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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710
|
//
// Copyright (C) 2004-2017 Greg Landrum and 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 <list>
#include <RDGeneral/RDLog.h>
#include "MolFileStereochem.h"
#include <Geometry/point.h>
#include <boost/dynamic_bitset.hpp>
#include <algorithm>
#include "MolFileStereochem.h"
#include <RDGeneral/Ranking.h>
namespace RDKit {
typedef std::list<double> DOUBLE_LIST;
// ----------------------------------- -----------------------------------
// This algorithm is identical to that used in the CombiCode Mol file
// parser (also developed by RD).
//
//
// SUMMARY:
// Derive a chiral code for an atom that has a wedged (or dashed) bond
// drawn to it.
//
// RETURNS:
// The chiral type
//
// CAVEATS:
// This is careful to ensure that the central atom has 4 neighbors and
// only single bonds to it, but that's about it.
//
// NOTE: this isn't careful at all about checking to make sure that
// things actually *should* be chiral. e.g. if the file has a
// 3-coordinate N with a wedged bond, it will make some erroneous
// assumptions about the chirality.
//
// ----------------------------------- -----------------------------------
Atom::ChiralType FindAtomStereochemistry(const RWMol &mol, const Bond *bond,
const Conformer *conf) {
PRECONDITION(bond, "no bond");
PRECONDITION(conf, "no conformer");
Bond::BondDir bondDir = bond->getBondDir();
PRECONDITION(bondDir == Bond::BEGINWEDGE || bondDir == Bond::BEGINDASH,
"bad bond direction");
// NOTE that according to the CT file spec, wedging assigns chirality
// to the atom at the point of the wedge, (atom 1 in the bond).
const Atom *atom = bond->getBeginAtom();
PRECONDITION(atom, "no atom");
// we can't do anything with atoms that have more than 4 neighbors:
if (atom->getDegree() > 4) {
return Atom::CHI_UNSPECIFIED;
}
const Atom *bondAtom = bond->getEndAtom();
Atom::ChiralType res = Atom::CHI_UNSPECIFIED;
INT_LIST neighborBondIndices;
RDGeom::Point3D centerLoc, tmpPt;
centerLoc = conf->getAtomPos(atom->getIdx());
tmpPt = conf->getAtomPos(bondAtom->getIdx());
centerLoc.z = 0.0;
tmpPt.z = 0.0;
RDGeom::Point3D refVect = centerLoc.directionVector(tmpPt);
//----------------------------------------------------------
//
// start by ensuring that all the bonds to neighboring atoms
// are single bonds and collecting a list of neighbor indices:
//
//----------------------------------------------------------
bool hSeen = false;
neighborBondIndices.push_back(bond->getIdx());
if (bondAtom->getAtomicNum() == 1 && bondAtom->getIsotope() == 0)
hSeen = true;
bool allSingle = true;
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const Bond *nbrBond = mol[*beg];
if (nbrBond->getBondType() != Bond::SINGLE) {
allSingle = false;
// break;
}
if (nbrBond != bond) {
if ((nbrBond->getOtherAtom(atom)->getAtomicNum() == 1 &&
nbrBond->getOtherAtom(atom)->getIsotope() == 0))
hSeen = true;
neighborBondIndices.push_back(nbrBond->getIdx());
}
++beg;
}
size_t nNbrs = neighborBondIndices.size();
//----------------------------------------------------------
//
// Return now if there aren't at least 3 non-H bonds to the atom.
// (we can implicitly add a single H to 3 coordinate atoms, but
// we're horked otherwise).
