This file is indexed.

/usr/include/rdkit/GraphMol/MolDrawing/MolDrawing.h is in librdkit-dev 201603.5-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  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
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
// $Id$
//
//  Copyright (C) 2009-2012 Greg Landrum
//
//   @@ 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.
//
//  Includes contributions from Dave Cosgrove (davidacosgroveaz@gmail.com)
//
#ifndef _RD_MOLDRAWING_H_
#define _RD_MOLDRAWING_H_

#include <vector>
#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <Geometry/point.h>

/***********
  Return Format: vector of ints

  RESOLUTION dots_per_angstrom
  BOUNDS x1 y1 x2 y2
  LINE width dashed atom1_atnum atom2_atnum x1 y1 x2 y2
  WEDGE dashed atom1_atnum atom2_atnum x1 y1 x2 y2 x3 y3
  ATOM idx atnum x y num_chars char1-charx orient



*************/

namespace RDKit {
namespace Drawing {
typedef int ElementType;

typedef enum { LINE = 1, WEDGE, ATOM, BOUNDS, RESOLUTION } PrimType;
typedef enum { C = 0, N, E, S, W } OrientType;

namespace detail {
// **************************************************************************
void drawLine(std::vector<ElementType> &res, int atnum1, int atnum2,
              int lineWidth, int dashed, double x1, double y1, double x2,
              double y2) {
  res.push_back(LINE);
  res.push_back(static_cast<ElementType>(lineWidth));
  res.push_back(dashed);
  res.push_back(static_cast<ElementType>(atnum1));
  res.push_back(static_cast<ElementType>(atnum2));
  res.push_back(static_cast<ElementType>(x1));
  res.push_back(static_cast<ElementType>(y1));
  res.push_back(static_cast<ElementType>(x2));
  res.push_back(static_cast<ElementType>(y2));
}
std::pair<std::string, OrientType> getAtomSymbolAndOrientation(
    const Atom &atom, RDGeom::Point2D nbrSum) {
  std::string symbol = "";
  OrientType orient = C;
  int isotope = atom.getIsotope();
  if (atom.getAtomicNum() != 6 || atom.getFormalCharge() != 0 || isotope ||
      atom.getNumRadicalElectrons() != 0 ||
      atom.hasProp(common_properties::molAtomMapNumber) ||
      atom.getDegree() == 0) {
    symbol = atom.getSymbol();
    bool leftToRight = true;
    if (atom.getDegree() == 1 && nbrSum.x > 0) {
      leftToRight = false;
    }
    if (isotope) {
      symbol = boost::lexical_cast<std::string>(isotope) + symbol;
    }
    if (atom.hasProp(common_properties::molAtomMapNumber)) {
      std::string mapNum;
      atom.getProp(common_properties::molAtomMapNumber, mapNum);
      symbol += ":" + mapNum;
    }
    int nHs = atom.getTotalNumHs();
    if (nHs > 0) {
      std::string h = "H";
      if (nHs > 1) {
        h += boost::lexical_cast<std::string>(nHs);
      }
      if (leftToRight)
        symbol += h;
      else
        symbol = h + symbol;
    }
    if (atom.getFormalCharge() != 0) {
      int chg = atom.getFormalCharge();
      std::string sgn = "+";
      if (chg < 0) {
        sgn = "-";
      }
      chg = abs(chg);
      if (chg > 1) {
        sgn += boost::lexical_cast<std::string>(chg);
      }
      if (leftToRight)
        symbol += sgn;
      else
        symbol = sgn + symbol;
    }

