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rdkit/Code/GraphMol/ChemTransforms/MolFragmenter.cpp
Brian Kelley 693796d7af Enhance molzip to properly handle RGroupDecompositions (#7202) 
* Fix zipping of rgroup decomps with broken rings

* Add utility to molzip rgroup rows

* Add RGroupRow molzip

* Fix typo in example and test

* Fix warning on integer size

* Don't use ssize_t

* a couple of suggestions

* Update Code/GraphMol/ChemTransforms/MolFragmenter.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/ChemTransforms/MolFragmenter.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Move molzip rgroup row from RGroupDecomp to ChemTransforms

* Fix exports

---------

Co-authored-by: Brian Kelley <bkelley@relaytx.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
2024-03-19 17:02:45 +01:00

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//
// Copyright (C) 2013-2018 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.
//
#include "MolFragmenter.h"
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/Exceptions.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/utils.h>
#include "ChemTransforms.h"
#include <RDGeneral/BoostStartInclude.h>
#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/dynamic_bitset.hpp>
#include <boost/flyweight.hpp>
#include <boost/flyweight/no_tracking.hpp>
#include <boost/functional/hash.hpp>
#include <boost/range/adaptor/reversed.hpp>
#include <boost/tokenizer.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <algorithm>
#include <cstdint>
#include <map>
#include <optional>
#include <sstream>
#include <vector>
namespace RDKit {
namespace MolFragmenter {
std::size_t hash_value(const FragmenterBondType &fbt) {
size_t res = boost::hash<int>()((int)fbt.bondType);
boost::hash_combine(res, fbt.atom1Label);
boost::hash_combine(res, fbt.atom2Label);
return res;
}
bool operator==(const FragmenterBondType &v1, const FragmenterBondType &v2) {
return (v1.atom1Label == v2.atom1Label) && (v1.atom2Label == v2.atom2Label) &&
(v1.bondType == v2.bondType);
}
void constructFragmenterAtomTypes(
std::istream *inStream, std::map<unsigned int, std::string> &defs,
const std::string &comment, bool validate,
std::map<unsigned int, ROMOL_SPTR> *environs) {
PRECONDITION(inStream, "no stream");
defs.clear();
unsigned int line = 0;
while (!inStream->eof() && !inStream->fail()) {
++line;
std::string tempStr = getLine(inStream);
if (tempStr == "" || tempStr.find(comment) == 0) {
continue;
}
std::vector<std::string> tokens;
boost::split(tokens, tempStr, boost::is_any_of(" \t"),
boost::token_compress_on);
if (tokens.size() < 2) {
BOOST_LOG(rdWarningLog)
<< "line " << line << " is too short" << std::endl;
continue;
}
auto idx = boost::lexical_cast<unsigned int>(tokens[0]);
if (defs.find(idx) != defs.end()) {
BOOST_LOG(rdWarningLog)
<< "definition #" << idx
<< " encountered more than once. Using the first occurrence."
<< std::endl;
continue;
}
if (validate || environs) {
ROMol *p = SmartsToMol(tokens[1]);
if (!p) {
BOOST_LOG(rdWarningLog) << "cannot convert SMARTS " << tokens[1]
<< " to molecule at line " << line << std::endl;
continue;
}
if (!environs) {
delete p;
} else {
(*environs)[idx] = ROMOL_SPTR(p);
}
}
defs[idx] = tokens[1];
}
}
void constructFragmenterAtomTypes(
const std::string &str, std::map<unsigned int, std::string> &defs,
const std::string &comment, bool validate,
std::map<unsigned int, ROMOL_SPTR> *environs) {
std::stringstream istr(str);
constructFragmenterAtomTypes(&istr, defs, comment, validate, environs);
}
void constructBRICSAtomTypes(std::map<unsigned int, std::string> &defs,
std::map<unsigned int, ROMOL_SPTR> *environs) {
/*
After some discussion, the L2 definitions ("N.pl3" in the original
paper) have been removed and incorporated into a (almost) general
purpose amine definition in L5 ("N.sp3" in the paper).
The problem is one of consistency.