//
//----------------------------------------------------------
if (nNbrs < 3 || (hSeen && nNbrs < 4)) {
return Atom::CHI_UNSPECIFIED;
}
//----------------------------------------------------------
//
// Continue if there are all single bonds or if we're considering
// 4-coordinate P or S
//
//----------------------------------------------------------
if (allSingle || atom->getAtomicNum() == 15 || atom->getAtomicNum() == 16) {
//------------------------------------------------------------
//
// Here we need to figure out the rotation direction between
// the neighbor bonds and the wedged bond:
//
//------------------------------------------------------------
bool isCCW = true;
double angle0, angle1, angle2;
const Bond *bond1, *bond2, *bond3;
RDGeom::Point3D atomVect0, atomVect1, atomVect2;
INT_LIST::const_iterator bondIter = neighborBondIndices.begin();
++bondIter;
bond1 = mol.getBondWithIdx(*bondIter);
int oaid = bond1->getOtherAtom(atom)->getIdx();
tmpPt = conf->getAtomPos(oaid);
tmpPt.z = 0;
atomVect0 = centerLoc.directionVector(tmpPt);
angle0 = refVect.signedAngleTo(atomVect0);
if (angle0 < 0) angle0 += 2. * M_PI;
++bondIter;
bond2 = mol.getBondWithIdx(*bondIter);
oaid = bond2->getOtherAtom(atom)->getIdx();
tmpPt = conf->getAtomPos(oaid);
tmpPt.z = 0;
atomVect1 = centerLoc.directionVector(tmpPt);
angle1 = refVect.signedAngleTo(atomVect1);
if (angle1 < 0) angle1 += 2. * M_PI;
// We proceed differently for 3 and 4 coordinate atoms:
double firstAngle, secondAngle;
if (nNbrs == 4) {
bool flipIt = false;
// grab the angle to the last neighbor:
++bondIter;
bond3 = mol.getBondWithIdx(*bondIter);
oaid = bond3->getOtherAtom(atom)->getIdx();
tmpPt = conf->getAtomPos(oaid);
tmpPt.z = 0;
atomVect2 = centerLoc.directionVector(tmpPt);
angle2 = refVect.signedAngleTo(atomVect2);
if (angle2 < 0) angle2 += 2. * M_PI;
// find the lowest and second-lowest angle and keep track of
// whether or not we have to do a non-cyclic permutation to
// get there:
if (angle0 < angle1) {
if (angle1 < angle2) {
// order is angle0 -> angle1 -> angle2
firstAngle = angle0;
secondAngle = angle1;
} else if (angle0 < angle2) {
// order is angle0 -> angle2 -> angle1
firstAngle = angle0;
secondAngle = angle2;
flipIt = true;
} else {
// order is angle2 -> angle0 -> angle1
firstAngle = angle2;
secondAngle = angle0;
}
} else if (angle0 < angle2) {
// order is angle1 -> angle0 -> angle2
firstAngle = angle1;
secondAngle = angle0;
flipIt = true;
} else {
if (angle1 < angle2) {
// order is angle1 -> angle2 -> angle0
firstAngle = angle1;
secondAngle = angle2;
} else {
// order is angle2 -> angle1 -> angle0
firstAngle = angle2;
secondAngle = angle1;
flipIt = true;
}
}
if (flipIt) {
isCCW = !isCCW;
}
} else {
// it's three coordinate. Things are a bit different here
// because we have to at least kind of figure out where the
// hydrogen might be.
// before getting started with that, use some of the inchi rules
// for contradictory stereochemistry
// (Table 10 in the InChi v1 technical manual)
angle2 = atomVect0.signedAngleTo(atomVect1);
if (angle2 < 0) angle2 += 2. * M_PI;
// this one is never allowed:
// 0 2
// \ /
// C
// *
// 1
if (angle0 < (M_PI - 1e-3) && angle1 < (M_PI - 1e-3) &&
angle2 < (M_PI - 1e-3)) {
if ((bond1->getBondDir() != Bond::NONE &&
bond1->getBeginAtomIdx() == bond->getBeginAtomIdx() &&
(bond1->getBondDir() != bond->getBondDir() ||
(bond2->getBondDir() != Bond::NONE &&
bond2->getBeginAtomIdx() == bond->getBeginAtomIdx() &&
bond2->getBondDir() != bond1->getBondDir()))) ||
(bond2->getBondDir() != Bond::NONE &&
bond2->getBeginAtomIdx() == bond->getBeginAtomIdx() &&
bond2->getBondDir() != bond->getBondDir())) {
BOOST_LOG(rdWarningLog)
<< "Warning: conflicting stereochemistry at atom "
<< bond->getBeginAtomIdx() << " ignored."
<< std::endl; // by rule 1." << std::endl;
return Atom::CHI_UNSPECIFIED;
}
}
if (bond1->getBondDir() != Bond::NONE &&
bond1->getBeginAtomIdx() == bond->getBeginAtomIdx()) {
if (!(bond2->getBondDir() != Bond::NONE &&
bond2->getBeginAtomIdx() == bond->getBeginAtomIdx())) {
BOOST_LOG(rdWarningLog)
<< "Warning: conflicting stereochemistry at atom "
<< bond->getBeginAtomIdx() << " ignored."
<< std::endl; // by rule 2a." << std::endl;
}
if (bond1->getBondDir() != bond->getBondDir()) {
// bond1 has a spec and does not match the bond0 spec.