    if (atom.getDegree() == 1) {
      double islope = 0;
      if (fabs(nbrSum.y) > 1) {
        islope = nbrSum.x / fabs(nbrSum.y);
      } else {
        islope = nbrSum.x;
      }
      if (fabs(islope) > .85) {
        if (islope > 0) {
          orient = W;
        } else {
          orient = E;
        }
      } else {
        if (nbrSum.y > 0) {
          orient = N;
        } else {
          orient = S;
        }
      }
    }
  }
  return std::make_pair(symbol, orient);
}
}  // end of detail namespace
// **************************************************************************
std::vector<ElementType> DrawMol(const ROMol &mol, int confId = -1,
                                 const std::vector<int> *highlightAtoms = 0,
                                 bool includeAtomCircles = false,
                                 unsigned int dotsPerAngstrom = 100,
                                 double dblBondOffset = 0.3,
                                 double dblBondLengthFrac = 0.8,
                                 double angstromsPerChar = 0.20) {
  if (!mol.getRingInfo()->isInitialized()) {
    MolOps::findSSSR(mol);
  }
  std::vector<ElementType> res;
  res.push_back(RESOLUTION);
  res.push_back(static_cast<ElementType>(dotsPerAngstrom));

  const Conformer &conf = mol.getConformer(confId);
  const RDGeom::POINT3D_VECT &locs = conf.getPositions();

  // get atom symbols and orientations
  // (we need them for the bounding box calculation)
  std::vector<std::pair<std::string, OrientType> > atomSymbols;
  ROMol::VERTEX_ITER bAts, eAts;
  boost::tie(bAts, eAts) = mol.getVertices();
  while (bAts != eAts) {
    ROMol::OEDGE_ITER nbr, endNbrs;
    RDGeom::Point2D nbrSum(0, 0);
    boost::tie(nbr, endNbrs) = mol.getAtomBonds(mol[*bAts].get());
    RDGeom::Point2D a1(locs[mol[*bAts]->getIdx()].x,
                       locs[mol[*bAts]->getIdx()].y);
    while (nbr != endNbrs) {
      const BOND_SPTR bond = mol[*nbr];
      ++nbr;
      int a2Idx = bond->getOtherAtomIdx(mol[*bAts]->getIdx());
      RDGeom::Point2D a2(locs[a2Idx].x, locs[a2Idx].y);
      nbrSum += a2 - a1;
    }
    atomSymbols.push_back(
        detail::getAtomSymbolAndOrientation(*mol[*bAts], nbrSum));
    ++bAts;
  }

  //------------
  // do the bounding box
  //------------
  double minx = 1e6, miny = 1e6, maxx = -1e6, maxy = -1e6;
  for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
    RDGeom::Point3D pt = locs[i];
    std::string symbol;
    OrientType orient;
    boost::tie(symbol, orient) = atomSymbols[i];
    if (symbol != "") {
      // account for a possible expansion of the bounding box by the symbol
      if (pt.x <= minx) {
        switch (orient) {
          case C:
          case N:
          case S:
          case E:
            minx = pt.x - symbol.size() / 2 * angstromsPerChar;
            break;
          case W:
            minx = pt.x - symbol.size() * angstromsPerChar;
            break;
        }
      }
      if (pt.x >= maxx) {
        switch (orient) {
          case C:
          case N:
          case S:
          case W:
            maxx = pt.x + symbol.size() / 2 * angstromsPerChar;
            break;
          case E:
            maxx = pt.x + symbol.size() * angstromsPerChar;
            break;
        }
      }

      if (pt.y <= miny) {
        miny = pt.y - 1.5 * angstromsPerChar;
      }
      if (pt.y >= maxy) {
        maxy = pt.y + angstromsPerChar;
      }
    } else {
      minx = std::min(pt.x, minx);
      miny = std::min(pt.y, miny);
      maxx = std::max(pt.x, maxx);
      maxy = std::max(pt.y, maxy);
    }
  }
  double dimx = (maxx - minx), dimy = (maxy - miny);
  res.push_back(BOUNDS);
  res.push_back(static_cast<ElementType>(dotsPerAngstrom * 0));
  res.push_back(static_cast<ElementType>(dotsPerAngstrom * 0));
  res.push_back(static_cast<ElementType>(dotsPerAngstrom * dimx));
  res.push_back(static_cast<ElementType>(dotsPerAngstrom * dimy));

