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//
//
// Copyright (C) 2020 Schrödinger, 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 <algorithm>
#include <memory>
#include <GraphMol/RDKitBase.h>
#include "CIPLabeler.h"
#include "CIPMol.h"
#include "configs/Sp2Bond.h"
#include "configs/Tetrahedral.h"
#include "configs/AtropisomerBond.h"
#include <boost/algorithm/string.hpp>
#include "rules/Rules.h"
#include "rules/Rule1a.h"
#include "rules/Rule1b.h"
#include "rules/Rule2.h"
#include "rules/Rule3.h"
#include "rules/Rule4a.h"
#include "rules/Rule4b.h"
#include "rules/Rule4c.h"
#include "rules/Rule5New.h"
#include "rules/Rule6.h"
#include <GraphMol/Chirality.h>
namespace RDKit {
namespace CIPLabeler {
namespace {
// constitutional rules
const Rules constitutional_rules({new Rule1a, new Rule1b, new Rule2});
// all rules (require aux calc)
const Rules all_rules({new Rule1a, new Rule1b, new Rule2, new Rule3, new Rule4a,
new Rule4b, new Rule4c, new Rule5New, new Rule6});
std::vector<std::unique_ptr<Configuration>> findConfigs(
CIPMol &mol, const boost::dynamic_bitset<> &atoms,
const boost::dynamic_bitset<> &bonds) {
std::vector<std::unique_ptr<Configuration>> configs;
for (auto index = atoms.find_first(); index != boost::dynamic_bitset<>::npos;
index = atoms.find_next(index)) {
auto atom = mol.getAtom(index);
auto chiraltag = atom->getChiralTag();
if (chiraltag == Atom::CHI_TETRAHEDRAL_CW ||
chiraltag == Atom::CHI_TETRAHEDRAL_CCW) {
std::unique_ptr<Tetrahedral> cfg{new Tetrahedral(mol, atom)};
configs.push_back(std::move(cfg));
}
}
for (auto index = bonds.find_first(); index != boost::dynamic_bitset<>::npos;
index = bonds.find_next(index)) {
auto bond = mol.getBond(index);
auto bond_cfg = bond->getStereo();
switch (bond_cfg) {
case Bond::STEREOE:
bond_cfg = Bond::STEREOTRANS;
break;
case Bond::STEREOZ:
bond_cfg = Bond::STEREOCIS;
break;
default:
break;
}
switch (bond_cfg) {
case Bond::STEREOTRANS:
case Bond::STEREOCIS: {
std::unique_ptr<Sp2Bond> cfg(new Sp2Bond(
mol, bond, bond->getBeginAtom(), bond->getEndAtom(), bond_cfg));
configs.push_back(std::move(cfg));
} break;
case Bond::STEREOATROPCCW:
case Bond::STEREOATROPCW: {
std::unique_ptr<AtropisomerBond> cfgAtrop(new AtropisomerBond(
mol, bond, bond->getBeginAtom(), bond->getEndAtom(), bond_cfg));
configs.push_back(std::move(cfgAtrop));
} break;
default:
break;
}
}
return configs;
}
bool labelAux(std::vector<std::unique_ptr<Configuration>> &configs,
const Rules &rules,
const std::unique_ptr<Configuration> ¢er) {
using Node_Cfg_Pair = std::pair<Node *, Configuration *>;
std::vector<Node_Cfg_Pair> aux;
auto &digraph = center->getDigraph();
for (const auto &config : configs) {
if (config == center) {
continue;
}
// FIXME: specific to each descriptor
const auto &foci = config->getFoci();
for (const auto &node : digraph.getNodes(foci[0])) {
if (node->isDuplicate()) {
continue;
}
auto low = node;
if (foci.size() == 2) {
for (const auto &edge : node->getEdges(foci[1])) {
const auto &other_node = edge->getOther(node);
if (other_node->getDistance() < node->getDistance()) {
low = other_node;
}
}
}
if (!low->isDuplicate()) {
aux.emplace_back(low, config.get());
}
}
}
auto farthest = [](const Node_Cfg_Pair &a, const Node_Cfg_Pair &b) {
return a.first->getDistance() > b.first->getDistance();
};
std::sort(aux.begin(), aux.end(), farthest);
// Using a boost::unordered_map because it is more performant
// than the STL version.
boost::unordered_map<Node *, Descriptor> queue;
int prev = std::numeric_limits<int>::max();
for (const auto &e : aux) {
const auto &node = e.first;
if (node->getDistance() < prev) {
for (const auto &e2 : queue) {
e2.first->setAux(e2.second);
}
queue.clear();
prev = node->getDistance();
}
const auto &config = e.second;
auto label = config->label(node, digraph, rules);
queue.emplace(node, label);
}
for (const auto &e : queue) {
e.first->setAux(e.second);
}
return true;
}
void label(std::vector<std::unique_ptr<Configuration>> &configs) {
for (const auto &conf : configs) {
auto desc = conf->label(constitutional_rules);
if (desc != Descriptor::UNKNOWN) {
conf->setPrimaryLabel(desc);
} else {
if (labelAux(configs, all_rules, conf)) {
desc = conf->label(all_rules);
if (desc != Descriptor::UNKNOWN) {
conf->setPrimaryLabel(desc);
}
}
}
}
}
thread_local unsigned int remainingCallCount = 0;
} // namespace
void assignCIPLabels(ROMol &mol, const boost::dynamic_bitset<> &atoms,
const boost::dynamic_bitset<> &bonds,
unsigned int maxRecursiveIterations) {
if (maxRecursiveIterations != 0) {
remainingCallCount = maxRecursiveIterations;
} else {
remainingCallCount = UINT_MAX; // really big - will never be hit
}
CIPMol cipmol{mol};
auto configs = findConfigs(cipmol, atoms, bonds);
label(configs);
}
void assignCIPLabels(ROMol &mol, unsigned int maxRecursiveIterations) {
boost::dynamic_bitset<> atoms(mol.getNumAtoms());
boost::dynamic_bitset<> bonds(mol.getNumBonds());
atoms.set();
bonds.set();
assignCIPLabels(mol, atoms, bonds, maxRecursiveIterations);
}
} // namespace CIPLabeler
namespace CIPLabeler_detail {
bool decrementRemainingCallCountAndCheck() {
return (--CIPLabeler::remainingCallCount) > 0;
}
} // namespace CIPLabeler_detail
} // namespace RDKit
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