File: bondtyper.cpp

package info (click to toggle)
openbabel 2.2.3-1
  • links: PTS, VCS
  • area: main
  • in suites: squeeze
  • size: 36,644 kB
  • ctags: 33,717
  • sloc: cpp: 242,528; ansic: 87,037; sh: 10,280; perl: 5,518; python: 5,156; pascal: 793; makefile: 747; cs: 392; xml: 97; ruby: 54; java: 23
file content (271 lines) | stat: -rw-r--r-- 8,333 bytes parent folder | download
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
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
/**********************************************************************
bondtyper.cpp - Bond typer to perceive connectivity and bond orders/types.

Copyright (C) 2003-2006 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>

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 version 2 of the License.
 
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.
***********************************************************************/
#include <openbabel/babelconfig.h>

#include <openbabel/mol.h>
#include <openbabel/bondtyper.h>

// data header with default parameters
#include "bondtyp.h"

using namespace std;

namespace OpenBabel
{

  //! Global OBBondTyper for perception of bond order assignment.
  OBBondTyper  bondtyper;

  /*! \class OBBondTyper bondtyper.h <openbabel/bondtyper.cpp>
    \brief Assigns bond types for file formats without bond information

    The OBBondTyper class is designed to read in a list of bond typing
    rules and apply them to molecules. It is called from the 
    OBMol::PerceiveBondOrders() method.
  */
  OBBondTyper::OBBondTyper()
  {
    _init = false;
    _dir = BABEL_DATADIR;
    _envvar = "BABEL_DATADIR";
    _filename = "bondtyp.txt";
    _subdir = "data";
    _dataptr = BondTypeData;
  }

  void OBBondTyper::ParseLine(const char *buffer)
  {
    vector<string> vs;
    vector<int>    bovector;
    OBSmartsPattern *sp;

    if (buffer[0] != '#')
      {
        tokenize(vs,buffer);
        // Make sure we actually have a SMARTS pattern plus at least one triple
        // and make sure we have the correct number of integers
        if (vs.empty() || vs.size() < 4)
          return; // just ignore empty (or short lines)
        else if (!vs.empty() && vs.size() >= 4 && (vs.size() % 3 != 1))
          {
            stringstream errorMsg;
            errorMsg << " Error in OBBondTyper. Pattern is incorrect, found "
                     << vs.size() << " tokens." << endl;
            errorMsg << " Buffer is: " << buffer << endl;
            obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo);
            return;
          }

        sp = new OBSmartsPattern;
        if (sp->Init(vs[0]))
          {
            for (unsigned int i = 1; i < vs.size() ; ++i)
              {
                bovector.push_back( atoi((char *)vs[i].c_str()) );
              }
            _fgbonds.push_back(pair<OBSmartsPattern*,vector<int> >
                               (sp, bovector));
          }
        else
          {
            delete sp;
            sp = NULL;
          }
      }
  }

  OBBondTyper::~OBBondTyper()
  {
    vector<pair<OBSmartsPattern*, vector<int> > >::iterator i;
    for (i = _fgbonds.begin();i != _fgbonds.end();++i)
      {
        delete i->first;
        i->first = NULL;
      }
  }

  void OBBondTyper::AssignFunctionalGroupBonds(OBMol &mol)
  {
    if (!_init)
      Init();

    OBSmartsPattern *currentPattern;
    OBBond *b1, *b2;
    OBAtom *a1,*a2, *a3;
    double angle, dist1, dist2;
    vector<int> assignments;
    vector<vector<int> > mlist;
    vector<vector<int> >::iterator matches, l;
    vector<pair<OBSmartsPattern*, vector<int> > >::iterator i;  
    unsigned int j;

    // Loop through for all the functional groups and assign bond orders
    for (i = _fgbonds.begin();i != _fgbonds.end();++i)
      {
        currentPattern = i->first;
        assignments = i->second;

        if (currentPattern && currentPattern->Match(mol))
          {
            mlist = currentPattern->GetUMapList();
            for (matches = mlist.begin(); matches != mlist.end(); ++matches)
              {
                // Now loop through the bonds to assign from _fgbonds
                for (j = 0; j < assignments.size(); j += 3)
                  {
                    // along the assignments vector: atomID1 atomID2 bondOrder
                    a1 = mol.GetAtom((*matches)[ assignments[j] ]);
                    a2 = mol.GetAtom((*matches)[ assignments[j+1 ] ]);
                    if (!a1 || !a2) continue;

                    b1 = a1->GetBond(a2);

                    if (!b1) continue;
                    b1->SetBO(assignments[j+2]);
                  } // bond order assignments
              } // each match
          } // current pattern matches