Based on the original definitions you should get the following
fragmentations:
C1CCCCC1NC(=O)C -> C1CCCCC1N[2*].[1*]C(=O)C
c1ccccc1NC(=O)C -> c1ccccc1[16*].[2*]N[2*].[1*]C(=O)C
This difference just didn't make sense to us. By switching to
the unified definition we end up with:
C1CCCCC1NC(=O)C -> C1CCCCC1[15*].[5*]N[5*].[1*]C(=O)C
c1ccccc1NC(=O)C -> c1ccccc1[16*].[5*]N[5*].[1*]C(=O)C
*/
const std::string BRICSdefs =
"1 [C;D3]([#0,#6,#7,#8])(=O)\n\
3 [O;D2]-;!@[#0,#6,#1]\n\
5 [N;!D1;!$(N=*);!$(N-[!#6;!#16;!#0;!#1]);!$([N;R]@[C;R]=O)]\n\
9 [n;+0;$(n(:[c,n,o,s]):[c,n,o,s])]\n\
10 [N;R;$(N(@C(=O))@[C,N,O,S])]\n\
11 [S;D2](-;!@[#0,#6])\n\
12 [S;D4]([#6,#0])(=O)(=O)\n\
6 [C;D3;!R](=O)-;!@[#0,#6,#7,#8]\n\
13 [C;$(C(-;@[C,N,O,S])-;@[N,O,S])]\n\
14 [c;$(c(:[c,n,o,s]):[n,o,s])]\n\
15 [C;$(C(-;@C)-;@C)]\n\
4 [C;!D1;!$(C=*)]-;!@[#6]\n\
7 [C;D2,D3]-[#6]\n\
8 [C;!R;!D1;!$(C!-*)]\n\
16 [c;$(c(:c):c)]";
constructFragmenterAtomTypes(BRICSdefs, defs, "//", true, environs);
}
void constructFragmenterBondTypes(
std::istream *inStream,
const std::map<unsigned int, std::string> &atomTypes,
std::vector<FragmenterBondType> &defs, const std::string &comment,
bool validate, bool labelByConnector) {
PRECONDITION(inStream, "no stream");
defs.clear();
defs.resize(0);
unsigned int line = 0;
while (!inStream->eof() && !inStream->fail()) {
++line;
std::string tempStr = getLine(inStream);
if (tempStr == "" || tempStr.find(comment) == 0) {
continue;
}
std::vector<std::string> tokens;
boost::split(tokens, tempStr, boost::is_any_of(" \t"),
boost::token_compress_on);
if (tokens.size() < 3) {
BOOST_LOG(rdWarningLog)
<< "line " << line << " is too short" << std::endl;
continue;
}
auto idx1 = boost::lexical_cast<unsigned int>(tokens[0]);
if (atomTypes.find(idx1) == atomTypes.end()) {
BOOST_LOG(rdWarningLog)
<< "atom type #" << idx1 << " not recognized." << std::endl;
continue;
}
auto idx2 = boost::lexical_cast<unsigned int>(tokens[1]);
if (atomTypes.find(idx2) == atomTypes.end()) {
BOOST_LOG(rdWarningLog)
<< "atom type #" << idx2 << " not recognized." << std::endl;
continue;
}
std::string sma1 = atomTypes.find(idx1)->second;
std::string sma2 = atomTypes.find(idx2)->second;
std::string smarts = "[$(" + sma1 + ")]" + tokens[2] + "[$(" + sma2 + ")]";
ROMol *p = SmartsToMol(smarts);
if (validate) {
if (!p) {
BOOST_LOG(rdWarningLog) << "cannot convert SMARTS " << smarts
<< " to molecule at line " << line << std::endl;
continue;
}
}
FragmenterBondType fbt;
fbt.atom1Type = idx1;
fbt.atom2Type = idx2;
if (labelByConnector) {
fbt.atom1Label = idx1;
fbt.atom2Label = idx2;
} else {
fbt.atom1Label = idx2;
fbt.atom2Label = idx1;
}
if (p) {
// for the purposes of replacing the bond, we'll use just the first
// character to set the bond type (if we recognize it):
switch (tokens[2][0]) {
case '-':
fbt.bondType = Bond::SINGLE;
break;
case '=':
fbt.bondType = Bond::DOUBLE;
break;
case '#':
fbt.bondType = Bond::TRIPLE;
break;
case ':':
fbt.bondType = Bond::AROMATIC;
break;
default:
fbt.bondType = p->getBondWithIdx(0)->getBondType();
}
fbt.query = ROMOL_SPTR(p);
} else {
fbt.bondType = Bond::UNSPECIFIED;
fbt.query = ROMOL_SPTR();
}
defs.push_back(fbt);
}
}
void constructFragmenterBondTypes(
const std::string &str,
const std::map<unsigned int, std::string> &atomTypes,
std::vector<FragmenterBondType> &defs, const std::string &comment,
bool validate, bool labelByConnector) {
std::stringstream istr(str);
constructFragmenterBondTypes(&istr, atomTypes, defs, comment, validate,
labelByConnector);
}
void constructBRICSBondTypes(std::vector<FragmenterBondType> &defs) {
const std::string BRICSdefs =
"// L1\n\
1 3 -;!@\n\
1 5 -;!@\n\
1 10 -;!@\n\
// L3 \n\
3 4 -;!@\n\
3 13 -;!@\n\
3 14 -;!@\n\
3 15 -;!@\n\
3 16 -;!@\n\
// L4\n\
4 5 -;!@\n\
4 11 -;!@\n\
// L5\n\
5 12 -;!@\n\
5 14 -;!@\n\
5 16 -;!@\n\
5 13 -;!@\n\
5 15 -;!@\n\
// L6\n\
6 13 -;!@\n\
6 14 -;!@\n\
6 15 -;!@\n\
6 16 -;!@\n\
// L7\n\
7 7 =;!@\n\
// L8\n\
8 9 -;!@\n\
8 10 -;!@\n\
8 13 -;!@\n\
8 14 -;!@\n\
8 15 -;!@\n\
8 16 -;!@\n\
// L9\n\
9 13 -;!@ // not in original paper\n\
9 14 -;!@ // not in original paper\n\
9 15 -;!@\n\
9 16 -;!@\n\
// L10\n\
10 13 -;!@\n\
10 14 -;!@\n\
10 15 -;!@\n\
10 16 -;!@\n\
// L11\n\
11 13 -;!@\n\
11 14 -;!@\n\
11 15 -;!@\n\
11 16 -;!@\n\
// L12\n\
// none left\n\
// L13\n\
13 14 -;!@\n\
13 15 -;!@\n\
13 16 -;!@\n\
// L14\n\
14 14 -;!@ // not in original paper\n\
14 15 -;!@\n\
14 16 -;!@\n\
// L15\n\
15 16 -;!@\n\
