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//
// Copyright (c) 2017-2023, Novartis Institutes for BioMedical Research Inc.
// and other RDKit contributors
//
// @@ 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 "RGroupData.h"
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>
#include <regex>
namespace RDKit {
void RGroupData::mergeIntoCombinedMol(const ROMOL_SPTR &mol) {
CHECK_INVARIANT(mol, "mol must not be null");
if (!combinedMol) {
combinedMol = RWMOL_SPTR(new RWMol(*mol));
} else {
combinedMol.reset(static_cast<RWMol *>(combineMols(*combinedMol, *mol)));
single_fragment = false;
}
smiles = getSmiles();
combinedMol->setProp(common_properties::internalRgroupSmiles, smiles);
std::vector<int> incomingAtomIndices;
std::vector<int> incomingBondIndices;
mol->getPropIfPresent(common_properties::_rgroupTargetAtoms,
incomingAtomIndices);
mol->getPropIfPresent(common_properties::_rgroupTargetBonds,
incomingBondIndices);
std::vector<int> existingAtomIndices;
std::vector<int> existingBondIndices;
combinedMol->getPropIfPresent(common_properties::_rgroupTargetAtoms,
existingAtomIndices);
combinedMol->getPropIfPresent(common_properties::_rgroupTargetBonds,
existingBondIndices);
if (!incomingAtomIndices.empty()) {
existingAtomIndices.insert(
existingAtomIndices.end(),
std::make_move_iterator(incomingAtomIndices.begin()),
std::make_move_iterator(incomingAtomIndices.end()));
}
if (!incomingBondIndices.empty()) {
existingBondIndices.insert(
existingBondIndices.end(),
std::make_move_iterator(existingBondIndices.begin()),
std::make_move_iterator(existingBondIndices.end()));
}
}
std::string RGroupData::getRGroupLabel(int rlabel) {
static const std::string RPREFIX = "R";
return RPREFIX + std::to_string(rlabel);
}
const std::string &RGroupData::getCoreLabel() {
static const std::string CORE = "Core";
return CORE;
}
const std::string &RGroupData::getMolLabel() {
static const std::string MOL = "Mol";
return MOL;
}
void RGroupData::add(const ROMOL_SPTR &newMol,
const std::vector<int> &rlabel_attachments) {
// some fragments can be added multiple times if they are cyclic
if (std::any_of(mols.begin(), mols.end(),
[&newMol](const auto &mol) { return newMol == mol; })) {
return;
}
if (!mols.empty()) {
// don't add extraneous hydrogens
if (isMolHydrogen(*newMol)) {
return;
}
if (is_hydrogen) {
// if we are adding a heavy attachment to hydrogens, discard the
// hydrogen and start over
combinedMol = nullptr;
smilesVect.clear();
attachments.clear();
mols.clear();
}
}
labelled = false;
std::copy(rlabel_attachments.begin(), rlabel_attachments.end(),
std::inserter(attachments, attachments.end()));
mols.push_back(newMol);
static const std::regex remove_isotopes_regex("\\[\\d*\\*\\]");
// remove the isotope labels from the SMILES string to avoid
// that identical R-group are perceived as different when
// MCS alignment is not used (NoAlign flag)
smilesVect.push_back(std::regex_replace(MolToSmiles(*newMol, true),
remove_isotopes_regex, "*"));
mergeIntoCombinedMol(newMol);
computeIsHydrogen();
is_linker = single_fragment && attachments.size() > 1;
}
std::map<int, int> RGroupData::getNumBondsToRlabels() const {
std::map<int, int> rlabelsUsedCount;
for (const auto atom : combinedMol->atoms()) {
int rlabel;
if (atom->getPropIfPresent<int>(RLABEL, rlabel)) {
++rlabelsUsedCount[rlabel];
}
}
return rlabelsUsedCount;
}
std::string RGroupData::toString() const {
auto attachmentString = std::accumulate(
attachments.cbegin(), attachments.cend(), std::string(),
[](std::string s, int a) {
return s.empty() ? std::to_string(a)
: std::move(s) + ',' + std::to_string(a);
});
std::stringstream ss;
ss << "RG " << attachmentString << " " << getSmiles();
return ss.str();
}
void RGroupData::computeIsHydrogen() { // is the rgroup all Hs
is_hydrogen = std::all_of(mols.begin(), mols.end(), [](const auto &mol) {
return RGroupData::isMolHydrogen(*mol);
});
}
bool RGroupData::isMolHydrogen(const ROMol &mol) {
auto atoms = mol.atoms();
return std::all_of(atoms.begin(), atoms.end(), [](const auto &atom) {
return (atom->getAtomicNum() == 1 ||
(atom->getAtomicNum() == 0 && atom->hasProp(SIDECHAIN_RLABELS)));
});
}
//! compute the canonical smiles for the attachments (bug: removes dupes since
//! we are using a set...)
std::string RGroupData::getSmiles() const {
std::string s;
for (const auto &it : smilesVect) {
if (s.length()) {
s += ".";
}
s += it;
}
return s;
}
} // namespace RDKit
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