// the only cases this is allowed are:
// 1 0 1 2
// * \*/
// 0 - C - 2 C
// and
// 1 2 1 0
// * \*/
// 2 - C - 0 C
//
if ((angle0 > M_PI && angle0 < angle1) ||
(angle0 < M_PI && angle0 > angle1)) {
BOOST_LOG(rdWarningLog)
<< "Warning: conflicting stereochemistry at atom "
<< bond->getBeginAtomIdx() << " ignored."
<< std::endl; // by rule 2b." << std::endl;
return Atom::CHI_UNSPECIFIED;
}
} else {
// bond1 matches, what about bond2 ?
if (bond2->getBondDir() != bond->getBondDir()) {
// the only cases this is allowed are:
// 2 0 2 1
// * \*/
// 0 - C - 1 C
// and
// 2 1 2 0
// * \*/
// 1 - C - 0 C
//
if ((angle1 > M_PI && angle1 < angle0) ||
(angle1 < M_PI && angle1 > angle0)) {
BOOST_LOG(rdWarningLog)
<< "Warning: conflicting stereochemistry at atom "
<< bond->getBeginAtomIdx() << " ignored."
<< std::endl; // by rule 2c." << std::endl;
return Atom::CHI_UNSPECIFIED;
}
}
}
} else if (bond2->getBondDir() != Bond::NONE &&
bond2->getBeginAtomIdx() == bond->getBeginAtomIdx() &&
bond2->getBondDir() != bond->getBondDir()) {
// bond2 has a spec and does not match the bond0 spec, but bond1
// is not set: this is never allowed.
BOOST_LOG(rdWarningLog)
<< "Warning: conflicting stereochemistry at atom "
<< bond->getBeginAtomIdx() << " ignored."
<< std::endl; // by rule 3." << std::endl;
return Atom::CHI_UNSPECIFIED;
}
if (angle0 < angle1) {
firstAngle = angle0;
secondAngle = angle1;
isCCW = true;
} else {
firstAngle = angle1;
secondAngle = angle0;
isCCW = false;
}
if (secondAngle - firstAngle >= (M_PI - 1e-4)) {
// it's a situation like one of these:
//
// 0 1 0 2
// * \*/
// 1 - C - 2 C
//
// In each of these cases, the implicit H is between atoms 1
// and 2, so we need to flip the rotation direction (go
// around the back).
isCCW = !isCCW;
}
}
// reverse the rotation direction if the reference is wedged down:
if (bondDir == Bond::BEGINDASH) {
isCCW = !isCCW;
}
// ----------------
//
// We now have the rotation direction using mol-file order.
// We need to convert that into the appropriate label for the
// central atom
//
// ----------------
int nSwaps = atom->getPerturbationOrder(neighborBondIndices);
if (nSwaps % 2) isCCW = !isCCW;
if (isCCW)
res = Atom::CHI_TETRAHEDRAL_CCW;
else
res = Atom::CHI_TETRAHEDRAL_CW;
}
return res;
}
void WedgeBond(Bond *bond, unsigned int fromAtomIdx, const Conformer *conf) {
PRECONDITION(bond, "no bond");
PRECONDITION(conf, "no conformer");
PRECONDITION(&conf->getOwningMol() == &bond->getOwningMol(),"bond and conformer do not belong to same molecule");
if(bond->getBondType() != Bond::SINGLE) return;
Bond::BondDir dir = DetermineBondWedgeState(bond, fromAtomIdx, conf);
if (dir == Bond::BEGINWEDGE || dir == Bond::BEGINDASH) {
bond->setBondDir(dir);
}
}
void WedgeMolBonds(ROMol &mol, const Conformer *conf) {
PRECONDITION(conf, "no conformer");
INT_MAP_INT wedgeBonds = pickBondsToWedge(mol);
for (ROMol::BondIterator bondIt = mol.beginBonds(); bondIt != mol.endBonds();
++bondIt) {
Bond *bond = *bondIt;
if (bond->getBondType() == Bond::SINGLE) {
Bond::BondDir dir = DetermineBondWedgeState(bond, wedgeBonds, conf);
if (dir == Bond::BEGINWEDGE || dir == Bond::BEGINDASH) {
bond->setBondDir(dir);
}
}
}
}
INT_MAP_INT pickBondsToWedge(const ROMol &mol) {
// we need ring information; make sure findSSSR has been called before
// if not call now
if (!mol.getRingInfo()->isInitialized()) {
MolOps::findSSSR(mol);
}
static int noNbrs = 100;
INT_VECT nChiralNbrs(mol.getNumAtoms(), noNbrs);
// start by looking for bonds that are already wedged
for (ROMol::ConstBondIterator cbi = mol.beginBonds(); cbi != mol.endBonds();
++cbi) {
const Bond *bond = *cbi;
