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rdkit/Code/GraphMol/FindRings.cpp

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// $Id$
//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include <RDKitBase.h>
#include <GraphMol/Rings.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <vector>
#include <set>
#include <algorithm>
typedef std::set<double> DOUBLE_SET;
typedef DOUBLE_SET::const_iterator DOUBLE_SET_CI;
namespace RingUtils {
using namespace RDKit;
void convertToBonds(VECT_INT_VECT &res, VECT_INT_VECT &brings, const ROMol &mol) {
VECT_INT_VECT_I ri;
int i, rsiz, bid;
for (ri = res.begin(); ri != res.end(); ri++) {
INT_VECT bring;
rsiz = (*ri).size();
for (i = 0; i < (rsiz-1); i++) {
bid = mol.getBondBetweenAtoms((*ri)[i], (*ri)[i+1])->getIdx();
bring.push_back(bid);
}
// bond from last to first atom
bid = mol.getBondBetweenAtoms((*ri)[rsiz-1], (*ri)[0])->getIdx();
bring.push_back(bid);
brings.push_back(bring);
}
}
} // end of namespace RingUtils
namespace FindRings {
using namespace RDKit;
int smallestRingsBfs(const ROMol &mol, int root, VECT_INT_VECT &rings,
INT_VECT *forbidden=0);
void trimBonds(int cand, RWMol &tMol, INT_SET &changed);
int _traceCycle(const ROMol &mol, int begIdx, int endIdx,
INT_VECT &ring,DOUBLE_SET &ringsSeen) {
#ifdef VERBOSE_SSSR
BOOST_LOG(rdDebugLog)<< "_trace: " << begIdx << " " << endIdx << std::endl;
BOOST_LOG(rdDebugLog)<< "seen: ";
std::copy(ringsSeen.begin(),ringsSeen.end(),std::ostream_iterator<double>(std::cout," "));
BOOST_LOG(rdDebugLog)<< std::endl;
#endif
int i;
int nAts = mol.getNumAtoms();
INT_VECT localParents;
localParents.resize(nAts);
for(INT_VECT::iterator ivIt = localParents.begin();ivIt!=localParents.end();ivIt++)
*ivIt = -1;
localParents[begIdx] = -2;
// ----------------------
//
// we're gonna do a BFS traversal starting from begIdx and running until we hit
// endIdx.
//
// ----------------------
std::deque<int> bfsQ;
ROMol::ADJ_ITER nbrIdx,endNbrs;
boost::tie(nbrIdx,endNbrs) = mol.getAtomNeighbors(mol.getAtomWithIdx(begIdx));
// push the start atom's neighbors onto the queue, but do not include
// the final atom.
while(nbrIdx!=endNbrs){
if(*nbrIdx!=endIdx){
//BOOST_LOG(rdDebugLog)<< "\tpush: " << *nbrIdx << "\t" << begIdx << std::endl;
bfsQ.push_back(*nbrIdx);
localParents[*nbrIdx] = begIdx;
}
nbrIdx++;
}
bool done=false;
while(!done && !bfsQ.empty()){
int activeIdx = bfsQ.front();
ROMol::GRAPH_NODE_CONST_TYPE atom = mol.getAtomWithIdx(activeIdx);
boost::tie(nbrIdx,endNbrs) = mol.getAtomNeighbors(atom);
while(nbrIdx != endNbrs){
if(*nbrIdx != endIdx){
if(localParents[*nbrIdx] == -1){
#ifdef VERBOSE_SSSR
BOOST_LOG(rdDebugLog)<< "push: " << *nbrIdx << std::endl;
#endif
localParents[*nbrIdx] = activeIdx;
bfsQ.push_back(*nbrIdx);
}
nbrIdx++;
} else {
// found the end of the ring
// figure out the primes product for the ring
double ringSum = 1.0;
localParents[endIdx] = activeIdx;
i = endIdx;
#ifdef VERBOSE_SSSR
BOOST_LOG(rdDebugLog)<< "trying: " << i;
#endif
while(i>=0 && i!=begIdx){
ringSum *= firstThousandPrimes[i];
i = localParents[i];
#ifdef VERBOSE_SSSR
BOOST_LOG(rdDebugLog)<< " " << i;
#endif
}
#ifdef VERBOSE_SSSR
BOOST_LOG(rdDebugLog)<< " ->" << ringSum << std::endl;
#endif
// if we've seen this ring already, then don't include it
