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
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
|
// $Id$
//
// Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/Depictor/RDDepictor.h>
namespace RDDepict {
void compute2DCoordsForReaction(RDKit::ChemicalReaction &rxn, double spacing,
bool updateProps, bool canonOrient,
unsigned int nFlipsPerSample,
unsigned int nSamples, int sampleSeed,
bool permuteDeg4Nodes) {
double xOffset = 0.0;
for (auto &reactant : rxn.getReactants()) {
if (updateProps) {
reactant->updatePropertyCache(false);
RDKit::MolOps::setConjugation(*reactant);
RDKit::MolOps::setHybridization(*reactant);
}
compute2DCoords(*reactant, nullptr, canonOrient, true, nFlipsPerSample,
nSamples, sampleSeed, permuteDeg4Nodes);
double minX = 1e8, maxX = -1e8;
for (auto &pt : reactant->getConformer().getPositions()) {
minX = std::min(pt.x, minX);
maxX = std::max(pt.x, maxX);
}
xOffset += (maxX - minX) / 2;
for (auto &pt : reactant->getConformer().getPositions()) {
pt.x += xOffset;
maxX = std::max(pt.x, maxX);
}
xOffset = maxX + spacing;
}
for (auto &product : rxn.getProducts()) {
if (updateProps) {
product->updatePropertyCache(false);
RDKit::MolOps::setConjugation(*product);
RDKit::MolOps::setHybridization(*product);
}
compute2DCoords(*product, nullptr, canonOrient, true, nFlipsPerSample,
nSamples, sampleSeed, permuteDeg4Nodes);
double minX = 100., maxX = -100.;
for (auto &pt : product->getConformer().getPositions()) {
minX = std::min(pt.x, minX);
maxX = std::max(pt.x, maxX);
}
xOffset += (maxX - minX) / 2;
for (auto &pt : product->getConformer().getPositions()) {
pt.x += xOffset;
maxX = std::max(pt.x, maxX);
}
xOffset = maxX + spacing;
}
}
} // namespace RDDepict
|