// L16\n\
16 16 -;!@ // not in original paper";
std::map<unsigned int, std::string> atTypes;
constructBRICSAtomTypes(atTypes);
constructFragmenterBondTypes(BRICSdefs, atTypes, defs, "//", true, false);
}
namespace {
boost::uint64_t nextBitCombo(boost::uint64_t v) {
// code from:
// http://graphics.stanford.edu/~seander/bithacks.html#NextBitPermutation
boost::uint64_t t = (v | (v - 1)) + 1;
return t | ((((t & -t) / (v & -v)) >> 1) - 1);
}
} // namespace
void fragmentOnSomeBonds(
const ROMol &mol, const std::vector<unsigned int> &bondIndices,
std::vector<ROMOL_SPTR> &resMols, unsigned int maxToCut, bool addDummies,
const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels,
const std::vector<Bond::BondType> *bondTypes,
std::vector<std::vector<unsigned int>> *nCutsPerAtom) {
PRECONDITION((!dummyLabels || dummyLabels->size() == bondIndices.size()),
"bad dummyLabel vector");
PRECONDITION((!bondTypes || bondTypes->size() == bondIndices.size()),
"bad bondType vector");
if (bondIndices.size() > 63) {
throw ValueErrorException("currently can only fragment on up to 63 bonds");
}
if (!maxToCut || !mol.getNumAtoms() || !bondIndices.size()) {
return;
}
boost::uint64_t state = (0x1L << maxToCut) - 1;
boost::uint64_t stop = 0x1L << bondIndices.size();
std::vector<unsigned int> fragmentHere(maxToCut);
std::vector<std::pair<unsigned int, unsigned int>> *dummyLabelsHere = nullptr;
if (dummyLabels) {
dummyLabelsHere =
new std::vector<std::pair<unsigned int, unsigned int>>(maxToCut);
}
std::vector<Bond::BondType> *bondTypesHere = nullptr;
if (bondTypes) {
bondTypesHere = new std::vector<Bond::BondType>(maxToCut);
}
while (state < stop) {
unsigned int nSeen = 0;
for (unsigned int i = 0; i < bondIndices.size() && nSeen < maxToCut; ++i) {
if (state & (0x1L << i)) {
fragmentHere[nSeen] = bondIndices[i];
if (dummyLabelsHere) {
(*dummyLabelsHere)[nSeen] = (*dummyLabels)[i];
}
if (bondTypesHere) {
(*bondTypesHere)[nSeen] = (*bondTypes)[i];
}
++nSeen;
}
}
std::vector<unsigned int> *lCutsPerAtom = nullptr;
if (nCutsPerAtom) {
nCutsPerAtom->push_back(std::vector<unsigned int>(mol.getNumAtoms()));
lCutsPerAtom = &(nCutsPerAtom->back());
}
ROMol *nm = fragmentOnBonds(mol, fragmentHere, addDummies, dummyLabelsHere,
bondTypesHere, lCutsPerAtom);
resMols.emplace_back(nm);
state = nextBitCombo(state);
}
delete dummyLabelsHere;
delete bondTypesHere;
}
namespace {
void checkChiralityPostMove(const ROMol &mol, const Atom *oAt, Atom *nAt,
const Bond *bond) {
static const std::string newBondOrder = "_newBondOrder";
INT_LIST newOrder;
INT_LIST incomingOrder;
const int check_bond_index = static_cast<int>(bond->getIdx());
// since we may call this function more than once, we need to keep track of
// whether or not we've already been called and what the new atom order is.
// we do this with a property.
// this was github #1734
if (nAt->getPropIfPresent(newBondOrder, incomingOrder)) {
for (int bidx : incomingOrder) {
if (bidx != check_bond_index) {
newOrder.push_back(bidx);
}
}
} else {
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(oAt);
while (beg != end) {
const Bond *obond = mol[*beg];
++beg;
if (obond == bond) {
continue;
}
newOrder.push_back(obond->getIdx());
}
}
newOrder.push_back(bond->getIdx());
nAt->setProp(newBondOrder, newOrder, true);
unsigned int nSwaps = oAt->getPerturbationOrder(newOrder);
// std::copy(newOrder.begin(), newOrder.end(),
// std::ostream_iterator<int>(std::cerr, ", "));
// std::cerr << std::endl;
// std::cerr<<"ccpm: "<<oAt->getIdx()<<"->"<<nAt->getIdx()<<" bond:
// "<<bond->getIdx()<<" swaps: "<<nSwaps<<std::endl;
nAt->setChiralTag(oAt->getChiralTag());
if (nSwaps % 2) {
nAt->invertChirality();
}
}
std::vector<std::pair<Bond *, std::vector<int>>> getNbrBondStereo(
RWMol &mol, const Bond *bnd) {
PRECONDITION(bnd, "null bond");
// loop over neighboring double bonds and remove their stereo atom
std::vector<std::pair<Bond *, std::vector<int>>> res;
const auto bgn = bnd->getBeginAtom();
const auto end = bnd->getEndAtom();
for (const auto *atom : {bgn, end}) {
ROMol::OEDGE_ITER a1, a2;
for (boost::tie(a1, a2) = mol.getAtomBonds(atom); a1 != a2; ++a1) {
Bond *obnd = mol[*a1];
if (obnd->getIdx() != bnd->getIdx() && !obnd->getStereoAtoms().empty()) {
res.emplace_back(obnd, obnd->getStereoAtoms());
}
}
}
return res;
}
} // namespace
ROMol *fragmentOnBonds(
const ROMol &mol, const std::vector<unsigned int> &bondIndices,
bool addDummies,