if(ringsSeen.find(ringSum) == ringsSeen.end()){
#ifdef VERBOSE_SSSR
BOOST_LOG(rdDebugLog)<< "accepted" << std::endl;
#endif
done = true;
localParents[endIdx] = activeIdx;
ringsSeen.insert(ringSum);
break;
} else {
localParents[endIdx] = -1;
nbrIdx++;
}
}
}
bfsQ.pop_front();
}
// ensure we actually finished
ASSERT_INVARIANT(done,"ring cycle not found");
// ----------------------
//
// now trace back up the tree using the parents array
//
// ----------------------
ring.resize(0);
done = false;
i=endIdx;
ring.push_back(endIdx);
while(i>=0 && i!=begIdx){
i = localParents[i];
ring.push_back(i);
}
#ifdef VERBOSE_SSSR
BOOST_LOG(rdDebugLog)<< "**** returning: ";
std::copy(ring.begin(),ring.end(),std::ostream_iterator<int>(std::cout," "));
BOOST_LOG(rdDebugLog)<< std::endl;
#endif
return ring.size();
};
void storeRingInfo(const ROMol &mol, const INT_VECT &ring) {
INT_VECT bondIndices;
INT_VECT_CI lastRai;
for(INT_VECT_CI rai=ring.begin();rai != ring.end();rai++){
if(rai!=ring.begin()){
bondIndices.push_back(mol.getBondBetweenAtoms(*rai,*lastRai)->getIdx());
}
lastRai = rai;
}
bondIndices.push_back(mol.getBondBetweenAtoms(*lastRai,*(ring.begin()))->getIdx());
mol.getRingInfo()->addRing(ring,bondIndices);
}
void storeRingsInfo(const ROMol &mol, const VECT_INT_VECT &rings) {
for (VECT_INT_VECT_CI ri = rings.begin(); ri != rings.end(); ri++) {
storeRingInfo(mol,*ri);
}
}
void markUselessD2s(int root, ROMol &tMol, INT_VECT &forb) {
// recursive function to mark any degree 2 nodes that are already represnted
// by root for the purpose of finding smallest rings.
ROMol::ADJ_ITER nbrIdx,endNbrs;
boost::tie(nbrIdx,endNbrs) = tMol.getAtomNeighbors(tMol.getAtomWithIdx(root));
Atom *at;
while(nbrIdx != endNbrs) {
if (std::find(forb.begin(), forb.end(), (*nbrIdx)) == forb.end()) {
at = tMol.getAtomWithIdx(*nbrIdx);
if (at->getDegree() == 2) {
forb.push_back(*nbrIdx);
markUselessD2s((*nbrIdx), tMol, forb);
}
}
nbrIdx++;
}
}
// FIX: this should probably be a local function,
void pickD2Nodes(ROMol &tMol, INT_VECT &d2nodes, const INT_VECT &currFrag) {
d2nodes.resize(0);
// FIX: ConstAtomIterator
ROMol::AtomIterator ai;
// forb contains all d2 nodes, not just the ones we want to keep
INT_VECT forb;
int root;
INT_VECT_CI axci;
Atom *at;
while (1) {
root = -1;
// FIX: should be looping only over atoms in fragment
//for (ai = tMol.beginAtoms(); ai != tMol.endAtoms(); ai++) {
// adx = (*ai)->getIdx();
for (axci = currFrag.begin(); axci != currFrag.end(); axci++) {
at = tMol.getAtomWithIdx(*axci);
if ( (at->getDegree() == 2 ) &&
(std::find(forb.begin(), forb.end(), (*axci)) == forb.end()) ) {
root = (*axci);
d2nodes.push_back(*axci);
forb.push_back(*axci);
break;
}
}
if (root == -1){
break;
}
else {
markUselessD2s(root, tMol, forb);
}
}
}
typedef std::map<double, INT_VECT> DOUBLE_INT_VECT_MAP;
typedef DOUBLE_INT_VECT_MAP::iterator DOUBLE_INT_VECT_MAP_I;
typedef DOUBLE_INT_VECT_MAP::const_iterator DOUBLE_INT_VECT_MAP_CI;
void findSSSRforDupCands(const RWMol &mol, VECT_INT_VECT &res,
DOUBLE_SET &invars, const INT_INT_VECT_MAP dupMap,
const DOUBLE_INT_VECT_MAP &dupD2Cands) {
INT_VECT_CI dni;
DOUBLE_INT_VECT_MAP_CI dvmi;
for (dvmi = dupD2Cands.begin(); dvmi != dupD2Cands.end(); dvmi++) {
INT_VECT dupCands = dvmi->second;
if (dupCands.size() > 1) {
// we have duplicate candidates.
