rdkit/Code/GraphMol/Descriptors/USRDescriptor.cpp

//
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#include <Geometry/point.h>
#include <Numerics/Vector.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include "USRDescriptor.h"

#include <boost/flyweight.hpp>
#include <boost/flyweight/key_value.hpp>
#include <boost/flyweight/no_tracking.hpp>

namespace RDKit {

namespace {
void calcDistances(const RDGeom::Point3DConstPtrVect &coords,
                   const RDGeom::Point3D &point,
                   std::vector<double> &distances) {
  distances.resize(coords.size());
  unsigned int i = 0;
  // loop over coordinates
  for (const auto *tpp : coords) {
    distances[i++] = (*tpp - point).length();
  }
}

void calcCentroid(const RDGeom::Point3DConstPtrVect &coords,
                  RDGeom::Point3D &pt) {
  PRECONDITION(!coords.empty(), "no coordinates");
  // set pt to zero
  pt *= 0.0;
  // loop over coordinates
  for (const auto *opt : coords) {
    pt += *opt;
  }
  pt /= coords.size();
}

unsigned int largestValId(const std::vector<double> &v) {
  PRECONDITION(!v.empty(), "no values");
  double res = v[0];
  unsigned int id = 0;
  for (unsigned int i = 1; i < v.size(); ++i) {
    if (v[i] > res) {
      res = v[i];
      id = i;
    }
  }
  return id;
}

unsigned int smallestValId(const std::vector<double> &v) {
  PRECONDITION(!v.empty(), "no values");
  double res = v[0];
  unsigned int id = 0;
  for (unsigned int i = 1; i < v.size(); ++i) {
    if (v[i] < res) {
      res = v[i];
      id = i;
    }
  }
  return id;
}

void calcMoments(const std::vector<double> &dist,
                 std::vector<double> &descriptor, int idx) {
  std::vector<double> moments(3, 0.0);
  unsigned int numPts = dist.size();
  if (numPts > 0) {
    // 1. moment: mean
    for (unsigned int i = 0; i < numPts; ++i) {
      moments[0] += dist[i];
    }
    moments[0] /= numPts;
    // 2. moment: standard deviation
    // 3. moment: cubic root of skewness
    for (unsigned int i = 0; i < numPts; ++i) {
      double diff = dist[i] - moments[0];
      moments[1] += diff * diff;
      moments[2] += diff * diff * diff;
    }
    moments[1] = sqrt(moments[1] / numPts);
    moments[2] /= numPts;
    if (moments[1] == 0) {
      moments[2] = 0.0;
    } else {
#ifdef WIN32
      moments[2] = moments[2] / (moments[1] * moments[1] * moments[1]);
      if (moments[2] >= 0)
        moments[2] = pow(moments[2], 1. / 3.);
      else
        moments[2] = -1. * pow(-1. * moments[2], 1. / 3.);
#else
      moments[2] = cbrt(moments[2] / (moments[1] * moments[1] * moments[1]));
#endif
    }
  }
  // add moments to descriptor
  std::copy(moments.begin(), moments.end(), descriptor.begin() + idx);
}

class ss_matcher {
 public:
  ss_matcher(){};
  ss_matcher(const std::string &pattern) {
    RDKit::RWMol *p = RDKit::SmartsToMol(pattern);
    TEST_ASSERT(p);
    m_matcher.reset(p);
  };
  const RDKit::ROMol *getMatcher() const { return m_matcher.get(); };

 private:
  RDKit::ROMOL_SPTR m_matcher;
};

// Definitions for feature points from
// https://bitbucket.org/aschreyer/usrcat/src/2aa77f970c2c/usrcat/__init__.py
const char *smartsPatterns[4] = {
    "[#6+0!$(*~[#7,#8,F]),SH0+0v2,s+0,S^3,Cl+0,Br+0,I+0]",  // hydrophobic
    "[a]",                                                  // aromatic
    "[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),\
$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]",  // acceptor
    "[N!H0v3,N!H0+v4,OH+0,SH+0,nH+0]"                              // donor
};
std::vector<std::string> featureSmarts(smartsPatterns, smartsPatterns + 4);
typedef boost::flyweight<boost::flyweights::key_value<std::string, ss_matcher>,
                         boost::flyweights::no_tracking>
    pattern_flyweight;

void getAtomIdsForFeatures(const ROMol &mol,
                           std::vector<std::vector<unsigned int>> &atomIds) {
  unsigned int numFeatures = featureSmarts.size();
  PRECONDITION(atomIds.size() == numFeatures,
               "atomIds must have be the same size as featureSmarts");
  std::vector<const ROMol *> featureMatchers;
  featureMatchers.reserve(numFeatures);
  for (const auto &feature : featureSmarts) {
    const ROMol *matcher = pattern_flyweight(feature).get().getMatcher();
    featureMatchers.push_back(matcher);
  }
  for (unsigned int i = 0; i < numFeatures; ++i) {
    std::vector<MatchVectType> matchVect;
    // to maintain thread safety, we have to copy the pattern molecules:
    SubstructMatch(mol, ROMol(*featureMatchers[i], true), matchVect);
    for (const auto &mv : matchVect) {
      for (auto mi : mv) {
        atomIds[i].push_back(mi.second);
      }
    }
  }  // end loop over features
}

