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53 lines
1.8 KiB
C++
53 lines
1.8 KiB
C++
// $Id: ShapeEncoder.cpp 4973 2006-02-18 00:42:14Z glandrum $
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//
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// Copyright (C) 2005-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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//
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#include <Geometry/Transform3D.h>
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#include <Geometry/UniformGrid3D.h>
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#include "ShapeEncoder.h"
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#include <Geometry/Transform3D.h>
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#include <Geometry/point.h>
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#include <Geometry/UniformGrid3D.h>
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//#include <GraphMol/ROMol.h>
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#include <GraphMol/Conformer.h>
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//#include <GraphMol/PeriodicTable.h>
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#include <GraphMol/RDKitBase.h>
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namespace RDKit {
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namespace MolShapes {
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void EncodeShape(const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId,
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const RDGeom::Transform3D *trans,
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double vdwScale, double stepSize, int maxLayers, bool ignoreHs) {
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const Conformer &conf = mol.getConformer(confId);
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EncodeShape(conf, grid, trans, vdwScale, stepSize, maxLayers, ignoreHs);
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}
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void EncodeShape(const Conformer &conf, RDGeom::UniformGrid3D &grid,
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const RDGeom::Transform3D *trans, double vdwScale,
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double stepSize, int maxLayers, bool ignoreHs) {
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const ROMol &mol = conf.getOwningMol();
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ROMol::ConstAtomIterator ai;
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double rad;
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unsigned int aid, anum;
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for (ai = mol.beginAtoms(); ai != mol.endAtoms(); ai++) {
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anum = (*ai)->getAtomicNum();
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if ((anum == 1) && (ignoreHs)) { //ignore hydrigens
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continue;
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}
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aid = (*ai)->getIdx();
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RDGeom::Point3D loc = conf.getAtomPos(aid);
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rad = PeriodicTable::getTable()->getRvdw(anum);
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if (trans) {
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trans->TransformPoint(loc);
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}
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grid.setSphereOccupancy(loc, vdwScale*rad, stepSize, maxLayers);
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}
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}
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}
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}
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