VECT_INT_VECT nrings;
VECT_INT_VECT_CI nri;
unsigned int minSiz = static_cast<unsigned int>(MAX_INT);
INT_VECT_CI dupi, dupj;
for (dupi = dupCands.begin(); dupi != dupCands.end(); dupi++) {
// now break bonds for all the d2 nodes for that give the same rings as with (*dupi) and recompute
// smallest ring with (*dupi)
// copy the molecule so that we can break teh bonds
ROMol pMol(mol,true);
RWMol &tMol = static_cast<RWMol &>(pMol);
INT_SET changed;
INT_INT_VECT_MAP_CI dmci = dupMap.find(*dupi);
for (dni = dmci->second.begin(); dni != dmci->second.end(); dni++) {
trimBonds((*dni), tMol, changed);
}
/*
for (dupj = dupCands.begin(); dupj != dupCands.end(); dupj++) {
if (dupj != dupi) {
MolOps::trimBonds((*dupj), tMol, changed);
}
}*/
// now find the smallest ring/s around (*dupi)
VECT_INT_VECT srings;
VECT_INT_VECT_CI sri;
int nsmall = smallestRingsBfs(tMol, (*dupi), srings);
for (sri = srings.begin(); sri != srings.end(); sri++) {
if (sri->size() < minSiz) {
minSiz = sri->size();
}
nrings.push_back((*sri));
}
}
for (nri = nrings.begin(); nri != nrings.end(); nri++) {
if (nri->size() == minSiz) {
double invr = computeIntVectPrimesProduct((*nri));
if (invars.find(invr) == invars.end()) {
res.push_back((*nri));
invars.insert(invr);
}
}
} // end of loop over new rings found
} // end if (dupCand.size() > 1)
} // end of loop over all set of duplicate candidates
}
bool compRings(const INT_VECT &ring1, const INT_VECT &ring2) {
return (ring1.size() < ring2.size());
}
void removeExtraRings(VECT_INT_VECT &res, unsigned int nexpt, const ROMol &mol) {
// convert each ring in res from a list of atom ids to list of bonds id
// sort on size
std::sort(res.begin(), res.end(), compRings);
// change the rings from atom IDs to bondIds
VECT_INT_VECT brings;
RingUtils::convertToBonds(res, brings, mol);
int tot = res.size();
VECT_INT_VECT_I ri;
INT_VECT_CI mi;
unsigned i, j, bid;
// the algorithm here is quite straightforward
// - take the union of bonds from all the rings
// - since we know how many SSSRs to expect, take the union of
// subsets of expected size.
// - if the union of bonds from the subset of rings give the entire union we
// have the SSSR set
// FIX: use the types.h union
// find the overall union
INT_VECT munion;
for (ri = brings.begin(); ri != brings.end(); ri++) {
for (mi = (*ri).begin(); mi != (*ri).end(); mi++) {
if (std::find(munion.begin(), munion.end(), (*mi)) == munion.end()) {
munion.push_back(*mi);
}
}
}
INT_VECT comb;
//comb.reserve(nexpt);
for (i = 0; i < nexpt; i++) {
comb.push_back(i);
}
bool found = false;
int pos;
while (!found) {
INT_VECT cunion;
found = true;
for (i = 0; i < nexpt; i++) {
INT_VECT bring = brings[comb[i]];
// FIX: use the types.h union
for (j = 0; j < bring.size(); j++) {
bid = bring[j];
if (std::find(cunion.begin(), cunion.end(), bid) == cunion.end()){
cunion.push_back(bid);
}
}
}
if (cunion.size() < munion.size()) {
pos = nextCombination(comb, tot);
CHECK_INVARIANT(pos >= 0,""); // we couldn't have run through all the combinations without removing any rings
found = false;
}
}
// remove the extra rings from res and store them on teh molecule in case we wish
// symmetrize the SSSRs later
VECT_INT_VECT extras;
VECT_INT_VECT temp = res;
res.resize(0);
for (i = 0; i < temp.size(); i++) {
if (std::find(comb.begin(), comb.end(), i) != comb.end()) {
res.push_back(temp[i]);
}
else {
extras.push_back(temp[i]);
}
}
// store the extra rings on teh molecule for later use like
// symmetrizing the SSSRs
mol.setProp("extraRings", extras, true);
}
void findRingsD2nodes(RWMol &tMol, VECT_INT_VECT &res,
DOUBLE_SET &invars, const INT_VECT &d2nodes) {
// place to record any duplicate rings discovered from the current d2 nodes