}  // end namespace

namespace Descriptors {

void USR(const ROMol &mol, std::vector<double> &descriptor, int confId) {
  PRECONDITION(descriptor.size() == 12, "descriptor must have 12 elements");
  unsigned int na = mol.getNumAtoms();
  // check that number of atoms > 3
  if (na < 3) {
    throw ValueErrorException("Number of atoms must be greater than 3");
  }
  // check that minimum a conformer exists
  if (mol.getNumConformers() == 0) {
    throw ConformerException("No conformations available on this molecule");
  }

  const Conformer &conf = mol.getConformer(confId);
  RDGeom::Point3DConstPtrVect coords(na);
  // loop over atoms
  for (unsigned int ai = 0; ai < na; ++ai) {
    coords[ai] = &conf.getAtomPos(ai);
  }
  // the four distances
  std::vector<std::vector<double>> dist(4);
  std::vector<RDGeom::Point3D> points(4);
  calcUSRDistributions(coords, dist, points);

  calcUSRFromDistributions(dist, descriptor);
}

void USRCAT(const ROMol &mol, std::vector<double> &descriptor,
            std::vector<std::vector<unsigned int>> &atomIds, int confId) {
  unsigned int na = mol.getNumAtoms();
  // check that number of atoms > 3
  if (na < 3) {
    throw ValueErrorException("Number of atoms must be greater than 3");
  }
  // check that minimum a conformer exists
  if (mol.getNumConformers() == 0) {
    throw ConformerException("No conformations available on this molecule");
  }

  // get atom selections
  unsigned int numClasses = atomIds.size();
  if (numClasses == 0) {  // no user input, use default values
    numClasses = featureSmarts.size();
    atomIds.resize(numClasses);
    getAtomIdsForFeatures(mol, atomIds);
  }
  PRECONDITION(descriptor.size() == 12 * (numClasses + 1),
               "descriptor wrong size");

  const Conformer &conf = mol.getConformer(confId);
  RDGeom::Point3DConstPtrVect coords(na);
  // loop over atoms
  for (unsigned int ai = 0; ai < na; ++ai) {
    coords[ai] = &conf.getAtomPos(ai);
  }
  // the original USR
  std::vector<std::vector<double>> distribs(4);
  std::vector<RDGeom::Point3D> points(4);
  calcUSRDistributions(coords, distribs, points);
  std::vector<double> tmpDescriptor(12);
  calcUSRFromDistributions(distribs, tmpDescriptor);
  std::copy(tmpDescriptor.begin(), tmpDescriptor.end(), descriptor.begin());

  // loop over the atom selections
  unsigned int featIdx = 12;
  for (const auto &atomsInClass : atomIds) {
    // reduce the coordinates to the atoms of interest
    RDGeom::Point3DConstPtrVect reducedCoords;
    reducedCoords.reserve(atomsInClass.size());
    for (const auto idx : atomsInClass) {
      reducedCoords.push_back(coords[idx]);
    }
    calcUSRDistributionsFromPoints(reducedCoords, points, distribs);
    calcUSRFromDistributions(distribs, tmpDescriptor);
    std::copy(tmpDescriptor.begin(), tmpDescriptor.end(),
              descriptor.begin() + featIdx);
    featIdx += 12;
  }
}

void calcUSRDistributions(const RDGeom::Point3DConstPtrVect &coords,
                          std::vector<std::vector<double>> &dist,
                          std::vector<RDGeom::Point3D> &points) {
  PRECONDITION(dist.size() == 4, "dist must have 4 elements");
  PRECONDITION(points.size() == 4, "points must have 4 elements");
  // ctd = centroid
  calcCentroid(coords, points[0]);
  calcDistances(coords, points[0], dist[0]);
  // catc = closest atom to centroid
  points[1] = (*coords[smallestValId(dist[0])]);
  calcDistances(coords, points[1], dist[1]);
  // fatc = farthest atom to centroid
  points[2] = (*coords[largestValId(dist[0])]);
  calcDistances(coords, points[2], dist[2]);
  // fatf = farthest atom to fatc
  points[3] = (*coords[largestValId(dist[2])]);
  calcDistances(coords, points[3], dist[3]);
}

void calcUSRDistributionsFromPoints(const RDGeom::Point3DConstPtrVect &coords,
                                    const std::vector<RDGeom::Point3D> &points,
                                    std::vector<std::vector<double>> &dist) {
  PRECONDITION(points.size() == dist.size(),
               "points and dist must have the same size");
  for (unsigned int i = 0; i < points.size(); ++i) {
    calcDistances(coords, points[i], dist[i]);
  }
}

void calcUSRFromDistributions(const std::vector<std::vector<double>> &dist,
                              std::vector<double> &descriptor) {
  PRECONDITION(descriptor.size() == 3 * dist.size(),
               "descriptor must have 3 times more elements than dist");
  for (unsigned int i = 0; i < dist.size(); ++i) {
    calcMoments(dist[i], descriptor, 3 * i);
  }
}

double calcUSRScore(const std::vector<double> &d1,
                    const std::vector<double> &d2,
                    const std::vector<double> &weights) {
  unsigned int num = 12;  // length of each subset
  PRECONDITION(d1.size() == d2.size(), "descriptors must have the same size");
  PRECONDITION(weights.size() == (d1.size() / num),
               "size of weights not correct");
  double score = 1.0;
  for (unsigned int w = 0; w < (d1.size() / num); ++w) {
    double tmpScore = 0.0;
    unsigned int offset = num * w;
    for (unsigned int i = 0; i < num; ++i) {
      tmpScore += fabs(d1[i + offset] - d2[i + offset]);
    }
    tmpScore /= num;
    score += weights[w] * tmpScore;
  }
  return 1.0 / score;
}

}  // end of namespace Descriptors
}  // end of namespace RDKit