const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels,
const std::vector<Bond::BondType> *bondTypes,
std::vector<unsigned int> *nCutsPerAtom) {
PRECONDITION((!dummyLabels || dummyLabels->size() == bondIndices.size()),
"bad dummyLabel vector");
PRECONDITION((!bondTypes || bondTypes->size() == bondIndices.size()),
"bad bondType vector");
PRECONDITION((!nCutsPerAtom || nCutsPerAtom->size() == mol.getNumAtoms()),
"bad nCutsPerAtom vector");
if (nCutsPerAtom) {
for (auto &nCuts : *nCutsPerAtom) {
nCuts = 0;
}
}
auto *res = new RWMol(mol);
if (!mol.getNumAtoms()) {
return res;
}
std::vector<Bond *> bondsToRemove;
bondsToRemove.reserve(bondIndices.size());
for (auto bondIdx : bondIndices) {
bondsToRemove.push_back(res->getBondWithIdx(bondIdx));
}
for (unsigned int i = 0; i < bondsToRemove.size(); ++i) {
const Bond *bond = bondsToRemove[i];
unsigned int bidx = bond->getBeginAtomIdx();
unsigned int eidx = bond->getEndAtomIdx();
Bond::BondType bT = bond->getBondType();
Bond::BondDir bD = bond->getBondDir();
unsigned int bondidx;
auto nbr_bond_stereo = getNbrBondStereo(*res, bond);
res->removeBond(bidx, eidx);
if (nCutsPerAtom) {
(*nCutsPerAtom)[bidx] += 1;
(*nCutsPerAtom)[eidx] += 1;
}
if (addDummies) {
Atom *at1, *at2;
at1 = new Atom(0);
at2 = new Atom(0);
if (dummyLabels) {
at1->setIsotope((*dummyLabels)[i].first);
at2->setIsotope((*dummyLabels)[i].second);
} else {
at1->setIsotope(bidx);
at2->setIsotope(eidx);
}
unsigned int idx1 = res->addAtom(at1, false, true);
if (bondTypes) {
bT = (*bondTypes)[i];
}
bondidx = res->addBond(at1->getIdx(), eidx, bT) - 1;
// the dummy replaces the original start atom, so the
// direction will be ok as long as it's one of the
// states associated with double bond stereo
if (bD == Bond::ENDDOWNRIGHT || bD == Bond::ENDUPRIGHT) {
res->getBondWithIdx(bondidx)->setBondDir(bD);
}
unsigned int idx2 = res->addAtom(at2, false, true);
bondidx = res->addBond(bidx, at2->getIdx(), bT) - 1;
// this bond starts at the same atom, so its direction should always be
// correct:
res->getBondWithIdx(bondidx)->setBondDir(bD);
// restore stereo atoms
for (auto &stereo_atoms : nbr_bond_stereo) {
std::replace(stereo_atoms.second.begin(), stereo_atoms.second.end(),
bidx, idx1);
std::replace(stereo_atoms.second.begin(), stereo_atoms.second.end(),
eidx, idx2);
stereo_atoms.first->getStereoAtoms().swap(stereo_atoms.second);
}
// figure out if we need to change the stereo tags on the atoms:
if (mol.getAtomWithIdx(bidx)->getChiralTag() ==
Atom::CHI_TETRAHEDRAL_CCW ||
mol.getAtomWithIdx(bidx)->getChiralTag() ==
Atom::CHI_TETRAHEDRAL_CW) {
checkChiralityPostMove(mol, mol.getAtomWithIdx(bidx),
res->getAtomWithIdx(bidx),
mol.getBondBetweenAtoms(bidx, eidx));
}
if (mol.getAtomWithIdx(eidx)->getChiralTag() ==
Atom::CHI_TETRAHEDRAL_CCW ||
mol.getAtomWithIdx(eidx)->getChiralTag() ==
Atom::CHI_TETRAHEDRAL_CW) {
checkChiralityPostMove(mol, mol.getAtomWithIdx(eidx),
res->getAtomWithIdx(eidx),
mol.getBondBetweenAtoms(bidx, eidx));
}
for (auto confIt = res->beginConformers(); confIt != res->endConformers();
++confIt) {
Conformer *conf = (*confIt).get();
conf->setAtomPos(idx1, conf->getAtomPos(bidx));
conf->setAtomPos(idx2, conf->getAtomPos(eidx));
}
} else {
// was github issues 429, 6034
for (auto idx : {bidx, eidx}) {
if (auto tatom = res->getAtomWithIdx(idx);
tatom->getNoImplicit() ||
(tatom->getIsAromatic() && tatom->getAtomicNum() != 6)) {
tatom->setNumExplicitHs(tatom->getNumExplicitHs() + 1);
} else {
tatom->updatePropertyCache(false);
}
}
}
}
res->clearComputedProps();
return static_cast<ROMol *>(res);
}
ROMol *fragmentOnBonds(const ROMol &mol,
const std::vector<FragmenterBondType> &bondPatterns,
const std::map<unsigned int, ROMOL_SPTR> *atomEnvirons,
std::vector<unsigned int> *nCutsPerAtom) {
PRECONDITION((!nCutsPerAtom || nCutsPerAtom->size() == mol.getNumAtoms()),
"bad nCutsPerAtom vector");
std::vector<unsigned int> bondIndices;
std::vector<std::pair<unsigned int, unsigned int>> dummyLabels;
std::vector<Bond::BondType> bondTypes;
std::map<unsigned int, bool> environsMatch;
if (atomEnvirons) {
for (const auto &atomEnviron : *atomEnvirons) {
MatchVectType mv;
environsMatch[atomEnviron.first] =
SubstructMatch(mol, *(atomEnviron.second), mv);
}
}
boost::dynamic_bitset<> bondsUsed(mol.getNumBonds(), 0);
// the bond definitions are organized (more or less) general -> specific, so
// loop over them backwards
for (const auto &fbt : boost::adaptors::reverse(bondPatterns)) {