  // loop over atoms:
  boost::tie(bAts, eAts) = mol.getVertices();
  while (bAts != eAts) {
    int a1Idx = mol[*bAts]->getIdx();
    RDGeom::Point2D a1(locs[a1Idx].x - minx, locs[a1Idx].y - miny);
    ROMol::OEDGE_ITER nbr, endNbrs;
    RDGeom::Point2D nbrSum(0, 0);
    boost::tie(nbr, endNbrs) = mol.getAtomBonds(mol[*bAts].get());
    while (nbr != endNbrs) {
      const BOND_SPTR bond = mol[*nbr];
      ++nbr;
      int a2Idx = bond->getOtherAtomIdx(a1Idx);
      int lineWidth = 1;
      if (highlightAtoms &&
          std::find(highlightAtoms->begin(), highlightAtoms->end(), a1Idx) !=
              highlightAtoms->end() &&
          std::find(highlightAtoms->begin(), highlightAtoms->end(), a2Idx) !=
              highlightAtoms->end()) {
        lineWidth = 3;
      }
      RDGeom::Point2D a2(locs[a2Idx].x - minx, locs[a2Idx].y - miny);
      nbrSum += a2 - a1;
      if (a2Idx < a1Idx) continue;

      // draw bond from a1 to a2.
      int atnum1 = mol[*bAts]->getAtomicNum();
      int atnum2 = mol.getAtomWithIdx(a2Idx)->getAtomicNum();

      if (!mol.getRingInfo()->numBondRings(bond->getIdx()) &&
          bond->getBondType() != Bond::AROMATIC) {
        // acyclic bonds
        RDGeom::Point2D obv = a2 - a1;
        RDGeom::Point2D perp = obv;
        perp.rotate90();
        perp.normalize();

        if (bond->getBondType() == Bond::DOUBLE ||
            bond->getBondType() == Bond::TRIPLE) {
          RDGeom::Point2D startP = a1, endP = a2;
          if (bond->getBondType() == Bond::TRIPLE) {
            perp *= dblBondOffset;
            startP += (obv * (1. - dblBondLengthFrac) / 2);
            endP -= (obv * (1. - dblBondLengthFrac) / 2);
          } else {
            perp *= 0.5 * dblBondOffset;
          }
          detail::drawLine(res, atnum1, atnum2, lineWidth, 0,
                           dotsPerAngstrom * (startP.x + perp.x),
                           dotsPerAngstrom * (startP.y + perp.y),
                           dotsPerAngstrom * (endP.x + perp.x),
                           dotsPerAngstrom * (endP.y + perp.y));
          if (bond->getBondType() != Bond::AROMATIC) {
            detail::drawLine(res, atnum1, atnum2, lineWidth, 0,
                             dotsPerAngstrom * (startP.x - perp.x),
                             dotsPerAngstrom * (startP.y - perp.y),
                             dotsPerAngstrom * (endP.x - perp.x),
                             dotsPerAngstrom * (endP.y - perp.y));
          } else {
            detail::drawLine(res, atnum1, atnum2, lineWidth, 1,
                             dotsPerAngstrom * (startP.x - perp.x),
                             dotsPerAngstrom * (startP.y - perp.y),
                             dotsPerAngstrom * (endP.x - perp.x),
                             dotsPerAngstrom * (endP.y - perp.y));
          }
        }
        if (bond->getBondType() == Bond::SINGLE ||
            bond->getBondType() == Bond::TRIPLE) {
          detail::drawLine(res, atnum1, atnum2, lineWidth, 0,
                           dotsPerAngstrom * (a1.x), dotsPerAngstrom * (a1.y),
                           dotsPerAngstrom * (a2.x), dotsPerAngstrom * (a2.y));
        } else if (bond->getBondType() != Bond::DOUBLE) {
          detail::drawLine(res, atnum1, atnum2, lineWidth, 2,
                           dotsPerAngstrom * (a1.x), dotsPerAngstrom * (a1.y),
                           dotsPerAngstrom * (a2.x), dotsPerAngstrom * (a2.y));
        }
      } else {
        // cyclic bonds
        detail::drawLine(res, atnum1, atnum2, lineWidth, 0,
                         dotsPerAngstrom * a1.x, dotsPerAngstrom * a1.y,
                         dotsPerAngstrom * a2.x, dotsPerAngstrom * a2.y);

