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
|
//
// Copyright (C) 2023 Schrödinger, 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 "Templates.h"
#include "RDDepictor.h"
namespace RDDepict {
void CoordinateTemplates::assertValidTemplate(RDKit::ROMol &mol,
const std::string &smiles) {
// template must have 2D coordinates
if (mol.getNumConformers() == 0) {
std::string msg = "Template missing coordinates: " + smiles;
throw RDDepict::DepictException(msg);
}
if (mol.getConformer().is3D()) {
std::string msg =
"Template has 3D coordinates, 2D coordinates required: " + smiles;
throw RDDepict::DepictException(msg);
}
// Make sure this template is a single ring system (spiro'd ring systems are
// OK). We can check this by ensuring that every bond is in a ring and that
// there is only one connected component in the molecular graph.
if (RDKit::MolOps::getMolFrags(mol).size() != 1) {
std::string msg =
"Template consists of multiple fragments, single fragment required: " +
smiles;
throw RDDepict::DepictException(msg);
}
if (mol.getNumAtoms() == 1) {
std::string msg = "Template is not a ring system: " + smiles;
throw RDDepict::DepictException(msg);
}
auto ri = mol.getRingInfo();
for (unsigned int i = 0; i < mol.getNumBonds(); ++i) {
if (!ri->numBondRings(i)) {
std::string msg = "Template is not a ring system: " + smiles;
throw RDDepict::DepictException(msg);
}
}
}
void CoordinateTemplates::loadTemplatesFromPath(
const std::string &templatePath,
std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
&templates) {
std::ifstream cxsmiles(templatePath);
if (!cxsmiles) {
std::string msg = "Could not open file " + templatePath;
throw RDDepict::DepictException(msg);
}
// Try loading templates in from this directory, if unsuccessful, keep current
// templates
std::string line;
while (std::getline(cxsmiles, line)) {
RDKit::ROMol *mol_ptr = RDKit::SmilesToMol(line);
if (!mol_ptr) {
std::string msg =
"Could not load templates from " + templatePath + ": Invalid smiles";
cxsmiles.close();
throw RDDepict::DepictException(msg);
}
std::shared_ptr<RDKit::ROMol> mol(mol_ptr);
try {
assertValidTemplate(*mol, line);
} catch (RDDepict::DepictException &e) {
cxsmiles.close();
throw e;
}
templates[mol->getNumAtoms()].push_back(mol);
}
cxsmiles.close();
}
void CoordinateTemplates::setRingSystemTemplates(
const std::string &templatePath) {
// Try loading templates in from this directory, if unsuccessful, keep current
// templates
std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
templates;
loadTemplatesFromPath(templatePath, templates);
clearTemplates();
m_templates = std::move(templates);
}
void CoordinateTemplates::addRingSystemTemplates(
const std::string &templatePath) {
// Try loading templates in from this directory, if unsuccessful, keep current
// templates
std::unordered_map<unsigned int, std::vector<std::shared_ptr<RDKit::ROMol>>>
templates;
loadTemplatesFromPath(templatePath, templates);
for (auto &kv : templates) {
m_templates[kv.first].insert(m_templates[kv.first].begin(),
kv.second.begin(), kv.second.end());
}
}
} // namespace RDDepict
|