if (fbt.query->getNumAtoms() != 2 || fbt.query->getNumBonds() != 1) {
BOOST_LOG(rdErrorLog)
<< "fragmentation queries must have 2 atoms and 1 bond" << std::endl;
continue;
}
if (atomEnvirons &&
(!environsMatch[fbt.atom1Type] || !environsMatch[fbt.atom2Type])) {
continue;
}
// std::cerr<<" >>> "<<fbt.atom1Label<<" "<<fbt.atom2Label<<std::endl;
std::vector<MatchVectType> bondMatches;
SubstructMatch(mol, *fbt.query.get(), bondMatches);
for (const auto &mv : bondMatches) {
const Bond *bond = mol.getBondBetweenAtoms(mv[0].second, mv[1].second);
// std::cerr<<" "<<bond->getIdx()<<std::endl;
TEST_ASSERT(bond);
if (bondsUsed[bond->getIdx()]) {
// BOOST_LOG(rdWarningLog)<<"bond #"<<bond->getIdx()<<" matched multiple
// times in decomposition. Later matches ignored."<<std::endl;
continue;
}
bondsUsed.set(bond->getIdx());
bondIndices.push_back(bond->getIdx());
if (bond->getBeginAtomIdx() == static_cast<unsigned int>(mv[0].second)) {
dummyLabels.emplace_back(fbt.atom1Label, fbt.atom2Label);
} else {
dummyLabels.emplace_back(fbt.atom2Label, fbt.atom1Label);
}
bondTypes.push_back(fbt.bondType);
}
}
return fragmentOnBonds(mol, bondIndices, true, &dummyLabels, &bondTypes,
nCutsPerAtom);
}
boost::flyweight<std::vector<FragmenterBondType>,
boost::flyweights::no_tracking>
bondPatterns;
boost::flyweight<std::map<unsigned int, ROMOL_SPTR>,
boost::flyweights::no_tracking>
atomEnvs;
ROMol *fragmentOnBRICSBonds(const ROMol &mol) {
if (bondPatterns.get().size() == 0) {
std::map<unsigned int, std::string> adefs;
std::map<unsigned int, ROMOL_SPTR> aenvs;
constructBRICSAtomTypes(adefs, &aenvs);
atomEnvs = aenvs;
std::vector<FragmenterBondType> tbondPatterns;
constructBRICSBondTypes(tbondPatterns);
bondPatterns = tbondPatterns;
}
return fragmentOnBonds(mol, bondPatterns, &(atomEnvs.get()));
}
} // namespace MolFragmenter
namespace {
const unsigned int NOLABEL = std::numeric_limits<unsigned int>::max();
// Get the atom label - this might be useful as a util class
unsigned int get_label(const Atom *a, const MolzipParams &p) {
PRECONDITION(a, "bad atom in MolZip::get_label")
unsigned int idx = NOLABEL;
switch (p.label) {
case MolzipLabel::AtomMapNumber:
if (a->getAtomicNum() == 0) {
auto mapno = a->getAtomMapNum();
return mapno ? mapno : NOLABEL;
}
break;
case MolzipLabel::Isotope:
if (a->getAtomicNum() == 0) {
auto iso = a->getIsotope();
return iso ? iso : NOLABEL;
}
break;
case MolzipLabel::AtomType:
idx = std::distance(p.atomSymbols.begin(),
std::find(p.atomSymbols.begin(), p.atomSymbols.end(),
a->getSymbol()));
if (idx == p.atomSymbols.size()) {
idx = NOLABEL;
}
break;
case MolzipLabel::FragmentOnBonds:
// shouldn't ever get here
CHECK_INVARIANT(
0, "FragmentOnBonds is not an atom label, it is an atom index");
break;
case MolzipLabel::AtomProperty:
a->getPropIfPresent<unsigned int>(p.atomProperty, idx);
break;
default:
CHECK_INVARIANT(0, "bogus MolZipLabel value in MolZip::get_label");
}
return idx;
}
// Return the connected atom
// n.b. There can be only one connection from a mapped atom
Atom *get_other_atom(Atom *a) {
PRECONDITION(a, "null atom in MolZip::get_other_atom");
auto &m = a->getOwningMol();
if (m.getAtomDegree(a) != 1) {
return nullptr;
}
return m[*m.getAtomNeighbors(a).first];
}
int num_swaps_to_interconvert(std::vector<unsigned int> &orders) {
int nswaps = 0;
std::vector<bool> seen(orders.size());
for (size_t i = 0; i < orders.size(); ++i) {
if (!seen[i]) {
auto j = i;
while (orders[j] != i) {
j = orders[j];
CHECK_INVARIANT(
j < orders.size(),
"molzip: bond index outside of number of bonds for atom")
seen[j] = true;
nswaps++;
}
}
}
return nswaps;
}
// Simple bookkeeping class to bond attachments and handle stereo
struct ZipBond {
Atom *a; // atom being bonded
Atom *a_dummy; // Labelled atom, i.e. [*:1]-C will bond the C to something
Atom *b; // atom being bonded
Atom *b_dummy; // Labelled atom, i.e. [*:1]-O will bond the O to something
// Backup the original chirality mark_chirality must be called first
// as it checks the datastructure for validity;
void mark_chirality() const {
PRECONDITION(a, "Must have a begin atom to bond");
PRECONDITION(b, "Must have an end atom to bond");
PRECONDITION(a_dummy, "Must have a begin dummy atom");
PRECONDITION(b_dummy, "Must have an end dummy atom");
mark(a, a_dummy, b);
mark(b, b_dummy, a);
}
// bond a<->b for now only use single bonds
// XXX FIX ME take the highest bond order.
