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
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
|
// Old-style test for Gasteiger charge model
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/babelconfig.h>
#include <fstream>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/chargemodel.h>
#include <openbabel/obutil.h>
using namespace std;
using namespace OpenBabel;
#ifdef TESTDATADIR
string atestdatadir = TESTDATADIR;
string aresults_file = atestdatadir + "charge-gasteiger.txt";
string adipole_file = atestdatadir + "dipole-gasteiger.txt";
string amolecules_file = atestdatadir + "forcefield.sdf";
#else
string aresults_file = "files/charge-gasteiger.txt";
string adipole_file = "files/dipole-gasteiger.txt";
string amolecules_file = "files/forcefield.sdf";
#endif
void GenerateGasteigerCharges();
int charge_gasteiger(int argc, char* argv[])
{
int defaultchoice = 1;
int choice = defaultchoice;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
cout << "# Testing GASTEIGER Charge Model..." << endl;
std::ifstream mifs;
if (!SafeOpen(mifs, amolecules_file.c_str()))
{
cout << "Bail out! Cannot read file " << amolecules_file << endl;
return -1; // test failed
}
std::ifstream rifs;
if (!SafeOpen(rifs, aresults_file.c_str()))
{
cout << "Bail out! Cannot read file " << aresults_file << endl;
return -1; // test failed
}
std::ifstream difs;
if (!SafeOpen(difs, adipole_file.c_str()))
{
cout << "Bail out! Cannot read file " << adipole_file << endl;
return -1; // test failed
}
char buffer[BUFF_SIZE];
vector<string> vs;
OBMol mol;
OBConversion conv(&mifs, &cout);
unsigned int currentTest = 0;
vector3 dipoleMoment, result;
std::vector<double> partialCharges;
OBChargeModel *pCM;
switch(choice) {
case 1:
if(! conv.SetInAndOutFormats("SDF","SDF"))
{
cout << "Bail out! SDF format is not loaded" << endl;
return -1; // test failed
}
pCM = OBChargeModel::FindType("gasteiger");
if (pCM == NULL) {
cerr << "Bail out! Cannot load charge model!" << endl;
return -1; // test failed
}
while(mifs)
{
mol.Clear();
conv.Read(&mol);
if (mol.Empty())
continue;
if (!difs.getline(buffer,BUFF_SIZE))
{
cout << "Bail out! error reading reference data" << endl;
return -1; // test failed
}
if (!pCM->ComputeCharges(mol)) {
cout << "Bail out! could not compute charges on " << mol.GetTitle() << endl;
return -1; // test failed
}
partialCharges = pCM->GetPartialCharges();
// compare the calculated energy to our reference data
tokenize(vs, buffer);
if (vs.size() < 3)
return -1;
dipoleMoment.SetX(atof(vs[0].c_str()));
dipoleMoment.SetY(atof(vs[1].c_str()));
dipoleMoment.SetZ(atof(vs[2].c_str()));
result = pCM->GetDipoleMoment(mol) - dipoleMoment;
if ( fabs(result.length_2()) > 1.0e-4)
{
cout << "not ok " << ++currentTest << " # calculated dipole incorrect "
<< " for molecule " << mol.GetTitle() << '\n';
}
else
cout << "ok " << ++currentTest << " # dipole\n";
FOR_ATOMS_OF_MOL(atom, mol) {
if (!rifs.getline(buffer,BUFF_SIZE)) {
cout << "Bail out! Cannot read reference data\n";
return -1; // test failed
}
if ( fabs(atom->GetPartialCharge() - atof(buffer)) > 1.0e-3 ) {
cout << "not ok " << ++currentTest << " # calculated charge incorrect "
<< " for molecule " << mol.GetTitle() << '\n';
cout << "# atom " << atom->GetIdx() << " expected " << buffer << " got "
<< atom->GetPartialCharge() << '\n';
} else {
cout << "ok " << ++currentTest << " # charge\n";
}
}
}
break;
case 99:
GenerateGasteigerCharges();
return 0;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
// Passed tests
return 0;
}
void GenerateGasteigerCharges()
{
std::ifstream ifs;
if (!SafeOpen(ifs, amolecules_file.c_str()))
return;
std::ofstream rofs;
if (!SafeOpen(rofs, aresults_file.c_str()))
return;
std::ofstream dofs;
if (!SafeOpen(dofs, adipole_file.c_str()))
return;
OBMol mol;
OBConversion conv(&ifs, &cout);
char buffer[BUFF_SIZE];
if(! conv.SetInAndOutFormats("SDF","SDF"))
{
cerr << "SDF format is not loaded" << endl;
return;
}
OBChargeModel *pCM = OBChargeModel::FindType("gasteiger");
if (pCM == NULL) {
cerr << "Cannot load charge model!" << endl;
return;
}
std::vector<double> partialCharges;
vector3 dipoleMoment;
for (;ifs;)
{
mol.Clear();
conv.Read(&mol);
if (mol.Empty())
continue;
if (pCM->ComputeCharges(mol)) {
partialCharges = pCM->GetPartialCharges();
}
// write out the dipole moment
dipoleMoment = pCM->GetDipoleMoment(mol);
sprintf(buffer, "%15.5f%15.5f%15.5f\n", dipoleMoment.x(), dipoleMoment.y(), dipoleMoment.z());
dofs << buffer;
// and write all the partial charges
FOR_ATOMS_OF_MOL(atom, mol) {
sprintf(buffer, "%15.5f\n", atom->GetPartialCharge());
rofs << buffer;
}
}
cerr << "Charges written successfully" << endl;
return;
}
|
