rdkit/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp

// $Id$
//
//   Copyright (C) 2005-2006 Rational Discovery LLC
//
//   @@ 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 "ShapeUtils.h"
#include "ShapeEncoder.h"
#include <Geometry/UniformGrid3D.h>
#include <GraphMol/RDKitBase.h>
#include <Geometry/Transform3D.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <Geometry/GridUtils.h>

namespace RDKit {
namespace MolShapes {

void computeConfBox(const Conformer &conf, RDGeom::Point3D &leftBottom,
                    RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans,
                    double padding) {
  double xmin, xmax, ymin, ymax, zmin, zmax;
  xmin = ymin = zmin = 1.e8;
  xmax = ymax = zmax = -1.e8;
  unsigned int i, nAtms = conf.getNumAtoms();
  for (i = 0; i < nAtms; ++i) {
    RDGeom::Point3D loc = conf.getAtomPos(i);
    if (trans) {
      trans->TransformPoint(loc);
    }
    xmax = std::max(xmax, loc.x);
    xmin = std::min(xmin, loc.x);
    ymax = std::max(ymax, loc.y);
    ymin = std::min(ymin, loc.y);
    zmax = std::max(zmax, loc.z);
    zmin = std::min(zmin, loc.z);
  }
  RDGeom::Point3D padPt(padding, padding, padding);
  leftBottom.x = xmin;
  leftBottom.y = ymin;
  leftBottom.z = zmin;
  rightTop.x = xmax;
  rightTop.y = ymax;
  rightTop.z = zmax;
  leftBottom -= padPt;
  rightTop += padPt;
}

void computeConfDimsAndOffset(const Conformer &conf, RDGeom::Point3D &dims,
                              RDGeom::Point3D &offSet,
                              const RDGeom::Transform3D *trans,
                              double padding) {
  // RDGeom::Point3D lb, rb;
  computeConfBox(conf, offSet, dims, trans, padding);
  dims -= offSet;
}

std::vector<double> getConfDimensions(const Conformer &conf, double padding,
                                      const RDGeom::Point3D *center,
                                      bool ignoreHs) {
  RDGeom::Point3D lb, rb;
  computeConfBox(conf, lb, rb, nullptr, padding);

  if (!center) {
    RDGeom::Point3D cpt = MolTransforms::computeCentroid(conf, ignoreHs);
    rb -= cpt;
    lb -= cpt;
  } else {
    rb -= (*center);
    lb -= (*center);
  }
  lb *= -1.0;
  double dimX = 2.0 * std::max(rb.x, lb.x);
  double dimY = 2.0 * std::max(rb.y, lb.y);
  double dimZ = 2.0 * std::max(rb.z, lb.z);
  std::vector<double> res;
  res.reserve(3);
  res.push_back(dimX);
  res.push_back(dimY);
  res.push_back(dimZ);
  return res;
}

void computeUnionBox(const RDGeom::Point3D &leftBottom1,
                     const RDGeom::Point3D &rightTop1,
                     const RDGeom::Point3D &leftBottom2,
                     const RDGeom::Point3D &rightTop2,
                     RDGeom::Point3D &uLeftBottom, RDGeom::Point3D &uRightTop) {
  uLeftBottom.x = std::min(leftBottom1.x, leftBottom2.x);
  uLeftBottom.y = std::min(leftBottom1.y, leftBottom2.y);
  uLeftBottom.z = std::min(leftBottom1.z, leftBottom2.z);

  uRightTop.x = std::max(rightTop1.x, rightTop2.x);
  uRightTop.y = std::max(rightTop1.y, rightTop2.y);
  uRightTop.z = std::max(rightTop1.z, rightTop2.z);
}

double tverskyIndex(const ROMol &mol1, const ROMol &mol2, double alpha, double beta, int confId1,
                        int confId2, double gridSpacing,
                        DiscreteValueVect::DiscreteValueType bitsPerPoint,
                        double vdwScale, double stepSize, int maxLayers,
                        bool ignoreHs) {
  const Conformer &conf1 = mol1.getConformer(confId1);
  const Conformer &conf2 = mol2.getConformer(confId2);
  return tverskyIndex(conf1, conf2, alpha, beta, gridSpacing, bitsPerPoint,
                          vdwScale, stepSize, maxLayers, ignoreHs);
}

double tverskyIndex(const Conformer &conf1, const Conformer &conf2, double alpha, double beta,
                        double gridSpacing,
                        DiscreteValueVect::DiscreteValueType bitsPerPoint,
                        double vdwScale, double stepSize, int maxLayers,
                        bool ignoreHs) {
  RDGeom::Transform3D *trans = MolTransforms::computeCanonicalTransform(conf1);

  // now use this transform and figure out what size grid we will need
  // find the lower-left and upper-right corners for each of the conformers
  // and take a union of these boxes - we will use this fo grid dimensions
  RDGeom::Point3D leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
      uRightTop;
  computeConfBox(conf1, leftBottom1, rightTop1, trans);
  computeConfBox(conf2, leftBottom2, rightTop2, trans);

  computeUnionBox(leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
                  uRightTop);

