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244 lines
9.8 KiB
C++
244 lines
9.8 KiB
C++
//
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// Copyright (C) 2005-2021 Greg Landrum and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "ShapeUtils.h"
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#include "ShapeEncoder.h"
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#include <Geometry/UniformGrid3D.h>
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#include <GraphMol/RDKitBase.h>
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#include <Geometry/Transform3D.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <Geometry/GridUtils.h>
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namespace RDKit {
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namespace MolShapes {
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void computeConfBox(const Conformer &conf, RDGeom::Point3D &leftBottom,
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RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans,
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double padding) {
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double xmin, xmax, ymin, ymax, zmin, zmax;
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xmin = ymin = zmin = 1.e8;
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xmax = ymax = zmax = -1.e8;
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unsigned int i, nAtms = conf.getNumAtoms();
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for (i = 0; i < nAtms; ++i) {
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RDGeom::Point3D loc = conf.getAtomPos(i);
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if (trans) {
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trans->TransformPoint(loc);
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}
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xmax = std::max(xmax, loc.x);
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xmin = std::min(xmin, loc.x);
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ymax = std::max(ymax, loc.y);
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ymin = std::min(ymin, loc.y);
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zmax = std::max(zmax, loc.z);
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zmin = std::min(zmin, loc.z);
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}
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RDGeom::Point3D padPt(padding, padding, padding);
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leftBottom.x = xmin;
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leftBottom.y = ymin;
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leftBottom.z = zmin;
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rightTop.x = xmax;
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rightTop.y = ymax;
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rightTop.z = zmax;
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leftBottom -= padPt;
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rightTop += padPt;
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}
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void computeConfDimsAndOffset(const Conformer &conf, RDGeom::Point3D &dims,
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RDGeom::Point3D &offSet,
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const RDGeom::Transform3D *trans,
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double padding) {
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// RDGeom::Point3D lb, rb;
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computeConfBox(conf, offSet, dims, trans, padding);
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dims -= offSet;
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}
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std::vector<double> getConfDimensions(const Conformer &conf, double padding,
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const RDGeom::Point3D *center,
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bool ignoreHs) {
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RDGeom::Point3D lb, rb;
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computeConfBox(conf, lb, rb, nullptr, padding);
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if (!center) {
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RDGeom::Point3D cpt = MolTransforms::computeCentroid(conf, ignoreHs);
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rb -= cpt;
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lb -= cpt;
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} else {
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rb -= (*center);
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lb -= (*center);
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}
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lb *= -1.0;
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double dimX = 2.0 * std::max(rb.x, lb.x);
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double dimY = 2.0 * std::max(rb.y, lb.y);
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double dimZ = 2.0 * std::max(rb.z, lb.z);
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std::vector<double> res;
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res.reserve(3);
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res.push_back(dimX);
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res.push_back(dimY);
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res.push_back(dimZ);
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return res;
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}
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void computeUnionBox(const RDGeom::Point3D &leftBottom1,
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const RDGeom::Point3D &rightTop1,
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const RDGeom::Point3D &leftBottom2,
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const RDGeom::Point3D &rightTop2,
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RDGeom::Point3D &uLeftBottom, RDGeom::Point3D &uRightTop) {
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uLeftBottom.x = std::min(leftBottom1.x, leftBottom2.x);
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uLeftBottom.y = std::min(leftBottom1.y, leftBottom2.y);
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uLeftBottom.z = std::min(leftBottom1.z, leftBottom2.z);
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uRightTop.x = std::max(rightTop1.x, rightTop2.x);
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uRightTop.y = std::max(rightTop1.y, rightTop2.y);
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uRightTop.z = std::max(rightTop1.z, rightTop2.z);
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}
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double tverskyIndex(const ROMol &mol1, const ROMol &mol2, double alpha,
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double beta, int confId1, int confId2, double gridSpacing,
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DiscreteValueVect::DiscreteValueType bitsPerPoint,
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double vdwScale, double stepSize, int maxLayers,
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bool ignoreHs) {
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const Conformer &conf1 = mol1.getConformer(confId1);
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const Conformer &conf2 = mol2.getConformer(confId2);
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return tverskyIndex(conf1, conf2, alpha, beta, gridSpacing, bitsPerPoint,
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vdwScale, stepSize, maxLayers, ignoreHs);
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}
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double tverskyIndex(const Conformer &conf1, const Conformer &conf2,
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double alpha, double beta, double gridSpacing,
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DiscreteValueVect::DiscreteValueType bitsPerPoint,
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double vdwScale, double stepSize, int maxLayers,
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bool ignoreHs) {
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RDGeom::Transform3D *trans = MolTransforms::computeCanonicalTransform(conf1);
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// now use this transform and figure out what size grid we will need
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// find the lower-left and upper-right corners for each of the conformers
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// and take a union of these boxes - we will use this fo grid dimensions
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RDGeom::Point3D leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
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uRightTop;
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computeConfBox(conf1, leftBottom1, rightTop1, trans);
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computeConfBox(conf2, leftBottom2, rightTop2, trans);
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computeUnionBox(leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
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uRightTop);