      } // for(functional groups)

    // FG with distance and/or bond criteria
    // Carbonyl oxygen C=O
    OBSmartsPattern carbo; carbo.Init("[#8D1][#6](*)(*)");
  
    if (carbo.Match(mol))
      {
        mlist = carbo.GetUMapList();
        for (l = mlist.begin(); l != mlist.end(); ++l)
          {
            a1 = mol.GetAtom((*l)[0]);
            a2 = mol.GetAtom((*l)[1]);
	   
            angle = a2->AverageBondAngle();
            dist1 = a1->GetDistance(a2);
	    
            // carbonyl geometries ?
            if (angle > 115 && angle < 150 && dist1 < 1.28) { 
	        
              if ( !a1->HasDoubleBond() ) {// no double bond already assigned
                b1 = a1->GetBond(a2); 

                if (!b1 ) continue;
                b1->SetBO(2);
              }
            }
          }
      } // Carbonyl oxygen

    // thione C=S
    OBSmartsPattern thione; thione.Init("[#16D1][#6](*)(*)");
  
    if (thione.Match(mol))
      {
        mlist = thione.GetUMapList();
        for (l = mlist.begin(); l != mlist.end(); ++l)
          {
            a1 = mol.GetAtom((*l)[0]);
            a2 = mol.GetAtom((*l)[1]);
	   
            angle = a2->AverageBondAngle();
            dist1 = a1->GetDistance(a2);
	    
            // thione geometries ?
            if (angle > 115 && angle < 150 && dist1 < 1.72) { 
	        
              if ( !a1->HasDoubleBond() ) {// no double bond already assigned
                b1 = a1->GetBond(a2); 

                if (!b1 ) continue;
                b1->SetBO(2);
              }
            }
          }
      } // thione

    // Isocyanate N=C=O or Isothiocyanate
    bool dist1OK;
    OBSmartsPattern isocyanate; isocyanate.Init("[#8,#16;D1][#6D2][#7D2]");
    if (isocyanate.Match(mol))
      {
        mlist = isocyanate.GetUMapList();
        for (l = mlist.begin(); l != mlist.end(); ++l)
          {
            a1 = mol.GetAtom((*l)[0]);
            a2 = mol.GetAtom((*l)[1]);
            a3 = mol.GetAtom((*l)[2]);

            angle = a2->AverageBondAngle();
            dist1 = a1->GetDistance(a2);
            dist2 = a2->GetDistance(a3);
	    
            // isocyanate geometry or Isotiocyanate geometry ?
            if (a1->IsOxygen()) 
              dist1OK =  dist1 < 1.28;
            else
              dist1OK =  dist1 < 1.72;
	    
            if (angle > 150 && dist1OK && dist2 < 1.34) { 
	          
              b1 = a1->GetBond(a2); 
              b2 = a2->GetBond(a3);
              if (!b1 || !b2) continue;
              b1->SetBO(2);
              b2->SetBO(2);
	        
            }
	    
          }      
      } // Isocyanate

    // oxime C=S
    OBSmartsPattern oxime; oxime.Init("[#6D3][#7D2][#8D2]");
  
    if (oxime.Match(mol))
      {
        mlist = oxime.GetUMapList();
        for (l = mlist.begin(); l != mlist.end(); ++l)
          {
            a1 = mol.GetAtom((*l)[0]);
            a2 = mol.GetAtom((*l)[1]);
	   
            angle = a2->AverageBondAngle();
            dist1 = a1->GetDistance(a2);
	    
            // thione geometries ?
            if (angle > 110 && angle < 150 && dist1 < 1.4) { 
	        
              if ( !a1->HasDoubleBond() ) {// no double bond already assigned
                b1 = a1->GetBond(a2); 

                if (!b1 ) continue;
                b1->SetBO(2);
              }
            }
          }
      } // oxime

  }

} //namespace OpenBabel;

//! \file bondtyper.cpp
//! \brief Bond typer to perceive connectivity and bond orders/types.
//! \todo Needs to add aromatic ring bond order assignment.
//!   Eventually need to migrate OBMol::PerceiveBondOrders(),
//!   OBMol::ConnectTheDots(), and possibly some of the Kekulize routines