bool bond(RWMol &newmol, const MolzipParams &params) const {
if (!a || !b || !a_dummy || !b_dummy) {
BOOST_LOG(rdWarningLog)
<< "Incomplete atom labelling, cannot make bond" << std::endl;
return false;
}
// Fragment on bonds allows multiple links to the same atom
// i.e. C.[1C].[1C]
// otherwise throw an invariant error
CHECK_INVARIANT(
params.label == MolzipLabel::FragmentOnBonds ||
!a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()),
"molzip: zipped Bond already exists, perhaps labels are duplicated");
if (!a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx())) {
CHECK_INVARIANT(&a->getOwningMol() == &newmol,
"Owning mol is not the combined molecule!!");
auto bnd = newmol.getBondBetweenAtoms(a->getIdx(), a_dummy->getIdx());
CHECK_INVARIANT(bnd != nullptr,
"molzip: begin atom and specified dummy atom connection "
"are not bonded.")
auto bond_type_a = bnd->getBondType();
auto bond_dir_a = bnd->getBondDir();
auto a_is_start = bnd->getBeginAtom() == a;
bnd = newmol.getBondBetweenAtoms(b->getIdx(), b_dummy->getIdx());
CHECK_INVARIANT(bnd != nullptr,
"molzip: end atom and specified dummy connection atom "
"are not bonded.")
auto bond_type_b = bnd->getBondType();
auto bond_dir_b = bnd->getBondDir();
auto b_is_start = bnd->getBeginAtom() == b;
unsigned int bnd_idx = 0;
// Fusion bond-dir logic table
// a-* b-* => a-b
// < = wedge
// a<* b-* => a<b
// a>* b-* => a>b
// a-* b>* => a<b
// a-* b<* => a>b
Bond::BondDir bond_dir{Bond::BondDir::NONE};
auto start = a;
auto end = b;
if (bond_dir_a != Bond::BondDir::NONE &&
bond_dir_b != Bond::BondDir::NONE) {
// are we consistent between the two bond orders check for the case of
// fragment on bonds where a<* and b>* or a>* and b<* when < is either a
// hash or wedge bond but not both.
bool consistent_directions = false;
if (bond_dir_a == bond_dir_b) {
if ((a_is_start != b_is_start)) {
consistent_directions = true;
}
}
if (!consistent_directions) {
BOOST_LOG(rdWarningLog)
<< "inconsistent bond directions when merging fragments, ignoring..."
<< std::endl;
bond_dir_a = bond_dir_b = Bond::BondDir::NONE;
} else {
bond_dir_b = Bond::BondDir::NONE;
}
}
if (bond_dir_a != Bond::BondDir::NONE) {
if (!a_is_start) {
start = b;
end = a;
}
bond_dir = bond_dir_a;
} else if (bond_dir_b != Bond::BondDir::NONE) {
if (b_is_start) {
start = b;
end = a;
}
bond_dir = bond_dir_b;
}
if (bond_type_a != Bond::BondType::SINGLE) {
bnd_idx = newmol.addBond(start, end, bond_type_a);
} else if (bond_type_b != Bond::BondType::SINGLE) {
bnd_idx = newmol.addBond(start, end, bond_type_b);
} else {
bnd_idx = newmol.addBond(start, end, Bond::BondType::SINGLE);
}
newmol.getBondWithIdx(bnd_idx - 1)->setBondDir(bond_dir);
}
a_dummy->setProp("__molzip_used", true);
b_dummy->setProp("__molzip_used", true);
return true;
}
// Restore the marked chirality (mark_chirality must be called first)
void restore_chirality(std::set<Atom *> &already_checked) const {
PRECONDITION(a, "Must have a begin atom to bond");
PRECONDITION(b, "Must have an end atom to bond");
PRECONDITION(a_dummy, "Must have a begin dummy atom");
PRECONDITION(b_dummy, "Must have an end dummy atom");
if (already_checked.find(a) == already_checked.end()) {
restore(a);
already_checked.insert(a);
}
if (already_checked.find(b) == already_checked.end()) {
restore(b);
already_checked.insert(b);
}
// now do bond stereo
std::string mark = "__molzip_bond_stereo_mark";
for (auto *bond : a->getOwningMol().bonds()) {
if (bond->hasProp(mark)) {
std::vector<int> atoms;
for (auto *atom : bond->getProp<std::vector<Atom *>>(mark)) {
atoms.push_back(rdcast<int>(atom->getIdx()));
}
bond->getStereoAtoms().swap(atoms);
bond->setStereo(
bond->getProp<Bond::BondStereo>("__molzip_bond_stereo"));
}
}
}
private:
// Mark the original order of the nbr atoms including the dummy
// The goal is to copy the dummy chiral order over to the
// atom being bonded
void mark(Atom *chiral_atom, Atom *dummy_atom, Atom *new_atom) const {
if (chiral_atom->getChiralTag()) {
std::string mark =
"__molzip_mark_" + std::to_string(chiral_atom->getIdx());
chiral_atom->setProp("__molzip_chiral_mark", mark);
int order = 0;
auto &m = chiral_atom->getOwningMol();
