mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
da6cd73168
* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
54 lines
1.8 KiB
C++
54 lines
1.8 KiB
C++
// $Id$
|
|
//
|
|
// 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 <Geometry/Transform3D.h>
|
|
#include <Geometry/UniformGrid3D.h>
|
|
|
|
#include "ShapeEncoder.h"
|
|
#include <Geometry/Transform3D.h>
|
|
#include <Geometry/point.h>
|
|
#include <Geometry/UniformGrid3D.h>
|
|
// #include <GraphMol/ROMol.h>
|
|
#include <GraphMol/Conformer.h>
|
|
// #include <GraphMol/PeriodicTable.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
namespace RDKit {
|
|
namespace MolShapes {
|
|
void EncodeShape(const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId,
|
|
const RDGeom::Transform3D *trans, double vdwScale,
|
|
double stepSize, int maxLayers, bool ignoreHs) {
|
|
const Conformer &conf = mol.getConformer(confId);
|
|
EncodeShape(conf, grid, trans, vdwScale, stepSize, maxLayers, ignoreHs);
|
|
}
|
|
|
|
void EncodeShape(const Conformer &conf, RDGeom::UniformGrid3D &grid,
|
|
const RDGeom::Transform3D *trans, double vdwScale,
|
|
double stepSize, int maxLayers, bool ignoreHs) {
|
|
const ROMol &mol = conf.getOwningMol();
|
|
ROMol::ConstAtomIterator ai;
|
|
double rad;
|
|
unsigned int aid, anum;
|
|
for (ai = mol.beginAtoms(); ai != mol.endAtoms(); ai++) {
|
|
anum = (*ai)->getAtomicNum();
|
|
if ((anum == 1) && (ignoreHs)) { // ignore hydrigens
|
|
continue;
|
|
}
|
|
aid = (*ai)->getIdx();
|
|
RDGeom::Point3D loc = conf.getAtomPos(aid);
|
|
rad = PeriodicTable::getTable()->getRvdw(anum);
|
|
if (trans) {
|
|
trans->TransformPoint(loc);
|
|
}
|
|
grid.setSphereOccupancy(loc, vdwScale * rad, stepSize, maxLayers);
|
|
}
|
|
}
|
|
} // namespace MolShapes
|
|
} // namespace RDKit
|