if (bond->getBondDir() == Bond::BEGINWEDGE ||
bond->getBondDir() == Bond::BEGINDASH ||
bond->getBondDir() == Bond::UNKNOWN) {
if (bond->getBeginAtom()->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
bond->getBeginAtom()->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW)
nChiralNbrs[bond->getBeginAtomIdx()] = noNbrs + 1;
else if (bond->getEndAtom()->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
bond->getEndAtom()->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW)
nChiralNbrs[bond->getEndAtomIdx()] = noNbrs + 1;
}
}
// now rank atoms by the number of chiral neighbors or Hs they have:
bool chiNbrs = false;
for (ROMol::ConstAtomIterator cai = mol.beginAtoms(); cai != mol.endAtoms();
++cai) {
const Atom *at = *cai;
if (nChiralNbrs[at->getIdx()] > noNbrs) {
// std::cerr << " SKIPPING1: " << at->getIdx() << std::endl;
continue;
}
Atom::ChiralType type = at->getChiralTag();
if (type != Atom::CHI_TETRAHEDRAL_CW && type != Atom::CHI_TETRAHEDRAL_CCW)
continue;
nChiralNbrs[at->getIdx()] = 0;
chiNbrs = true;
ROMol::ADJ_ITER nbrIdx, endNbrs;
boost::tie(nbrIdx, endNbrs) = mol.getAtomNeighbors(at);
while (nbrIdx != endNbrs) {
const Atom* nat = mol[*nbrIdx];
++nbrIdx;
if (nat->getAtomicNum() == 1) {
// special case: it's an H... we weight these especially high:
nChiralNbrs[at->getIdx()] -= 10;
continue;
}
type = nat->getChiralTag();
if (type != Atom::CHI_TETRAHEDRAL_CW && type != Atom::CHI_TETRAHEDRAL_CCW)
continue;
nChiralNbrs[at->getIdx()] -= 1;
}
}
std::vector<unsigned int> indices(mol.getNumAtoms());
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) indices[i] = i;
if (chiNbrs) {
std::sort(indices.begin(), indices.end(),
Rankers::argless<INT_VECT>(nChiralNbrs));
}
#if 0
std::cerr << " nbrs: ";
std::copy(nChiralNbrs.begin(), nChiralNbrs.end(),
std::ostream_iterator<int>(std::cerr, " "));
std::cerr << std::endl;
std::cerr << " order: ";
std::copy(indices.begin(), indices.end(),
std::ostream_iterator<int>(std::cerr, " "));
std::cerr << std::endl;
#endif
// picks a bond for each atom that we will wedge when we write the mol file
// here is what we are going to do
// - at each chiral center look for a bond that is begins at the atom and
// is not yet picked to be wedged for a different chiral center, preferring
// bonds to Hs
// - if we do not find a bond that begins at the chiral center - we will take
// the first bond that is not yet picked by any other chiral centers
// we use the orders calculated above to determine which order to do the
// wedging
INT_MAP_INT res;
BOOST_FOREACH (unsigned int idx, indices) {
if (nChiralNbrs[idx] > noNbrs) {
// std::cerr << " SKIPPING2: " << idx << std::endl;
continue; // already have a wedged bond here
}
const Atom *atom = mol.getAtomWithIdx(idx);
Atom::ChiralType type = atom->getChiralTag();
// the indices are ordered such that all chiral atoms come first. If
// this has no chiral flag, we can stop the whole loop:
if (type != Atom::CHI_TETRAHEDRAL_CW && type != Atom::CHI_TETRAHEDRAL_CCW)
break;
RDKit::ROMol::OBOND_ITER_PAIR atomBonds = mol.getAtomBonds(atom);
std::vector<std::pair<int, int>> nbrScores;
while (atomBonds.first != atomBonds.second) {
const Bond *bond = mol[*atomBonds.first];
++atomBonds.first;
// can only wedge single bonds:
if (bond->getBondType() != Bond::SINGLE) continue;
int bid = bond->getIdx();
if (res.find(bid) == res.end()) {
// very strong preference for Hs:
if (bond->getOtherAtom(atom)->getAtomicNum() == 1) {
nbrScores.push_back(std::make_pair(
-1000000, bid)); // lower than anything else can be
continue;
}
// prefer lower atomic numbers with lower degrees and no specified
// chirality:
const Atom *oatom = bond->getOtherAtom(atom);
int nbrScore = oatom->getAtomicNum() + 10 * oatom->getDegree() +
100 * ((oatom->getChiralTag() != Atom::CHI_UNSPECIFIED));
// prefer neighbors that are nonchiral or have as few chiral neighbors
// as possible:
int oIdx = oatom->getIdx();
if (nChiralNbrs[oIdx] < noNbrs) {
// the counts are negative, so we have to subtract them off
nbrScore -= 10000 * nChiralNbrs[oIdx];
}
// prefer bonds to non-ring atoms:
nbrScore += 1000 * mol.getRingInfo()->numAtomRings(oIdx);
// prefer non-ring bonds;
nbrScore += 1000 * mol.getRingInfo()->numBondRings(bid);
// std::cerr << " nrbScore: " << idx << " - " << oIdx << " : "
// << nbrScore << " nChiralNbrs: " << nChiralNbrs[oIdx]
// << std::endl;
nbrScores.push_back(std::make_pair(nbrScore, bid));
}
}
// There's still one situation where this whole thing can fail: an unlucky
// situation where all neighbors of all neighbors of an atom are chiral and
// that atom ends up being the last one picked for stereochem assignment.
//
// We'll catch that as an error here and hope that it's as unlikely to occur
// as it seems like it is. (I'm going into this knowing that it's bound to
// happen; I'll kick myself and do the hard solution at that point.)
CHECK_INVARIANT(nbrScores.size(),
"no eligible neighbors for chiral center");
std::sort(nbrScores.begin(), nbrScores.end(),
Rankers::pairLess<int, int>());
res[nbrScores[0].second] = idx;
}
return res;
}
//
// Determine bond wedge state
///
Bond::BondDir DetermineBondWedgeState(const Bond *bond,
unsigned int fromAtomIdx,
const Conformer *conf) {
PRECONDITION(bond, "no bond");
PRECONDITION(bond->getBondType() == Bond::SINGLE,
"bad bond order for wedging");
const ROMol *mol = &(bond->getOwningMol());
PRECONDITION(mol, "no mol");
Bond::BondDir res = bond->getBondDir();
if (!conf) {
return res;
}
Atom *atom, *bondAtom; // = bond->getBeginAtom();
if (bond->getBeginAtom()->getIdx() == fromAtomIdx) {
atom = bond->getBeginAtom();
bondAtom = bond->getEndAtom();
} else {
atom = bond->getEndAtom();
bondAtom = bond->getBeginAtom();
}
Atom::ChiralType chiralType = atom->getChiralTag();
CHECK_INVARIANT(chiralType == Atom::CHI_TETRAHEDRAL_CW ||
chiralType == Atom::CHI_TETRAHEDRAL_CCW,
"");
// if we got this far, we really need to think about it:
INT_LIST neighborBondIndices;
DOUBLE_LIST neighborBondAngles;
RDGeom::Point3D centerLoc, tmpPt;
centerLoc = conf->getAtomPos(atom->getIdx());
tmpPt = conf->getAtomPos(bondAtom->getIdx());
centerLoc.z = 0.0;
tmpPt.z = 0.0;
RDGeom::Point3D refVect = centerLoc.directionVector(tmpPt);
neighborBondIndices.push_back(bond->getIdx());
neighborBondAngles.push_back(0.0);
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol->getAtomBonds(atom);
while (beg != end) {
const Bond *nbrBond = (*mol)[*beg];
Atom *otherAtom = nbrBond->getOtherAtom(atom);
if (nbrBond != bond) {
tmpPt = conf->getAtomPos(otherAtom->getIdx());
tmpPt.z = 0.0;
RDGeom::Point3D tmpVect = centerLoc.directionVector(tmpPt);
double angle = refVect.signedAngleTo(tmpVect);
if (angle < 0.0) angle += 2. * M_PI;
auto nbrIt = neighborBondIndices.begin();
auto angleIt = neighborBondAngles.begin();
// find the location of this neighbor in our angle-sorted list
// of neighbors:
while (angleIt != neighborBondAngles.end() && angle > (*angleIt)) {
++angleIt;
++nbrIt;
}
neighborBondAngles.insert(angleIt, angle);
neighborBondIndices.insert(nbrIt, nbrBond->getIdx());
}
++beg;
}
// at this point, neighborBondIndices contains a list of bond
// indices from the central atom. They are arranged starting
// at the reference bond in CCW order (based on the current
// depiction).