DOUBLE_INT_VECT_MAP dupD2Cands;
int cand, nsmall;
double invr;
INT_VECT_CI d2i;
INT_INT_VECT_MAP dupMap;
// here is an example of molecule where the this scheme of finding other node that
// result in duplicates is necessary : C12=CON=C1C(C4)CC3CC2CC4C3
// It would help to draw this molecule, and number the atoms but here is what happen
// - there are 6 d2 node - 1, 6, 7, 9, 11, 13
// - both 6 and 7 find the same ring (5,6,12,13,8,7) but we do not find the 7 membered ring
// (5,7,8,9,10,0,4)
// - similarly 9 and 11 find a duplicate ring (9,10,11,12,13)
// - when we move to 13 both the above duplicate rings are found
// - so we will keep track for each d2 all the other node that resulted in duplicate rings
// - the bonds to these nodes will be broken and we attempt to find a new ring, for e.g. by breaking
// bonds to 7 and 13, we will find a 7 membered ring with 6 (this is done in findSSSRforDupCands)
std::map<int, DOUBLE_VECT> nodeInvars;
std::map<int, DOUBLE_VECT>::const_iterator nici;
DOUBLE_VECT_CI ici;
for (d2i = d2nodes.begin(); d2i != d2nodes.end(); d2i++) {
cand = (*d2i);
VECT_INT_VECT srings;
VECT_INT_VECT_CI sri;
// we have to find all non duplicate possible smallest rings for each node
//rsiz = MolOps::findSmallestRing(cand, tMol, ring, invars);
nsmall = smallestRingsBfs(tMol, cand, srings);
for (sri = srings.begin(); sri != srings.end(); sri++) {
INT_VECT nring = (*sri);
invr = computeIntVectPrimesProduct(nring);
if (invars.find(invr) == invars.end()) {
res.push_back(nring);
invars.insert(invr);
}
nodeInvars[cand].push_back(invr);
// check if this ring is duplicate with something else
for (nici = nodeInvars.begin(); nici != nodeInvars.end(); nici++) {
if (nici->first != cand) {
if (std::find(nici->second.begin(), nici->second.end(), invr) != nici->second.end()) {
// ok we discovered this ring via another node before
// add that node as duplicate to this node and and vice versa
dupMap[cand].push_back(nici->first);
dupMap[nici->first].push_back(cand);
}
}
}
dupD2Cands[invr].push_back(cand);
}
// We don't want to trim the bonds connecting cand here - this can disrupt
// a second small ring. Here is an example SC(C3C1CC(C3)CC(C2S)(O)C1)2S
// by trimming the bond connecting to atom #4 , we loose the smallest ring that
// contains atom #7. Issue 134
//MolOps::trimBonds(cand, tMol, changed);
}
// now deal with any d2 nodes that resulted in duplicate rings before trimming their bonds.
// it is possible that one of these nodes is involved a different small ring, that is not found
// because the first nodes has not be trimmed. Here is an example molecule:
// CC1=CC=C(C=C1)S(=O)(=O)O[CH]2[CH]3CO[CH](O3)[CH]4OC(C)(C)O[CH]24
findSSSRforDupCands(tMol, res, invars, dupMap, dupD2Cands);
}
void findRingsD3Node(RWMol &tMol, VECT_INT_VECT &res, DOUBLE_SET &invars, int cand) {
// this is brutal - we have no degree 2 nodes - find the first possible degree 3 node
int nsmall;
double invr;
// We've got a degree three node. The goal of what follows is to find the
// three rings in which it's involved, push those onto our results, and
// then remove the node from consideration. This will create a bunch of degree
// 2 nodes, which we can then chew off the next time around the loop.
// this part is a bit different fromt he Figueras algorithm
// here we try to find all the rings the rings that have a potential for contributing to
// SSSR - i.e. we try to find 3 rings for this node.
// - each bond (that contributres to the degree 3 ) is allowed to participate in exactly
// two of these rings.
// - also any rings that are inclusive in alsready found rings are ingnored
// ASSUME: every connection from a degree three node at this point is a
// ring bond
// REVIEW: Is this valid?