  // make the grid object to store the encoding
  uRightTop -= uLeftBottom;  // uRightTop now has grid dimensions

  RDGeom::UniformGrid3D grd1(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
                             bitsPerPoint, &uLeftBottom);
  RDGeom::UniformGrid3D grd2(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
                             bitsPerPoint, &uLeftBottom);

  EncodeShape(conf1, grd1, trans, vdwScale, stepSize, maxLayers, ignoreHs);
  EncodeShape(conf2, grd2, trans, vdwScale, stepSize, maxLayers, ignoreHs);

  delete trans;
  return RDGeom::tverskyIndex(grd1, grd2, alpha, beta);
}


double tanimotoDistance(const ROMol &mol1, const ROMol &mol2, int confId1,
                        int confId2, double gridSpacing,
                        DiscreteValueVect::DiscreteValueType bitsPerPoint,
                        double vdwScale, double stepSize, int maxLayers,
                        bool ignoreHs) {
  const Conformer &conf1 = mol1.getConformer(confId1);
  const Conformer &conf2 = mol2.getConformer(confId2);
  return tanimotoDistance(conf1, conf2, gridSpacing = 0.5, bitsPerPoint,
                          vdwScale, stepSize, maxLayers, ignoreHs);
}

double tanimotoDistance(const Conformer &conf1, const Conformer &conf2,
                        double gridSpacing,
                        DiscreteValueVect::DiscreteValueType bitsPerPoint,
                        double vdwScale, double stepSize, int maxLayers,
                        bool ignoreHs) {
  RDGeom::Transform3D *trans = MolTransforms::computeCanonicalTransform(conf1);

  // now use this transform and figure out what size grid we will need
  // find the lower-left and upper-right corners for each of the conformers
  // and take a union of these boxes - we will use this fo grid dimensions
  RDGeom::Point3D leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
      uRightTop;
  computeConfBox(conf1, leftBottom1, rightTop1, trans);
  computeConfBox(conf2, leftBottom2, rightTop2, trans);

  computeUnionBox(leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
                  uRightTop);

  // make the grid object to store the encoding
  uRightTop -= uLeftBottom;  // uRightTop now has grid dimensions

  RDGeom::UniformGrid3D grd1(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
                             bitsPerPoint, &uLeftBottom);
  RDGeom::UniformGrid3D grd2(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
                             bitsPerPoint, &uLeftBottom);

  EncodeShape(conf1, grd1, trans, vdwScale, stepSize, maxLayers, ignoreHs);
  EncodeShape(conf2, grd2, trans, vdwScale, stepSize, maxLayers, ignoreHs);

  delete trans;
  return RDGeom::tanimotoDistance(grd1, grd2);
}

double protrudeDistance(const ROMol &mol1, const ROMol &mol2, int confId1,
                        int confId2, double gridSpacing,
                        DiscreteValueVect::DiscreteValueType bitsPerPoint,
                        double vdwScale, double stepSize, int maxLayers,
                        bool ignoreHs, bool allowReordering) {
  const Conformer &conf1 = mol1.getConformer(confId1);
  const Conformer &conf2 = mol2.getConformer(confId2);
  return protrudeDistance(conf1, conf2, gridSpacing = 0.5, bitsPerPoint,
                          vdwScale, stepSize, maxLayers, ignoreHs,
                          allowReordering);
}

double protrudeDistance(const Conformer &conf1, const Conformer &conf2,
                        double gridSpacing,
                        DiscreteValueVect::DiscreteValueType bitsPerPoint,
                        double vdwScale, double stepSize, int maxLayers,
                        bool ignoreHs, bool allowReordering) {
  //
  // FIX: all this duplicated code needs to be refactored out.
  //
  RDGeom::Transform3D *trans = MolTransforms::computeCanonicalTransform(conf1);

  // now use this transform and figure out what size grid we will need
  // find the lower-left and upper-right corners for each of the conformers
  // and take a union of these boxes - we will use this fo grid dimensions
  RDGeom::Point3D leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
      uRightTop;
  computeConfBox(conf1, leftBottom1, rightTop1, trans);
  computeConfBox(conf2, leftBottom2, rightTop2, trans);

  computeUnionBox(leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
                  uRightTop);

  // make the grid object to store the encoding
  uRightTop -= uLeftBottom;  // uRightTop now has grid dimensions

  RDGeom::UniformGrid3D grd1(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
                             bitsPerPoint, &uLeftBottom);
  RDGeom::UniformGrid3D grd2(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
                             bitsPerPoint, &uLeftBottom);

  EncodeShape(conf1, grd1, trans, vdwScale, stepSize, maxLayers, ignoreHs);
  EncodeShape(conf2, grd2, trans, vdwScale, stepSize, maxLayers, ignoreHs);
  delete trans;

  double res;
  if (allowReordering && (grd2.getOccupancyVect()->getTotalVal() <
                          grd1.getOccupancyVect()->getTotalVal())) {
    res = RDGeom::protrudeDistance(grd2, grd1);
  } else {
    res = RDGeom::protrudeDistance(grd1, grd2);
  }
  return res;
}
}
}