forked from UnixJunkie/pharmer
-
Notifications
You must be signed in to change notification settings - Fork 2
/
ReadMCMol.h
194 lines (171 loc) · 4.25 KB
/
ReadMCMol.h
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
/*
Pharmer: Efficient and Exact 3D Pharmacophore Search
Copyright (C) 2011 David Ryan Koes and the University of Pittsburgh
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
/*
* ReadMCMol.h
*
* Created on: Feb 2, 2011
* Author: dkoes
*/
#ifndef READMCMOL_H_
#define READMCMOL_H_
#include <openbabel/mol.h>
//openbabel currently doesn't have native support of multiple conformer input
//this just assumes sequential mols with the same name are conformers
//the read-ahead mol is cached
class ReadMCMol
{
istream& infile;
unsigned stride;
unsigned offset;
unsigned reduceConfs;
OpenBabel::OBConversion conv;
unsigned molcnt;
struct MInfo
{
string title;
OpenBabel::OBMol mol;
string data;
bool valid;
MInfo(): valid(false) {}
bool load(OpenBabel::OBConversion& conv)
{
title.clear();
mol.Clear();
data.clear();
valid = false;
//openbabel is SLOW due to (unneccessary I think) perception routines that
//get run when construction an obmol from an sdf, so optimize for it separately
if(strcmp(conv.GetInFormat()->GetID(), "sdf") == 0)
{
//parse out a mol ourselves
istream* in = conv.GetInStream();
getline(*in, title);
stringstream d;
d << title << "\n";
char c;
unsigned dollarcnt = 0;
while(in->get(c))
{
d.put(c);
if(c == '$') dollarcnt++;
else if(dollarcnt == 4) //readnewline
break;
else
dollarcnt = 0;
}
if(dollarcnt != 4)
return false;
data = d.str();
valid = (bool)*in;
return valid;
}
else
{
if(!conv.Read(&mol))
return false;
title = mol.GetTitle();
}
valid = true;
return true;
}
OpenBabel::OBMol& getMol()
{
if(data.length() > 0)
{
OpenBabel::OBConversion strconv;
strconv.SetInFormat("sdf");
strconv.ReadString(&mol, data);
data.clear();
}
return mol;
}
bool isValid()
{
return valid;
}
};
MInfo next;
public:
ReadMCMol(istream& in, OpenBabel::OBFormat* f, unsigned st, unsigned o, unsigned reduce) :
infile(in), stride(st), offset(o), reduceConfs(reduce > 0 ? reduce : UINT_MAX), molcnt(0)
{
conv.SetInFormat(f);
conv.SetOutFormat("sdf");
//must do a read to setup conv
conv.Read(&next.mol, &infile);
next.title = next.mol.GetTitle();
next.valid = true;
}
//put multi-conformer molecule in mol
//include weight to ensure value used for filtering matches stored value
bool read(OpenBabel::OBMol& mol)
{
mol.Clear();
if (!next.isValid())
return false; //nothing else
while(next.isValid())
{
if((molcnt % stride) == offset)
{
molcnt++;
unsigned confcnt = 1;
//read the rest of conformers for next
mol = next.getMol();
unsigned N = mol.NumAtoms();
string curtitle = next.title;
while (next.load(conv))
{
if (next.title == curtitle)
{
if (confcnt < reduceConfs)
{
if (next.getMol().NumAtoms() != N)
{
cerr
<< "Warning: Invalid Input. Sequential molecules with the same name should be conformers.\n";
break; //don't fail, just ignore
}
double *confdata = new double[N * 3];
memcpy(confdata, next.getMol().GetConformer(0),
sizeof(double) * N * 3);
mol.AddConformer(confdata); //mol is now managing the memory
}
confcnt++;
}
else //all done
{
break;
}
}
return true;
}
else
{
//read next mc mol
molcnt++;
string curtitle = next.title;
while(next.load(conv))
{
if(next.title != curtitle)
break;
}
}
}
return false;
}
unsigned molsRead() const { return molcnt; }
};
#endif /* READMCMOL_H_ */