// first find all smallest possible rings
VECT_INT_VECT srings;
nsmall = smallestRingsBfs(tMol, cand, srings);
VECT_INT_VECT_CI sri;
for (sri = srings.begin(); sri != srings.end(); sri++) {
INT_VECT nring = (*sri);
invr = computeIntVectPrimesProduct(nring);
if (invars.find(invr) == invars.end()) {
res.push_back(nring);
invars.insert(invr);
}
}
// if already found >3 rings we are done with this degree 3 node
// if we found less than 3 we have to find other potential ring/s
if (nsmall < 3) {
int n1, n2, n3;
ROMol::ADJ_ITER nbrIdx,endNbrs;
boost::tie(nbrIdx,endNbrs) = tMol.getAtomNeighbors(tMol.getAtomWithIdx(cand));
n1 = (*nbrIdx); nbrIdx++;
n2 = (*nbrIdx); nbrIdx++;
n3 = (*nbrIdx);
if (nsmall == 2) {
// we found two rings find the third one
// first find the neighbor that is common to the two ring we found so far
int f;
if ( (std::find(srings[0].begin(), srings[0].end(), n1) != srings[0].end())
& (std::find(srings[1].begin(), srings[1].end(), n1) != srings[1].end()) ) {
f = n1;
}
else if ( (std::find(srings[0].begin(), srings[0].end(), n2) != srings[0].end())
& (std::find(srings[1].begin(), srings[1].end(), n2) != srings[1].end()) ) {
f = n2;
}
else if ( (std::find(srings[0].begin(), srings[0].end(), n3) != srings[0].end())
& (std::find(srings[1].begin(), srings[1].end(), n3) != srings[1].end()) ) {
f = n3;
}
// now find the smallest possible ring that does not contain f
VECT_INT_VECT trings;
INT_VECT forb;
forb.push_back(f);
int nrngs = smallestRingsBfs(tMol, cand, trings, &forb);
for (sri = trings.begin(); sri != trings.end(); sri++) {
INT_VECT nring = (*sri);
invr = computeIntVectPrimesProduct(nring);
if (invars.find(invr) == invars.end()) {
res.push_back(nring);
invars.insert(invr);
}
}
} // doing degree 3 node - end of 2 smallest rings found for cand
if (nsmall == 1) {
// we found 1 ring - we need to find two more that involve the 3rd neighbor
int f1, f2;
// Which of our three neighbors are in the small ring?
// these are f1 and f2
if (std::find(srings[0].begin(), srings[0].end(), n1) == srings[0].end()) {
f1 = n2, f2 = n3;
}
else if (std::find(srings[0].begin(), srings[0].end(), n2) == srings[0].end()) {
f1 = n1; f2 = n3;
}
else if (std::find(srings[0].begin(), srings[0].end(), n3) == srings[0].end()) {
f1 = n1; f2 = n2;
}
// now find two rings that include cand, one of these rings should include f1
// and the other should include f2
// first ring with f1 and no f2
VECT_INT_VECT trings;
INT_VECT forb;
forb.push_back(f2);
int nrngs = smallestRingsBfs(tMol, cand, trings, &forb);
for (sri = trings.begin(); sri != trings.end(); sri++) {
INT_VECT nring = (*sri);
invr = computeIntVectPrimesProduct(nring);
if (invars.find(invr) == invars.end()) {
res.push_back(nring);
invars.insert(invr);
}
}
// next the ring with f2 and no f1
trings.clear();
forb.clear();
forb.push_back(f1);
nrngs = smallestRingsBfs(tMol, cand, trings, &forb);
for (sri = trings.begin(); sri != trings.end(); sri++) {
INT_VECT nring = (*sri);
invr = computeIntVectPrimesProduct(nring);
if (invars.find(invr) == invars.end()) {
res.push_back(nring);
invars.insert(invr);
}
}
} // doing node of degree 3 - end of found only 1 smallest ring
} // end of found less than 3 smallest ring for the degree 3 node
//doneAts.push_back(cand);
//MolOps::trimBonds(cand, tMol, changed);
}
int greatestComFac(long curfac, long nfac) {
long small;
long large;
long rem;
// Determine which of the numbers is the larger, and which is the smaller
large = (curfac > nfac) ? curfac : nfac;
small = (curfac < nfac) ? curfac : nfac;
// Keep looping until no remainder, as this means it is a factor of both
while (small != 0){
// Set the larger var to the smaller, and set the smaller to the remainder of (large / small)
rem = (large % small);
large = small;
small = rem;
}
// By here nLarge will hold the largest common factor, so just return it
return large;
}
/******************************************************************************
* SUMMARY:
* remove the bond in the molecule that connect to the spcified atom
*
* ARGUMENTS:
* cand - the node(atom) of interest
* tMol - molecule of interest
* changed - list of the atoms that are effected the bond removal
* this may be accumulated over multiple calls to trimBonds
* it basically forms a list of atom that need to be searched for
* the next round of pruning
*
******************************************************************************/
void trimBonds(int cand, RWMol &tMol, INT_SET &changed) {
// basically loop over the bonds for cand and mark the neighbors if any of them after
// bond removal become degree 1 or 0
ROMol::ADJ_ITER nbrIdx,endNbrs;
boost::tie(nbrIdx,endNbrs) = tMol.getAtomNeighbors(tMol.getAtomWithIdx(cand));
INT_VECT neighs;
while (nbrIdx != endNbrs) {
neighs.push_back(*nbrIdx);
nbrIdx++;
}
for (INT_VECT_CI nci = neighs.begin(); nci != neighs.end(); nci++) {
Atom *nat = tMol.getAtomWithIdx(*nci);
if (nat->getDegree() <= 2) {
changed.insert(*nci);
}
tMol.removeBond(cand, (*nci));
}
}
/*******************************************************************************
* SUMMARY:
* this again is a modified version of the BFS algorihtm in Figueras paper to find
* the smallest ring with a specified root atom.