int nSwaps = atom->getPerturbationOrder(neighborBondIndices);
// in the case of three-coordinated atoms we may have to worry about
// the location of the implicit hydrogen - Issue 209
// Check if we have one of these situation
//
// 0 1 0 2
// * \*/
// 1 - C - 2 C
//
// here the hydrogen will be between 1 and 2 and we need to add an additional
// swap
if (neighborBondAngles.size() == 3) {
// three coordinated
auto angleIt = neighborBondAngles.begin();
++angleIt; // the first is the 0 (or reference bond - we will ignoire that
double angle1 = (*angleIt);
++angleIt;
double angle2 = (*angleIt);
if (angle2 - angle1 >= (M_PI - 1e-4)) {
// we have the above situation
nSwaps++;
}
}
#ifdef VERBOSE_STEREOCHEM
BOOST_LOG(rdDebugLog) << "--------- " << nSwaps << std::endl;
std::copy(neighborBondIndices.begin(), neighborBondIndices.end(),
std::ostream_iterator<int>(BOOST_LOG(rdDebugLog), " "));
BOOST_LOG(rdDebugLog) << std::endl;
std::copy(neighborBondAngles.begin(), neighborBondAngles.end(),
std::ostream_iterator<double>(BOOST_LOG(rdDebugLog), " "));
BOOST_LOG(rdDebugLog) << std::endl;
#endif
if (chiralType == Atom::CHI_TETRAHEDRAL_CCW) {
if (nSwaps % 2 == 1) { // ^ reverse) {
res = Bond::BEGINDASH;
} else {
res = Bond::BEGINWEDGE;
}
} else {
if (nSwaps % 2 == 1) { // ^ reverse) {
res = Bond::BEGINWEDGE;
} else {
res = Bond::BEGINDASH;
}
}
return res;
}
Bond::BondDir DetermineBondWedgeState(const Bond *bond,
const INT_MAP_INT &wedgeBonds,
const Conformer *conf) {
PRECONDITION(bond, "no bond");
int bid = bond->getIdx();
auto wbi = wedgeBonds.find(bid);
if (wbi == wedgeBonds.end()) {
return bond->getBondDir();
}
unsigned int waid = wbi->second;
return DetermineBondWedgeState(bond,waid,conf);
}
// handles stereochem markers set by the Mol file parser and
// converts them to the RD standard:
void DetectAtomStereoChemistry(RWMol &mol, const Conformer *conf) {
PRECONDITION(conf, "no conformer");
for (RWMol::BondIterator bondIt = mol.beginBonds(); bondIt != mol.endBonds();
++bondIt) {
Bond *bond = *bondIt;
if (bond->getBondDir() != Bond::UNKNOWN) {
Bond::BondDir dir = bond->getBondDir();
// the bond is marked as chiral:
if (dir == Bond::BEGINWEDGE || dir == Bond::BEGINDASH) {
Atom *atom = bond->getBeginAtom();
if (atom->getImplicitValence() == -1) {
atom->calcExplicitValence(false);
atom->calcImplicitValence(false);
}
Atom::ChiralType code = FindAtomStereochemistry(mol, bond, conf);
atom->setChiralTag(code);
// within the RD representation, if a three-coordinate atom
// is chiral and has an implicit H, that H needs to be made explicit:
if (atom->getDegree() == 3 && !atom->getNumExplicitHs() &&
atom->getNumImplicitHs() == 1) {
atom->setNumExplicitHs(1);
// recalculated number of implicit Hs:
atom->updatePropertyCache();
}
}
}
}
}
void ClearSingleBondDirFlags(ROMol &mol) {
for (RWMol::BondIterator bondIt = mol.beginBonds(); bondIt != mol.endBonds();
++bondIt) {
if ((*bondIt)->getBondType() == Bond::SINGLE) {
if ((*bondIt)->getBondDir() == Bond::UNKNOWN)
(*bondIt)->setProp(common_properties::_UnknownStereo, 1);
(*bondIt)->setBondDir(Bond::NONE);
}
}
}
void DetectBondStereoChemistry(ROMol &mol, const Conformer *conf) {
PRECONDITION(conf, "no conformer");
PRECONDITION(&(conf->getOwningMol()) == &mol,
"conformer does not belong to molecule");
MolOps::detectBondStereochemistry(mol, conf->getId());
}
}
|