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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 <list>
#include <sstream>
#include "Digraph.h"
#include "CIPMol.h"
#include "Node.h"
#include "Edge.h"
namespace RDKit {
namespace CIPLabeler {
namespace {
/**
* Upper limit on the size of the digraph, stops out of memory error with a
* more graceful failure. 0=Infinite
*/
const int MAX_NODE_COUNT = 100000;
/**
* Used for debugging only, 0=Infinite
*/
const int MAX_NODE_DIST = 0;
} // namespace
Node &Digraph::addNode(std::vector<char> &&visit, Atom *atom,
boost::rational<int> &&frac, int dist, int flags) {
d_nodes.emplace_back(this, std::move(visit), atom, std::move(frac), dist,
flags);
return d_nodes.back();
}
void Digraph::addEdge(Node *beg, Bond *bond, Node *end) {
d_edges.emplace_back(beg, end, bond);
auto &e = d_edges.back();
beg->add(&e);
end->add(&e);
}
Digraph::Digraph(const CIPMol &mol, Atom *atom, bool atropisomerMode)
: d_mol{mol} {
PRECONDITION(atom, "cannot init digraph on a nullptr")
auto visit = std::vector<char>(d_mol.getNumAtoms());
visit[atom->getIdx()] = 1;
auto dist = 1;
auto flags = 0x0;
auto atomic_num = atom->getAtomicNum();
dp_root = &addNode(std::move(visit), atom, atomic_num, dist, flags);
dp_origin = dp_root;
d_atropisomerMode = atropisomerMode;
}
const CIPMol &Digraph::getMol() const { return d_mol; };
Node *Digraph::getOriginalRoot() const { return dp_origin; };
Node *Digraph::getCurrentRoot() const { return dp_root; }
int Digraph::getNumNodes() const { return d_nodes.size(); }
std::vector<Node *> Digraph::getNodes(Atom *atom) const {
std::vector<Node *> result;
std::vector<Node*> queue = {getCurrentRoot()};
for (size_t i=0; i<queue.size(); ++i) {
auto node = queue[i];
if (atom == node->getAtom()) {
result.push_back(node);
}
for (const auto &e : node->getEdges()) {
if (!e->isBeg(node)) {
continue;
}
queue.push_back(e->getEnd());
}
}
return result;
}
/**
* Access the reference atom for Rule 6 (if one is set).
*/
Atom *Digraph::getRule6Ref() const { return dp_rule6Ref; }
/**
* Used exclusively for Rule 6, we set one atom as the reference.
* @param ref reference atom
*/
void Digraph::setRule6Ref(Atom *ref) { dp_rule6Ref = ref; }
/**
* Sets the root node of this digraph by flipping the directions
* of edges as required.
*
* @param newroot the new root
*/
void Digraph::changeRoot(Node *newroot) {
std::vector<Edge *> toflip;
auto queue = std::list<Node *>({newroot});
for (const auto &node : queue) {
for (const auto &e : node->getEdges()) {
if (e->isEnd(node)) {
toflip.push_back(e);
queue.push_back(e->getBeg());
}
}
}
for (auto &e : toflip) {
e->flip();
}
dp_root = newroot;
}
void Digraph::expand(Node *beg) {
const auto &atom = beg->getAtom();
const auto &edges = beg->getEdges();
const auto &prev =
edges.size() > 0 && !edges[0]->isBeg(beg) ? edges[0]->getBond() : nullptr;
if (MAX_NODE_DIST > 0 && beg->getDistance() > MAX_NODE_DIST) {
return;
}
if (MAX_NODE_COUNT > 0 && d_nodes.size() >= MAX_NODE_COUNT) {
std::stringstream errmsg;
errmsg << "Digraph generation failed: more than " << MAX_NODE_COUNT
<< "nodes found.";
throw TooManyNodesException(errmsg.str());
}
// create 'explicit' nodes
for (const auto &bond : d_mol.getBonds(atom)) {
const auto &nbr = bond->getOtherAtom(atom);
const int nbrIdx = nbr->getIdx();
const int bord = d_mol.getBondOrder(bond);
const int virtual_nodes = bord - 1;
if (!beg->isVisited(nbrIdx)) {
auto end = beg->newChild(nbrIdx, nbr);
addEdge(beg, bond, end);
// duplicate nodes for bond orders (except for root atoms...)
// for example >S=O
if (dp_origin != beg || d_atropisomerMode) {
if (atom->getFormalCharge() < 0 &&
d_mol.getFractionalAtomicNum(atom).denominator() > 1) {
end = beg->newBondDuplicateChild(nbrIdx, nbr);
addEdge(beg, bond, end);
} else {
for (int i = 0; i < virtual_nodes; ++i) {
end = beg->newBondDuplicateChild(nbrIdx, nbr);
addEdge(beg, bond, end);
}
}
}
} else if (bond == prev) { // bond order expansion (backwards)
if (dp_origin->getAtom() != nbr || d_atropisomerMode) {
for (int i = 0; i < virtual_nodes; ++i) {
auto end = beg->newBondDuplicateChild(nbrIdx, nbr);
addEdge(beg, bond, end);
}
}
} else { // ring closures
auto end = beg->newRingDuplicateChild(nbrIdx, nbr);
addEdge(beg, bond, end);
if (atom->getFormalCharge() < 0 &&
d_mol.getFractionalAtomicNum(atom).denominator() > 1) {
end = beg->newBondDuplicateChild(nbrIdx, nbr);
addEdge(beg, bond, end);
} else {
for (int i = 0; i < virtual_nodes; ++i) {
end = beg->newBondDuplicateChild(nbrIdx, nbr);
addEdge(beg, bond, end);
}
}
}
}
// Create implicit hydrogen nodes
const int hcnt = atom->getTotalNumHs();
for (int i = 0; i < hcnt; ++i) {
auto end = beg->newImplicitHydrogenChild();
addEdge(beg, nullptr, end);
}
}
} // namespace CIPLabeler
} // namespace RDKit
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