* JCICS, Vol. 30, No. 5, 1996, 986-991
* The follwing are changes from the original algorithm
* - find all smallest rings around a node not just one
* - once can provided a list of node IDs that should not be include in the discovered rings
*
* ARGUMENTS:
* mol - molecule of interest
* root - Atom ID of the node of interest
* rings - list of rings into which the results are entered
* forbidden - list of atoms ID that should be avoided
*
* RETURNS:
* number of smallest rings found
***********************************************************************************/
int smallestRingsBfs(const ROMol &mol, int root, VECT_INT_VECT &rings, INT_VECT *forbidden) {
// this function finds the smallest ring with the given root atom.
// if multiple smallest rings are found all of them are return
// if any atoms are specified in the forbidden list, those atoms are avoided.
// FIX: this should be number of atoms in the fragment (if it's required at all, see below)
const int WHITE=0,GRAY=1,BLACK=2;
unsigned nats = mol.getNumAtoms();
INT_VECT done(mol.getNumAtoms(),WHITE);
if (forbidden) {
for (INT_VECT_CI dci = forbidden->begin(); dci != forbidden->end(); dci++) {
done[*dci]=BLACK;
}
}
// it would be "nicer" to use a map for this, but that ends up being too slow:
VECT_INT_VECT atPaths(mol.getNumAtoms());
INT_VECT rpath(1,root);
atPaths[root] = rpath;
std::deque<int> bfsq;
bfsq.push_back(root);
int curr=-1;
unsigned int curSize=256;
while (bfsq.size() > 0) {
curr = bfsq.front();
bfsq.pop_front();
done[curr]=BLACK;
INT_VECT &cpath = atPaths[curr];
ROMol::ADJ_ITER nbr,endNbrs;
boost::tie(nbr,endNbrs) = mol.getAtomNeighbors(mol.getAtomWithIdx(curr));
while(nbr != endNbrs) {
int nbrIdx=(*nbr);
if ((std::find(cpath.begin(), cpath.end(), nbrIdx) == cpath.end())
&& done[nbrIdx]!=BLACK ){
// i.e. we are not at a node that is making up the current path
// and we are not a node that has been completely explored before
// (it has been a curr node before)
// FIX: can we avoid this find by coloring atoms gray when they go into
// the queue and just looking up the colors?
if (done[nbrIdx]==WHITE) {
// we have never been to this node before through via any path
atPaths[nbrIdx] = cpath;
atPaths[nbrIdx].push_back(nbrIdx);
done[nbrIdx]=GRAY;
bfsq.push_back(nbrIdx);
} // end of found a untouched node
else {
// we have been here via a different path
// there is a potential for ring closure here
INT_VECT npath = atPaths[nbrIdx];
// make sure that the intersections of cpath and npath give exactl one
// element and that should be the root element for correct ring closure
int id, com = 0;
INT_VECT_CI ci;
for (ci = cpath.begin(); ci != cpath.end(); ci++) {
if (std::find(npath.begin(), npath.end(), (*ci)) != npath.end()) {
com++;
id = (*ci);
if((*ci)!=root) break;
}
} // end of found stuff in common with neighbor
if (id == root){ // we found a ring
// make the ring
INT_VECT ring = cpath;
// FIX: we can set the reserve on ring here to minimize reallocs
// remove the root node and attach the other half of the ring from npath
// reverse this piece so that the ring is traversed correctly
// FIX: we're probably assured that root is the first node, so we can
// just pop it from the front
npath.erase(std::remove(npath.begin(), npath.end(), root));
#ifndef WIN32
ring.insert(ring.end(), npath.rbegin(), npath.rend());
#else // I <heart> MSVC++ v6
std::reverse(npath.begin(), npath.end());
ring.insert(ring.end(), npath.begin(), npath.end());
#endif
if (ring.size() <= curSize) {
curSize = ring.size();
rings.push_back(ring) ;
}
else {
// we are done with the smallest rings
return rings.size();
}
} // end of found a ring
} // end of we have seen this neighbor before
} // end of nbrIdx not part of current path and not a done atom
nbr++;
} // end of loop over neighbors of current atom
