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
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
|
// $Id$
//
// Copyright (C) 2003-2006 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 <RDGeneral/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <RDGeneral/types.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Substruct/SubstructMatch.h>
using namespace RDKit;
std::string getSmiles(std::string line, std::string &smi) {
int x = line.find("\t");
if (x == -1) {
x = line.find(" ");
}
smi = line.substr(0, x);
std::string rem = line.substr(x + 1, line.length() - x);
x = rem.find(" ");
std::string name;
name = rem.substr(0, x);
return name;
}
void switchAtoms(RWMol *mol, int idx) {
ROMol::ADJ_ITER nbrIdx, endNbrs;
boost::tie(nbrIdx, endNbrs) = mol->getAtomNeighbors(mol->getAtomWithIdx(idx));
INT_VECT neighs;
std::map<int, Bond *> nbBnd;
std::map<int, Bond *>::const_iterator nbi;
// before removing the atom keep track of the bonds and neighboring atoms
while (nbrIdx != endNbrs) {
auto *bnd = new Bond(*(mol->getBondBetweenAtoms(idx, (*nbrIdx))));
nbBnd[*nbrIdx] = bnd;
nbrIdx++;
}
Atom *oatom = mol->getAtomWithIdx(idx);
auto *natom = new Atom(*oatom);
// remove teh aroignal atom
mol->removeAtom(idx);
// delete oatom;
// now add it to the end of the molecule
int nid = mol->addAtom(natom);
// then reconnect to the old neighbors with the same bonds we stored
// keep in mind that if a old neighbor index is greater than that of the
// removed atom, the id changed by -1
int nbid;
for (nbi = nbBnd.begin(); nbi != nbBnd.end(); nbi++) {
nbid = nbi->first;
if (nbid > idx) {
nbid--;
}
auto *bnd = new Bond(*(nbi->second));
bnd->setBeginAtomIdx(nid);
bnd->setEndAtomIdx(nbid);
mol->addBond(bnd, true);
}
for (nbi = nbBnd.begin(); nbi != nbBnd.end(); nbi++) {
delete nbi->second;
}
nbBnd.clear();
}
void permuteAtoms(RWMol *mol) {
int nats = mol->getNumAtoms();
INT_VECT picks;
INT_VECT_CI pri;
int i, aid;
for (i = 0; i < 5; i++) {
aid = rand() % nats;
if (std::find(picks.begin(), picks.end(), aid) == picks.end()) {
picks.push_back(aid);
}
}
for (pri = picks.begin(); pri != picks.end(); pri++) {
switchAtoms(mol, *pri);
}
if (mol->hasProp("SubstructGraphPtr")) mol->clearProp("SubstructGraphPtr");
}
int main(int argc, char *argv[]) {
RDLog::InitLogs();
std::string fname;
if (argc > 1) {
fname = argv[1];
} else {
BOOST_LOG(rdErrorLog) << "Pass in the list of smiles\n";
}
std::ifstream inStream(fname.c_str());
const int MAX_LINE_LEN = 512;
char inLine[MAX_LINE_LEN];
std::string tmpstr;
std::string smi;
inStream.getline(inLine, MAX_LINE_LEN, '\n');
tmpstr = inLine;
// MolOps molop;
int lineCount = 0;
while (tmpstr.size() > 0) {
lineCount++;
if (!(lineCount % 100)) {
BOOST_LOG(rdErrorLog) << "Doing: " << lineCount << std::endl;
}
if (tmpstr[0] != '#') {
std::string name = getSmiles(tmpstr, smi);
#ifdef VERBOSE_CANON
BOOST_LOG(rdInfoLog) << "\n-----------------\nSTART: " << smi
<< std::endl;
#endif
// std::cout << " \n";
RWMol *om = SmilesToMol(smi, 0, 0);
RWMol *m = SmilesToMol(smi, 0, 0);
if (m && om) {
try {
MolOps::sanitizeMol(*m);
MolOps::sanitizeMol(*om);
for (int iter = 0; iter < 5; iter++) {
std::string preSmi = MolToSmiles(*om);
#if 1
permuteAtoms(m);
std::string postSmi = MolToSmiles(*m);
#else
BOOST_LOG(rdInfoLog) << " ----------------- 2 --------------"
<< std::endl;
std::string postSmi = MolToSmiles(*SmilesToMol(preSmi));
#endif
std::vector<MatchVectType> fgpMatches;
int nmat = SubstructMatch(*om, *m, fgpMatches);
if (preSmi != postSmi) {
BOOST_LOG(rdInfoLog) << lineCount << " " << name << " " << smi
<< " " << preSmi << " " << postSmi
<< std::endl;
iter = 100;
std::cout << "\n\n";
m->debugMol(std::cout);
std::cout << "-*-*-*- MAP -*-*-*-" << std::endl;
MatchVectType::const_iterator matchI;
for (matchI = fgpMatches[0].begin();
matchI != fgpMatches[0].end(); matchI++) {
BOOST_LOG(rdInfoLog) << "\t" << matchI->second << "\t"
<< matchI->first << std::endl;
}
break;
}
if (nmat < 1) {
BOOST_LOG(rdInfoLog) << lineCount << " Not the same mol: " << name
<< "\n";
exit(-1);
}
}
delete om;
delete m;
} catch (MolSanitizeException &) {
BOOST_LOG(rdErrorLog) << smi << "\n";
delete om;
delete m;
}
} else {
BOOST_LOG(rdErrorLog) << lineCount << " Parse Failed: " << smi
<< std::endl;
}
}
inStream.getline(inLine, MAX_LINE_LEN, '\n');
tmpstr = inLine;
}
BOOST_LOG(rdErrorLog) << "FINISHED after " << lineCount << " lines."
<< std::endl;
return 0;
}
|