        if (bond->getBondType() == Bond::DOUBLE ||
            bond->getBondType() == Bond::AROMATIC ||
            bond->getBondType() == Bond::TRIPLE) {
          RDGeom::Point2D obv = a2 - a1;
          RDGeom::Point2D perp = obv;
          perp.rotate90();
          perp.normalize();

          if ((bond->getBondType() == Bond::DOUBLE ||
               bond->getBondType() == Bond::AROMATIC) &&
              mol.getRingInfo()->numBondRings(bond->getIdx())) {
            // we're in a ring... we might need to flip sides:
            ROMol::OEDGE_ITER nbr2, endNbrs2;
            boost::tie(nbr2, endNbrs2) = mol.getAtomBonds(mol[*bAts].get());
            while (nbr2 != endNbrs2) {
              const BOND_SPTR bond2 = mol[*nbr2];
              ++nbr2;
              if (bond2->getIdx() == bond->getIdx() ||
                  !mol.getRingInfo()->numBondRings(bond2->getIdx()))
                continue;
              bool sharedRing = false;
              BOOST_FOREACH (const INT_VECT &ring,
                             mol.getRingInfo()->bondRings()) {
                if (std::find(ring.begin(), ring.end(), bond->getIdx()) !=
                        ring.end() &&
                    std::find(ring.begin(), ring.end(), bond2->getIdx()) !=
                        ring.end()) {
                  sharedRing = true;
                  break;
                }
              }
              if (sharedRing) {
                // these two bonds share a ring.
                int a3Idx = bond2->getOtherAtomIdx(a1Idx);
                if (a3Idx != a2Idx) {
                  RDGeom::Point2D a3(locs[a3Idx].x - minx,
                                     locs[a3Idx].y - miny);
                  RDGeom::Point2D obv2 = a3 - a1;
                  if (obv2.dotProduct(perp) < 0) {
                    perp *= -1;
                  }
                }
              }
            }
          }
          perp *= dblBondOffset;

          RDGeom::Point2D offsetStart =
              a1 + obv * (.5 * (1. - dblBondLengthFrac));

          obv *= dblBondLengthFrac;

          detail::drawLine(res, atnum1, atnum2, lineWidth,
                           (bond->getBondType() == Bond::AROMATIC),
                           dotsPerAngstrom * (offsetStart.x + perp.x),
                           dotsPerAngstrom * (offsetStart.y + perp.y),
                           dotsPerAngstrom * (offsetStart.x + obv.x + perp.x),
                           dotsPerAngstrom * (offsetStart.y + obv.y + perp.y));
        }
      }
    }
    std::string symbol;
    OrientType orient;
    boost::tie(symbol, orient) = atomSymbols[a1Idx];
    if (symbol != "" || includeAtomCircles) {
      res.push_back(ATOM);
      res.push_back(mol[*bAts]->getAtomicNum());
      res.push_back(static_cast<ElementType>(dotsPerAngstrom * a1.x));
      res.push_back(static_cast<ElementType>(dotsPerAngstrom * a1.y));
      res.push_back(static_cast<ElementType>(symbol.length()));
      if (symbol.length()) {
        BOOST_FOREACH (char c, symbol) {
          res.push_back(static_cast<ElementType>(c));
        }
      }
      res.push_back(static_cast<ElementType>(orient));
    }

    ++bAts;
  }

  return res;
}

std::vector<int> MolToDrawing(const RDKit::ROMol &mol,
                              const std::vector<int> *highlightAtoms = 0,
                              bool kekulize = true,
                              bool includeAtomCircles = false) {
  RDKit::RWMol *cp = new RDKit::RWMol(mol);
  if (kekulize) {
    try {
      RDKit::MolOps::Kekulize(*cp);
    } catch (...) {
      delete cp;
      cp = new RDKit::RWMol(mol);
    }
  }
  if (!mol.getNumConformers()) {
    RDDepict::compute2DCoords(*cp);
  }
  std::vector<int> drawing =
      DrawMol(*cp, -1, highlightAtoms, includeAtomCircles);
  delete cp;
  return drawing;
}

}  // end of namespace Drawing
}  // end of namespace RDKit

#endif