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47 lines
1.6 KiB
C++
47 lines
1.6 KiB
C++
//
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// Copyright (C) 2005-2025 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 <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/Conformer.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, double vdwScale,
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double stepSize, int maxLayers, bool ignoreHs) {
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const auto &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 auto &mol = conf.getOwningMol();
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for (const auto &atom : mol.atoms()) {
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auto anum = atom->getAtomicNum();
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if (anum == 1 && ignoreHs) { // ignore hydrigens
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continue;
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}
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auto rad = PeriodicTable::getTable()->getRvdw(anum);
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RDGeom::Point3D loc = conf.getAtomPos(atom->getIdx());
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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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} // namespace MolShapes
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} // namespace RDKit
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