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// make the grid object to store the encoding
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uRightTop -= uLeftBottom; // uRightTop now has grid dimensions
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RDGeom::UniformGrid3D grd1(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
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bitsPerPoint, &uLeftBottom);
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RDGeom::UniformGrid3D grd2(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
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bitsPerPoint, &uLeftBottom);
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EncodeShape(conf1, grd1, trans, vdwScale, stepSize, maxLayers, ignoreHs);
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EncodeShape(conf2, grd2, trans, vdwScale, stepSize, maxLayers, ignoreHs);
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delete trans;
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return RDGeom::tverskyIndex(grd1, grd2, alpha, beta);
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}
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double tanimotoDistance(const ROMol &mol1, const ROMol &mol2, int confId1,
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int confId2, double gridSpacing,
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DiscreteValueVect::DiscreteValueType bitsPerPoint,
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double vdwScale, double stepSize, int maxLayers,
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bool ignoreHs) {
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const Conformer &conf1 = mol1.getConformer(confId1);
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const Conformer &conf2 = mol2.getConformer(confId2);
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return tanimotoDistance(conf1, conf2, gridSpacing, bitsPerPoint, vdwScale,
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stepSize, maxLayers, ignoreHs);
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}
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double tanimotoDistance(const Conformer &conf1, const Conformer &conf2,
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double gridSpacing,
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DiscreteValueVect::DiscreteValueType bitsPerPoint,
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double vdwScale, double stepSize, int maxLayers,
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bool ignoreHs) {
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RDGeom::Transform3D *trans = MolTransforms::computeCanonicalTransform(conf1);
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// now use this transform and figure out what size grid we will need
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// find the lower-left and upper-right corners for each of the conformers
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// and take a union of these boxes - we will use this fo grid dimensions
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RDGeom::Point3D leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
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uRightTop;
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computeConfBox(conf1, leftBottom1, rightTop1, trans);
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computeConfBox(conf2, leftBottom2, rightTop2, trans);
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computeUnionBox(leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
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uRightTop);
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// make the grid object to store the encoding
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uRightTop -= uLeftBottom; // uRightTop now has grid dimensions
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RDGeom::UniformGrid3D grd1(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
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bitsPerPoint, &uLeftBottom);
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RDGeom::UniformGrid3D grd2(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
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bitsPerPoint, &uLeftBottom);
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EncodeShape(conf1, grd1, trans, vdwScale, stepSize, maxLayers, ignoreHs);
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EncodeShape(conf2, grd2, trans, vdwScale, stepSize, maxLayers, ignoreHs);
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delete trans;
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return RDGeom::tanimotoDistance(grd1, grd2);
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}
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double protrudeDistance(const ROMol &mol1, const ROMol &mol2, int confId1,
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int confId2, double gridSpacing,
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DiscreteValueVect::DiscreteValueType bitsPerPoint,
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double vdwScale, double stepSize, int maxLayers,
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bool ignoreHs, bool allowReordering) {
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const Conformer &conf1 = mol1.getConformer(confId1);
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const Conformer &conf2 = mol2.getConformer(confId2);
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return protrudeDistance(conf1, conf2, gridSpacing = 0.5, bitsPerPoint,
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vdwScale, stepSize, maxLayers, ignoreHs,
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allowReordering);
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}
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double protrudeDistance(const Conformer &conf1, const Conformer &conf2,
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double gridSpacing,
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DiscreteValueVect::DiscreteValueType bitsPerPoint,
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double vdwScale, double stepSize, int maxLayers,
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bool ignoreHs, bool allowReordering) {
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//
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// FIX: all this duplicated code needs to be refactored out.
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//
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RDGeom::Transform3D *trans = MolTransforms::computeCanonicalTransform(conf1);
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// now use this transform and figure out what size grid we will need
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// find the lower-left and upper-right corners for each of the conformers
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// and take a union of these boxes - we will use this fo grid dimensions
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RDGeom::Point3D leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
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uRightTop;
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computeConfBox(conf1, leftBottom1, rightTop1, trans);
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computeConfBox(conf2, leftBottom2, rightTop2, trans);
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computeUnionBox(leftBottom1, rightTop1, leftBottom2, rightTop2, uLeftBottom,
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uRightTop);
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// make the grid object to store the encoding
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uRightTop -= uLeftBottom; // uRightTop now has grid dimensions
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RDGeom::UniformGrid3D grd1(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
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bitsPerPoint, &uLeftBottom);
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RDGeom::UniformGrid3D grd2(uRightTop.x, uRightTop.y, uRightTop.z, gridSpacing,
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bitsPerPoint, &uLeftBottom);
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EncodeShape(conf1, grd1, trans, vdwScale, stepSize, maxLayers, ignoreHs);
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EncodeShape(conf2, grd2, trans, vdwScale, stepSize, maxLayers, ignoreHs);
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delete trans;
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double res;
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if (allowReordering && (grd2.getOccupancyVect()->getTotalVal() <
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grd1.getOccupancyVect()->getTotalVal())) {
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res = RDGeom::protrudeDistance(grd2, grd1);
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} else {
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res = RDGeom::protrudeDistance(grd1, grd2);
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}
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return res;
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}
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} // namespace MolShapes
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} // namespace RDKit
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