1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
|
// $Id: ShapeEncoder.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// 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);
}
}
}
}
|