} // moving to the next node
return rings.size(); // if we are here we should have founf everything around the node
}
void _ringFindDFS(const ROMol &mol,INT_VECT &traversePath,INT_VECT &atomsSeen,
INT_VECT &bondsSeen,int atomIdx,int depth,
INT_SET &ringAtoms,INT_SET &ringBonds){
PRECONDITION(!atomsSeen[atomIdx]||depth>0,"");
if(atomsSeen[atomIdx]){
//-----
// we've been here before -> it's a ring atom
//-----
// reconstruct the path and mark atoms and bonds as being in rings
depth -= 1;
ringBonds.insert(traversePath[depth]);
while(--depth >= 0 ){
int bIdx = traversePath[depth];
// mark the bond itself as being in a ring
ringBonds.insert(bIdx);
// and now do the atoms to which it's attached
const Bond *b=mol.getBondWithIdx(bIdx);
ringAtoms.insert(b->getBeginAtomIdx());
ringAtoms.insert(b->getEndAtomIdx());
if(b->getBeginAtomIdx() == atomIdx || b->getEndAtomIdx() == atomIdx){
// back where we started, terminate this branch
break;
}
}
} else {
//-----
// continue the DFS traverse
//-----
atomsSeen[atomIdx] = 1;
const Atom *atom = mol.getAtomWithIdx(atomIdx);
ROMol::OEDGE_ITER beg,end;
boost::tie(beg,end) = mol.getAtomBonds(atom);
ROMol::GRAPH_MOL_BOND_PMAP::const_type pMap = mol.getBondPMap();
while(beg!=end){
int bondIdx = pMap[*beg]->getIdx();
if(!bondsSeen[bondIdx]){
traversePath[depth] = bondIdx;
bondsSeen[bondIdx] = 1;
_ringFindDFS(mol,traversePath,atomsSeen,bondsSeen,
pMap[*beg]->getOtherAtomIdx(atomIdx),
depth+1,ringAtoms,ringBonds);
}
beg++;
}
}
}
} // end of FindRings namespace
namespace RDKit {
namespace MolOps {
int findSSSR(const ROMol &mol, VECT_INT_VECT *res) {
if (!res) {
VECT_INT_VECT rings;
return findSSSR(mol, rings);
}
else {
return findSSSR(mol,(*res));
}
}
int findSSSR(const ROMol &mol, VECT_INT_VECT &res) {
res.resize(0);
// check if SSSR's are already on the molecule
if(mol.getRingInfo()->isInitialized()){
res = mol.getRingInfo()->atomRings();
return res.size();
} else {
mol.getRingInfo()->initialize();
}
DOUBLE_SET invars;
//DOUBLE_VECT invars;
// make a copy of the molecule that we can chop around
// mind you we will never remove atoms to avoid numbering issues
// only bonds are removed
ROMol pMol(mol,true);
RWMol &tMol = static_cast<RWMol &>(pMol);
int nats = tMol.getNumAtoms();
int nbnds = tMol.getNumBonds();
// find the number of fragments in the molecule - we will loop over them
VECT_INT_VECT frags;
INT_VECT curFrag;
int fi, nfrags = getMolFrags(tMol, frags);
for (fi = 0; fi < nfrags; fi++) { // loop over the fragments in a molecule
curFrag = frags[fi];
// the following is the list of atoms that are useful in the next round of trimming
// basically atoms that become degree 0 or 1 because of bond removals
// initialized with atoms of degrees 0 and 1
INT_VECT doneAts; // atoms that we already dealt with int he fragment
INT_SET changed;
INT_VECT_CI aidi;
int deg, cand;
for (aidi = curFrag.begin(); aidi != curFrag.end(); aidi++) {
deg = tMol.getAtomWithIdx((*aidi))->getDegree();
if ((deg == 0) || (deg == 1)) {
changed.insert((*aidi));
}
}
while (doneAts.size() < curFrag.size()) {
//trim all bonds that connect to degree 0 and 1 bonds
while (changed.size() > 0) {
cand = *(changed.begin());
changed.erase(changed.begin());
if (std::find(doneAts.begin(), doneAts.end(), cand) == doneAts.end()) {
doneAts.push_back(cand);
FindRings::trimBonds(cand, tMol, changed);
}
}
// all atoms left in the fragment should atleast have a degree >= 2
// collect all the degree two nodes;
INT_VECT d2nodes;
// pick all the d2nodes from the current fragment
FindRings::pickD2Nodes(tMol, d2nodes, curFrag);
if (d2nodes.size() > 0) { // deal with the current degree two nodes
// place to record any duplicate rings discovered from the current d2 nodes
FindRings::findRingsD2nodes(tMol, res, invars, d2nodes);
INT_VECT_CI d2i;
