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//
// Copyright (C) 2020 Greg Landrum and T5 Informatics GmbH
//
// @@ 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 "MolEnumerator.h"
#include <RDGeneral/Exceptions.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <boost/lexical_cast.hpp>
#include <boost/tokenizer.hpp>
#include <boost/format.hpp>
#include <algorithm>
typedef boost::tokenizer<boost::char_separator<char>> tokenizer;
namespace RDKit {
namespace MolEnumerator {
void LinkNodeOp::initFromMol(const ROMol &mol) {
dp_mol.reset(new ROMol(mol));
initFromMol();
}
void LinkNodeOp::initFromMol() {
if (!dp_mol) {
return;
}
std::string pval;
if (!dp_mol->getPropIfPresent(common_properties::molFileLinkNodes, pval)) {
return;
}
std::vector<int> mapping;
if (MolOps::getMolFrags(*dp_mol, mapping) > 1) {
throw ValueErrorException(
"LINKNODE enumeration only supported for molecules with a single "
"fragment.");
}
dp_frame.reset(new RWMol(*dp_mol));
boost::char_separator<char> pipesep("|");
boost::char_separator<char> spacesep(" ");
std::string attachSmarts = "";
std::vector<std::string> linkEnums;
std::vector<std::string> molEnums;
d_variations.clear();
d_pointRanges.clear();
d_isotopeMap.clear();
for (auto linknode : tokenizer(pval, pipesep)) {
std::string productSmarts = "";
tokenizer tokens(linknode, spacesep);
std::vector<unsigned int> data;
try {
std::transform(tokens.begin(), tokens.end(), std::back_inserter(data),
[](const std::string &token) -> unsigned int {
return boost::lexical_cast<unsigned int>(token);
});
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert values in LINKNODE '" << linknode
<< "' to unsigned ints";
throw ValueErrorException(errout.str());
}
// the second test here is for the atom-pairs defining the bonds
// data[2] contains the number of bonds
if (data.size() < 5 || data.size() < 3 + 2 * data[2]) {
std::ostringstream errout;
errout << "not enough values in LINKNODE '" << linknode << "'";
throw ValueErrorException(errout.str());
}
unsigned int minRep = data[0];
unsigned int maxRep = data[1];
if (minRep == 0 || maxRep < minRep) {
std::ostringstream errout;
errout << "bad counts in LINKNODE '" << linknode << "'";
throw ValueErrorException(errout.str());
}
d_countAtEachPoint.push_back(maxRep - minRep + 1);
d_pointRanges.push_back(std::make_pair(minRep, maxRep));
unsigned int nBonds = data[2];
if (nBonds != 2) {
UNDER_CONSTRUCTION(
"only link nodes with 2 bonds are currently supported");
}
// both bonds must start from the same atom:
if (data[3] != data[5]) {
std::ostringstream errout;
errout << "bonds don't start at the same atom for LINKNODE '" << linknode
<< "'";
throw ValueErrorException(errout.str());
}
auto varAtom = dp_frame->getAtomWithIdx(data[3] - 1);
auto attach1 = dp_frame->getAtomWithIdx(data[4] - 1);
auto attach2 = dp_frame->getAtomWithIdx(data[6] - 1);
if (!dp_frame->getBondBetweenAtoms(data[4] - 1, data[3] - 1) ||
!dp_frame->getBondBetweenAtoms(data[4] - 1, data[3] - 1)) {
std::ostringstream errout;
errout << "bond not found between atoms in LINKNODE '" << linknode << "'";
throw ValueErrorException(errout.str());
}
// save the isotope values:
if (d_isotopeMap.find(1000 * data[3]) == d_isotopeMap.end()) {
d_isotopeMap[1000 * data[3]] = varAtom->getIsotope();
}
if (d_isotopeMap.find(1000 * data[4]) == d_isotopeMap.end()) {
d_isotopeMap[1000 * data[4]] = attach1->getIsotope();
}
if (d_isotopeMap.find(1000 * data[6]) == d_isotopeMap.end()) {
d_isotopeMap[1000 * data[6]] = attach2->getIsotope();
}
varAtom->setIsotope(1000 * data[3]);
attach1->setIsotope(1000 * data[4]);
attach2->setIsotope(1000 * data[6]);
d_variations.push_back(
std::make_tuple(1000 * data[3], 1000 * data[4], 1000 * data[6]));
}
}
std::vector<size_t> LinkNodeOp::getVariationCounts() const {
return d_countAtEachPoint;
}
std::unique_ptr<ROMol> LinkNodeOp::operator()(
const std::vector<size_t> &which) const {
PRECONDITION(dp_mol, "no molecule");
PRECONDITION(dp_frame, "not initialized");
if (which.size() != d_countAtEachPoint.size()) {
throw ValueErrorException("bad element choice in enumeration");
}
// quick error checking before we do any work:
for (size_t i = 0; i < which.size(); ++i) {
if (which[i] >= d_countAtEachPoint[i]) {
throw ValueErrorException("bad element value in enumeration");
}
}
// we do the enumeration of each of the variation points independantly
ROMOL_SPTR res(new ROMol(*dp_frame));
for (size_t i = 0; i < which.size(); ++i) {
auto variationIdx = i + 1;
auto variationCount = d_pointRanges[i].first + which[i];
auto reactFormat =
boost::format("[%d*:%d]-[%d*:%d]-[%d*:%d]") %
(std::get<1>(d_variations[i])) % (variationIdx * 100 + 1) %
(std::get<0>(d_variations[i])) % (variationIdx * 100) %
(std::get<2>(d_variations[i])) % (variationIdx * 100 + 2);
auto reacts = reactFormat.str();
auto prodFormat = boost::format("[*:%d]") % (variationIdx * 100 + 1);
auto prods = prodFormat.str();
for (size_t j = 0; j < variationCount - 1; ++j) {
prods += (boost::format("-[*:%d]") % (variationIdx * 100)).str();
}
prods +=
(boost::format("-[%d*:%d]-[*:%d]") % (std::get<0>(d_variations[i])) %
(variationIdx * 100) % (variationIdx * 100 + 2))
.str();
auto reactSmarts = reacts + ">>" + prods;
// std::cerr << "variation index: " << variationIdx
// << " count: " << variationCount << " reaction " << reactSmarts
// << std::endl;
std::unique_ptr<ChemicalReaction> rxn(
RxnSmartsToChemicalReaction(reactSmarts));
ASSERT_INVARIANT(rxn, "reaction could not be constructed");
// we expect warnings for these alchemical reactions. :-)
bool silent = true;
rxn->initReactantMatchers(silent);
ROMOL_SPTR reactant(new ROMol(*res));
std::vector<MOL_SPTR_VECT> ps;
{
RDLog::BlockLogs blocker;
ps = rxn->runReactant(reactant, 0);
}
ASSERT_INVARIANT(!ps.empty(), "no products from reaction");
ASSERT_INVARIANT(ps[0].size() == 1, "too many products from reaction");
res = ps[0][0];
// std::cerr << " APPLICATION: " << MolToSmiles(*res) << std::endl;
}
// reset the original isotopes
for (auto atom : res->atoms()) {
if (atom->getIsotope() >= 1000) {
auto iter = d_isotopeMap.find(atom->getIsotope());
if (iter != d_isotopeMap.end()) {
atom->setIsotope(iter->second);
}
}
}
return std::unique_ptr<ROMol>(new ROMol(*res));
}
} // namespace MolEnumerator
} // namespace RDKit
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