for (auto nbrIdx :
boost::make_iterator_range(m.getAtomNeighbors(chiral_atom))) {
m[nbrIdx]->setProp(mark, order);
++order;
}
new_atom->setProp(mark, dummy_atom->getProp<int>(mark));
}
// check bond stereo
auto &m = chiral_atom->getOwningMol();
for (auto nbrIdx :
boost::make_iterator_range(m.getAtomNeighbors(chiral_atom))) {
auto bond = m.getBondBetweenAtoms(chiral_atom->getIdx(), nbrIdx);
if (bond->getStereo()) {
std::string mark = "__molzip_bond_stereo_mark";
std::vector<Atom *> atoms;
bool has_dummy = false;
for (auto idx : bond->getStereoAtoms()) {
if (static_cast<unsigned>(idx) == dummy_atom->getIdx()) {
atoms.push_back(new_atom);
has_dummy = true;
} else {
atoms.push_back(m.getAtomWithIdx(idx));
}
}
if (has_dummy) {
bond->setProp(mark, atoms);
bond->setProp<Bond::BondStereo>("__molzip_bond_stereo",
bond->getStereo());
}
}
}
}
// Restore the atom's chirality by comparing the original order
// to the current
void restore(Atom *chiral_atom) const {
if (!chiral_atom->getChiralTag()) {
return;
}
std::string mark =
chiral_atom->getProp<std::string>("__molzip_chiral_mark");
// std::vector<unsigned int> orders1;
std::vector<unsigned int> orders2;
auto &m = chiral_atom->getOwningMol();
for (auto nbrIdx :
boost::make_iterator_range(m.getAtomNeighbors(chiral_atom))) {
orders2.push_back(m[nbrIdx]->getProp<int>(mark));
}
if (num_swaps_to_interconvert(orders2) % 2 == 1) {
chiral_atom->invertChirality();
}
}
};
} // namespace
static const std::string indexPropName("__zipIndex");
std::unique_ptr<ROMol> molzip(
const ROMol &a, const ROMol &b, const MolzipParams &params,
std::optional<std::map<int, int>> &attachmentMapping) {
if (attachmentMapping) {
attachmentMapping->clear();
}
std::unique_ptr<RWMol> newmol;
if (b.getNumAtoms()) {
newmol.reset(static_cast<RWMol *>(combineMols(a, b)));
} else {
newmol.reset(new RWMol(a));
}
std::map<unsigned int, ZipBond> mappings;
std::map<Atom *, std::vector<const ZipBond *>> mappings_by_atom;
std::vector<Atom *> deletions;
if (params.label == MolzipLabel::FragmentOnBonds) {
for (auto *atom : newmol->atoms()) {
if (atom->getAtomicNum() == 0) {
auto molno = atom->getIsotope();
auto attached_atom = get_other_atom(atom);
auto &bond = mappings[molno];
bond.a = attached_atom;
bond.a_dummy = atom;
bond.b = newmol->getAtomWithIdx(molno);
for (auto nbrIdx :
boost::make_iterator_range(newmol->getAtomNeighbors(bond.b))) {
auto *nbr = (*newmol)[nbrIdx];
if (nbr->getAtomicNum() == 0 &&
nbr->getIsotope() == attached_atom->getIdx()) {
bond.b_dummy = nbr;
break;
}
}
if (!bond.b_dummy) {
BOOST_LOG(rdErrorLog)
<< "Cannot find atom to bond using FragmentOnBond labelling"
<< std::endl;
return std::unique_ptr<ROMol>();
}
mappings_by_atom[atom].push_back(&bond);
deletions.push_back(atom);
if (attachmentMapping) {
if (int otherIndex, dummyIndex;
atom->getPropIfPresent(indexPropName, dummyIndex) &&
bond.b->getPropIfPresent(indexPropName, otherIndex)) {
(*attachmentMapping)[dummyIndex] = otherIndex;
}
}
}
}
} else {
for (auto *atom : newmol->atoms()) {
auto molno = get_label(atom, params);
if (molno != NOLABEL) {
auto attached_atom = get_other_atom(atom);
if (mappings.find(molno) == mappings.end()) {
auto &bond = mappings[molno];
CHECK_INVARIANT(
!bond.a,
"molzip: bond info already setup for bgn atom with label:" +
std::to_string(molno));
bond.a = attached_atom;
bond.a_dummy = atom;
} else {
auto &bond = mappings[molno];
CHECK_INVARIANT(
bond.a,
"molzip: bond info not properly setup for bgn atom with label:" +
std::to_string(molno));
CHECK_INVARIANT(
!bond.b,
"molzip: bond info already exists for end atom with label:" +
std::to_string(molno));
bond.b = attached_atom;
bond.b_dummy = atom;
mappings_by_atom[bond.a].push_back(&bond);
if (attachmentMapping) {
if (int otherIndex, dummyIndex;
bond.a_dummy->getPropIfPresent(indexPropName, dummyIndex) &&
bond.b->getPropIfPresent(indexPropName, otherIndex)) {
(*attachmentMapping)[dummyIndex] = otherIndex;
}
if (int otherIndex, dummyIndex;
bond.b_dummy->getPropIfPresent(indexPropName, dummyIndex) &&
bond.a->getPropIfPresent(indexPropName, otherIndex)) {
(*attachmentMapping)[dummyIndex] = otherIndex;
}
}
}
