O3A(ROMol &prbMol, const ROMol &refMol, void *prbProp, void *refProp,
      AtomTypeScheme atomTypes = MMFF94, const int prbCid = -1,
      const int refCid = -1, const bool reflect = false,
      const unsigned int maxIters = 50, unsigned int options = 0,
      const MatchVectType *constraintMap = nullptr,
      const RDNumeric::DoubleVector *constraintWeights = nullptr,
      LAP *extLAP = nullptr, MolHistogram *extPrbHist = nullptr,
      MolHistogram *extRefHist = nullptr);
  O3A(int (*costFunc)(const unsigned int, const unsigned int, double, void *),
      double (*weightFunc)(const unsigned int, const unsigned int, void *),
      double (*scoringFunc)(const unsigned int, const unsigned int, void *),
      void *data, ROMol &prbMol, const ROMol &refMol, const int prbCid,
      const int refCid, const boost::dynamic_bitset<> &prbHvyAtoms,
      const boost::dynamic_bitset<> &refHvyAtoms, const bool reflect = false,
      const unsigned int maxIters = 50, unsigned int options = 0,
      O3AConstraintVect *o3aConstraintVect = nullptr,
      ROMol *extWorkPrbMol = nullptr, LAP *extLAP = nullptr,
      MolHistogram *extPrbHist = nullptr, MolHistogram *extRefHist = nullptr);
  ~O3A() {
    if (d_o3aMatchVect) {
      delete d_o3aMatchVect;
    }
    if (d_o3aWeights) {
      delete d_o3aWeights;
    }
  }
  double align();
  double trans(RDGeom::Transform3D &trans);
  double score() { return d_o3aScore; }
  const RDKit::MatchVectType *matches() { return d_o3aMatchVect; }
  const RDNumeric::DoubleVector *weights() { return d_o3aWeights; }
 
 private:
  ROMol *d_prbMol;
  const ROMol *d_refMol;
  int d_prbCid;
  int d_refCid;
  bool d_reflect;
  unsigned int d_maxIters;
  const RDKit::MatchVectType *d_o3aMatchVect;
  const RDNumeric::DoubleVector *d_o3aWeights;
  double d_o3aScore;
};
 
RDKIT_MOLALIGN_EXPORT void randomTransform(ROMol &mol, const int cid = -1,
                                           const int seed = -1);
RDKIT_MOLALIGN_EXPORT const RDGeom::POINT3D_VECT *reflect(
    const Conformer &conf);
RDKIT_MOLALIGN_EXPORT int o3aMMFFCostFunc(const unsigned int prbIdx,
                                          const unsigned int refIdx,
                                          double hSum, void *data);
RDKIT_MOLALIGN_EXPORT double o3aMMFFWeightFunc(const unsigned int prbIdx,
                                               const unsigned int refIdx,
                                               void *data);
RDKIT_MOLALIGN_EXPORT double o3aMMFFScoringFunc(const unsigned int prbIdx,
                                                const unsigned int refIdx,
                                                void *data);
RDKIT_MOLALIGN_EXPORT int o3aCrippenCostFunc(const unsigned int prbIdx,
                                             const unsigned int refIdx,
                                             double hSum, void *data);
RDKIT_MOLALIGN_EXPORT double o3aCrippenWeightFunc(const unsigned int prbIdx,
                                                  const unsigned int refIdx,
                                                  void *data);
RDKIT_MOLALIGN_EXPORT double o3aCrippenScoringFunc(const unsigned int prbIdx,
                                                   const unsigned int refIdx,
                                                   void *data);
 
RDKIT_MOLALIGN_EXPORT void getO3AForProbeConfs(
    ROMol &prbMol, const ROMol &refMol, void *prbProp, void *refProp,
    std::vector<boost::shared_ptr<O3A>> &res, int numThreads = 1,
    O3A::AtomTypeScheme atomTypes = O3A::MMFF94, const int refCid = -1,
    const bool reflect = false, const unsigned int maxIters = 50,
    unsigned int options = 0, const MatchVectType *constraintMap = nullptr,
    const RDNumeric::DoubleVector *constraintWeights = nullptr);
}  // namespace MolAlign
}  // namespace RDKit
#endif