// trim after we have dealt with all the current d2 nodes,
for (d2i = d2nodes.begin(); d2i != d2nodes.end(); d2i++) {
doneAts.push_back((*d2i));
FindRings::trimBonds((*d2i), tMol, changed);
}
} // end of degree two nodes
else if ( doneAts.size() < curFrag.size() ) { // now deal with higher degree nodes
//INT_VECT ring;
// this is brutal - we have no degree 2 nodes - find the first possible degree 3 node
cand = -1;
for (aidi = curFrag.begin(); aidi != curFrag.end(); aidi++) {
deg = tMol.getAtomWithIdx((*aidi))->getDegree();
if (deg == 3){
cand = (*aidi);
break;
}
}
// if we did not find a degree 3 node we are done
// REVIEW:
//if (cand == -1) {
// break;
//}
FindRings::findRingsD3Node(tMol, res, invars, cand);
doneAts.push_back(cand);
FindRings::trimBonds(cand, tMol, changed);
} // done with degree 3 node
} // done finding rings in this fragement
} // done with all fragments
// calculate the Frere-Jacque number
int nexpt = (nbnds - nats + nfrags);
int ssiz = res.size();
// first check that we got more than or equal to the number of expected rings
CHECK_INVARIANT(ssiz>=nexpt,"");
// if we have more than expected we need to do some cleanup
// otherwise do som celan up work
if (ssiz > nexpt) {
FindRings::removeExtraRings(res, nexpt, mol);
}
FindRings::storeRingsInfo(mol,res);
// update the ring memberships of atoms and bonds in the molecule:
// store the SSSR rings on the the molecule as a property
// we will ignore any existing SSSRs ont eh molecule - simply overwrite
return res.size();
}
int symmetrizeSSSR(ROMol &mol, VECT_INT_VECT &res) {
res.clear();res.resize(0);
int nsssr;
VECT_INT_VECT sssrs;
// FIX: need to set flag here the symmetrization has been done in order to avoid
// repeating this work
if(!mol.getRingInfo()->isInitialized()){
nsssr = findSSSR(mol, sssrs);
} else {
sssrs = mol.getRingInfo()->atomRings();
nsssr = sssrs.size();
}
VECT_INT_VECT_CI srci;
INT_VECT copr;
for (srci = sssrs.begin(); srci != sssrs.end(); srci++) {
copr = (*srci);
res.push_back(copr);
}
// now check if there are any extra rings on the molecule
VECT_INT_VECT extras;
if (!mol.hasProp("extraRings")) {
// no extra rings nothign to be done
return res.size();
}
else {
mol.getProp("extraRings", extras);
}
// convert the rings to bond ids
VECT_INT_VECT bsrs, bextra;
RingUtils::convertToBonds(sssrs, bsrs, mol);
RingUtils::convertToBonds(extras, bextra, mol);
INT_VECT munion, nunion, symids;
Union(bsrs, munion);
INT_VECT sr, exr;
INT_VECT_CI eri;
int eid, srid, ssiz;
int next = bextra.size();
// now the trick is the following
// we will replace each ring of size ssiz from the SSSR with
// one of the same size rings in the extras. Compute the union of of the new set
// if all the union elements of the new set if same as munion we found a symmetric ring
for (srid = 0; srid < nsssr; srid++) {
sr = bsrs[srid];
ssiz = sr.size();
INT_VECT exrid;
exrid.push_back(srid);
Union(bsrs, nunion, &exrid);
for (eid = 0; eid < next; eid++) {
// if we already added this ring continue
// FIX: if the ring has already been added,it probably shouldn't be
// in the list at all? Is this perhaps the most efficient way?
if (std::find(symids.begin(), symids.end(), eid) != symids.end()){
continue;
}
exr = bextra[eid];
if (ssiz == exr.size()) {
INT_VECT eunion;
Union(nunion, exr, eunion);
// now check if the eunion is same as the original union from the SSSRs
if (eunion.size() == munion.size()) {
//we found a symmetric ring
symids.push_back(eid);
}
}
}
}
// add the symmertic rings
for (eri = symids.begin(); eri != symids.end(); eri++) {
exr = extras[*eri];
res.push_back(exr);
FindRings::storeRingInfo(mol, exr);
}
if (mol.hasProp("extraRings")) {
mol.clearProp("extraRings");
}
return res.size();
}
}// end of MolOps namespace
} // end of RDKit namespace
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