deletions.push_back(atom);
}
}
}
for (auto &kv : mappings_by_atom) {
for (auto &bond : kv.second) {
bond->mark_chirality();
}
}
for (auto &kv : mappings) {
kv.second.bond(*newmol, params);
}
newmol->beginBatchEdit();
for (auto &atom : deletions) {
if (atom->hasProp("__molzip_used")) {
newmol->removeAtom(atom);
}
}
newmol->commitBatchEdit();
std::set<Atom *> already_checked;
for (auto &kv : mappings_by_atom) {
for (auto &bond : kv.second) {
bond->restore_chirality(already_checked);
}
}
// remove all molzip tags
for (auto *atom : newmol->atoms()) {
auto propnames = atom->getPropList();
for (auto &prop : propnames) {
if (prop.find("__molzip") == 0) {
atom->clearProp(prop);
}
}
}
for (auto *bond : newmol->bonds()) {
auto propnames = bond->getPropList();
for (auto &prop : propnames) {
if (prop.find("__molzip") == 0) {
bond->clearProp(prop);
}
}
}
newmol->updatePropertyCache(params.enforceValenceRules);
newmol->setProp(common_properties::_StereochemDone, true);
return newmol;
}
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr<ROMol> molzip(
const ROMol &a, const ROMol &b, const MolzipParams &params) {
std::optional<std::map<int, int>> opt(std::nullopt);
return molzip(a, b, params, opt);
}
std::unique_ptr<ROMol> molzip(const ROMol &a, const MolzipParams &params) {
const static ROMol b;
return molzip(a, b, params);
}
std::unique_ptr<ROMol> molzip(std::vector<ROMOL_SPTR> &decomposition,
const MolzipParams &params) {
if (params.generateCoordinates) {
int index = 0;
for (const auto &mol : decomposition) {
for (const auto atom : mol->atoms()) {
atom->setProp(indexPropName, index++);
}
}
}
if (decomposition.empty()) {
return nullptr;
}
// When the rgroup decomposition splits a ring, it puts it in both
// rgroups, so remove these
std::vector<ROMOL_SPTR> mols;
if (params.label != MolzipLabel::FragmentOnBonds &&
decomposition.size() > 1) {
std::vector<std::string> existing_smiles;
for (size_t idx = 1; idx < decomposition.size(); ++idx) {
auto &mol = decomposition[idx];
auto smiles = MolToSmiles(*mol);
if (std::find(existing_smiles.begin(), existing_smiles.end(), smiles) ==
existing_smiles.end()) {
mols.push_back(mol);
existing_smiles.push_back(smiles);
}
}
}
auto combinedMol = decomposition[0];
if (!mols.empty()) {
combinedMol.reset(
std::accumulate(mols.begin(), mols.end(), decomposition[0].get(),
[](const auto *combined, const auto &mol) {
return combineMols(*combined, *mol);
}));
}
const static ROMol b;
std::optional attachmentMappingOption = std::map<int, int>();
auto zippedMol = molzip(*combinedMol, b, params, attachmentMappingOption);
if (params.generateCoordinates && zippedMol->getNumAtoms() > 0) {
const auto confId = RDDepict::compute2DCoords(*zippedMol);
const auto zippedConf = zippedMol->getConformer(confId);
auto attachmentMapping = *attachmentMappingOption;
for (auto &mol : decomposition) {
const auto newConf = new Conformer(mol->getNumAtoms());
newConf->set3D(false);
for (const auto atom : mol->atoms()) {
int zippedIndex = atom->getProp<int>(indexPropName);
atom->clearProp(indexPropName);
if (const auto attachment = attachmentMapping.find(zippedIndex);
attachment != attachmentMapping.end()) {
zippedIndex = (*attachment).second;
}
auto zipppedAtoms = zippedMol->atoms();
auto zippedAtom = std::find_if(
zipppedAtoms.begin(), zipppedAtoms.end(),
[zippedIndex](const Atom *zippedAtom) {
const auto index = zippedAtom->getProp<int>(indexPropName);
return index == zippedIndex;
});
newConf->setAtomPos(atom->getIdx(),
zippedConf.getAtomPos((*zippedAtom)->getIdx()));
}
mol->addConformer(newConf, true);
}
for (const auto atom : zippedMol->atoms()) {
atom->clearProp(indexPropName);
}
return zippedMol;
}
return zippedMol;
}
std::unique_ptr<ROMol> molzip(const std::map<std::string, ROMOL_SPTR> &row,
const MolzipParams &params) {
auto core = row.find("Core");
PRECONDITION(core != row.end(), "RGroup has no Core, cannot molzip");
std::vector<ROMOL_SPTR> mols;
mols.push_back(core->second);
for (auto it : row) {
if (it.first != "Core") {
mols.push_back(it.second);
}
}
return molzip(mols, params);
}
} // end of namespace RDKit
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