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
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
//
// Copyright (C) 2020 Greg Landrum and T5 Informatics GmbH
//
// @@ 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 "MolEnumerator.h"
#include <RDGeneral/Exceptions.h>
#include <GraphMol/FileParsers/MolSGroupParsing.h>
namespace RDKit {
namespace MolEnumerator {
void PositionVariationOp::initFromMol(const ROMol &mol) {
dp_mol.reset(new ROMol(mol));
initFromMol();
}
void PositionVariationOp::initFromMol() {
d_variationPoints.clear();
if (!dp_mol) {
return;
}
if (!dp_mol->hasProp(detail::idxPropName)) {
detail::preserveOrigIndices(*dp_mol);
}
for (const auto bond : dp_mol->bonds()) {
std::string endpts;
std::string attach;
if (bond->getPropIfPresent(common_properties::_MolFileBondEndPts, endpts) &&
bond->getPropIfPresent(common_properties::_MolFileBondAttach, attach) &&
attach == "ANY") {
const Atom *atom = bond->getBeginAtom();
if (atom->getAtomicNum() == 0) {
atom = bond->getEndAtom();
if (atom->getAtomicNum() == 0) {
// marvin sketch seems to place the position-variation dummy at the
// beginning of the bond, so we're going to favor taking the end atom.
// In case other tools construct this differently, we have an
// exception to that if the end atom is an AtomNull query and the
// beginning atom is not one.
if (atom->hasQuery() &&
atom->getQuery()->getDescription() == "AtomNull" &&
bond->getBeginAtom()->hasQuery() &&
bond->getBeginAtom()->getQuery()->getDescription() !=
"AtomNull") {
atom = bond->getBeginAtom();
}
}
}
d_dummiesAtEachPoint.push_back(bond->getOtherAtomIdx(atom->getIdx()));
std::vector<unsigned int> oats =
RDKit::SGroupParsing::ParseV3000Array<unsigned int>(
endpts, dp_mol->getNumAtoms(), false);
// decrement the indices and do error checking and whatever additional
// cleanup is required:
for (auto &oat : oats) {
if (oat == 0 || oat > dp_mol->getNumAtoms()) {
throw ValueErrorException("Bad variation point index");
}
--oat;
// github #4381: if we're connecting to an aromatic heteroatom which
// has implicit Hs, we should remove those
auto attachAtom = dp_mol->getAtomWithIdx(oat);
if (attachAtom->getIsAromatic() && attachAtom->getAtomicNum() != 6) {
attachAtom->setNumExplicitHs(0);
}
}
d_variationPoints.push_back(std::make_pair(atom->getIdx(), oats));
}
}
}
std::vector<size_t> PositionVariationOp::getVariationCounts() const {
std::vector<size_t> res(d_variationPoints.size());
std::transform(d_variationPoints.begin(), d_variationPoints.end(),
res.begin(),
[](const auto &pr) -> size_t { return pr.second.size(); });
return res;
}
std::unique_ptr<ROMol> PositionVariationOp::operator()(
const std::vector<size_t> &which) const {
PRECONDITION(dp_mol, "no molecule");
if (which.size() != d_variationPoints.size()) {
throw ValueErrorException("bad element choice in enumeration");
}
// a bit of quick error checking before starting the real work
for (unsigned int i = 0; i < d_variationPoints.size(); ++i) {
if (which[i] >= d_variationPoints[i].second.size()) {
throw ValueErrorException("bad element value in enumeration");
}
}
RWMol *res = new RWMol(*dp_mol);
for (unsigned int i = 0; i < d_variationPoints.size(); ++i) {
const auto tpl = d_variationPoints[i];
auto begAtomIdx = tpl.first;
auto endAtomIdx = tpl.second[which[i]];
// do we already have a bond?
if (res->getBondBetweenAtoms(begAtomIdx, endAtomIdx)) {
continue;
}
res->addBond(begAtomIdx, endAtomIdx, Bond::BondType::SINGLE);
}
// now remove the dummies:
res->beginBatchEdit();
for (auto idx : d_dummiesAtEachPoint) {
res->removeAtom(idx);
}
res->commitBatchEdit();
return std::unique_ptr<ROMol>(static_cast<ROMol *>(res));
}
} // namespace MolEnumerator
} // namespace RDKit
|
