mirror of
https://github.com/rdkit/rdkit.git
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6615ae5a01
Conformer.cpp: make sure we don't ask for space for zero atoms. Kekulize.cpp: don't complain about marked bonds if we aren't removing markers. molopstest.cpp: bad smiles corrected in one test.exe ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along) Wrap/MolOps.cpp: docs for replacesubstructs.
623 lines
18 KiB
C++
Executable File
623 lines
18 KiB
C++
Executable File
// $Id$
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//
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// Copyright (C) 2003-2006 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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//
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#include <iostream>
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// our stuff
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include "ROMol.h"
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#include "Atom.h"
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#include "QueryAtom.h"
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#include "Bond.h"
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#include "QueryBond.h"
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#include "MolPickler.h"
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#include "AtomIterators.h"
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#include "BondIterators.h"
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#include "Conformer.h"
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namespace RDKit{
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const int ci_RIGHTMOST_ATOM=-0xBADBEEF;
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const int ci_LEADING_BOND=-0xBADBEEF+1;
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const int ci_ATOM_HOLDER=-0xDEADD06;
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void ROMol::destroy(){
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// blow out atoms
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ROMol::ATOM_ITER_PAIR atItP = getVertices();
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ROMol::GRAPH_MOL_ATOM_PMAP::type atMap = getAtomPMap();
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while(atItP.first != atItP.second ){
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delete atMap[*(atItP.first++)];
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}
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// and the bonds:
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ROMol::BOND_ITER_PAIR bondItP = getEdges();
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ROMol::GRAPH_MOL_BOND_PMAP::type bondMap = getBondPMap();
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int nSoFar = 0;
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while(bondItP.first != bondItP.second ){
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delete bondMap[*(bondItP.first++)];
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}
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d_atomBookmarks.clear();
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d_bondBookmarks.clear();
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d_graph.clear();
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if (dp_props) {
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delete dp_props;
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dp_props=0;
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}
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if (dp_ringInfo) {
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delete dp_ringInfo;
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dp_ringInfo=0;
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}
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};
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ROMol::ROMol(const std::string &pickle) {
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initMol();
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MolPickler::molFromPickle(pickle,*this);
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}
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ROMol::ROMol(const ROMol &other,bool quickCopy){
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initMol();
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// copy over the atoms
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ROMol::ATOM_ITER_PAIR atItP = other.getVertices();
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ROMol::GRAPH_MOL_ATOM_PMAP::const_type atMap = other.getAtomPMap();
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while(atItP.first != atItP.second ){
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addAtom(atMap[*(atItP.first++)]->copy(),false,true);
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}
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// and the bonds:
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ROMol::BOND_ITER_PAIR bondItP = other.getEdges();
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ROMol::GRAPH_MOL_BOND_PMAP::const_type bondMap = other.getBondPMap();
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int nSoFar = 0;
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while(bondItP.first != bondItP.second ){
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addBond(bondMap[*(bondItP.first++)]->copy(),true);
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}
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// ring information
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if(dp_ringInfo) delete dp_ringInfo;
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if(other.dp_ringInfo){
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dp_ringInfo = new RingInfo(*(other.dp_ringInfo));
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} else {
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dp_ringInfo = 0;
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}
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if(!quickCopy){
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// copy conformations
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ConstConformerIterator ci;
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for (ci = other.beginConformers(); ci != other.endConformers(); ci++) {
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Conformer *conf = new Conformer(*(*ci));
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this->addConformer(conf);
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}
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if (other.dp_props) {
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if (dp_props) {
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delete dp_props;
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}
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dp_props = new Dict(*other.dp_props);
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}
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// Bookmarks should be copied as well:
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ATOM_BOOKMARK_MAP::const_iterator abmI;
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for(abmI=other.d_atomBookmarks.begin();abmI!=other.d_atomBookmarks.end();abmI++){
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ATOM_PTR_LIST::const_iterator aplI;
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for(aplI=abmI->second.begin();aplI!=abmI->second.end();aplI++){
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int idx=(*aplI)->getIdx();
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int first=abmI->first;
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Atom *at=getAtomWithIdx(idx);
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setAtomBookmark(at,first);
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}
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}
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BOND_BOOKMARK_MAP::const_iterator bbmI;
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for(bbmI=other.d_bondBookmarks.begin();bbmI!=other.d_bondBookmarks.end();bbmI++){
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BOND_PTR_LIST::const_iterator bplI;
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for(bplI=bbmI->second.begin();bplI!=bbmI->second.end();bplI++){
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setBondBookmark(getBondWithIdx((*bplI)->getIdx()),bbmI->first);
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}
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}
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}
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}
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void ROMol::initMol() {
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dp_props = new Dict();
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dp_ringInfo = new RingInfo();
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// ok every bond contains a property entry called "computedProps" which provides
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// list of property keys that correspond to value that have been computed
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// this can used to blow out all computed properties while leaving the rest along
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// initialize this list to an empty vector of strings
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STR_VECT computed;
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dp_props->setVal("computedProps", computed);
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}
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unsigned int ROMol::getAtomDegree(const Atom *at) const {
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return (boost::out_degree(at->getIdx(),d_graph));
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};
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unsigned int ROMol::getAtomDegree(Atom::ATOM_SPTR at) const {
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return getAtomDegree(at.get());
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};
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unsigned int ROMol::getNumAtoms(bool onlyHeavy) const {
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int res = boost::num_vertices(d_graph);
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if (!onlyHeavy) {
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// if we are interested in hydrogens as well add them up from
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// each heavy atom
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ConstAtomIterator ai;
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for (ai = beginAtoms(); ai != endAtoms(); ai++) {
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res += (*ai)->getTotalNumHs();
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}
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}
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return res;
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};
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ROMol::GRAPH_NODE_TYPE ROMol::getAtomWithIdx(unsigned int idx)
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{
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RANGE_CHECK(0,idx,getNumAtoms()-1);
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int vd = boost::vertex(idx,d_graph);
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GRAPH_MOL_ATOM_PMAP::type pMap = boost::get(vertex_atom_t(),d_graph);
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ROMol::GRAPH_NODE_TYPE res = pMap[vd];
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return res;
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}
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ROMol::GRAPH_NODE_CONST_TYPE ROMol::getAtomWithIdx(unsigned int idx) const
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{
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RANGE_CHECK(0,idx,getNumAtoms()-1);
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int vd = boost::vertex(idx,d_graph);
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GRAPH_MOL_ATOM_PMAP::const_type pMap = boost::get(vertex_atom_t(),d_graph);
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return pMap[vd];
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}
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// returns the first inserted atom with the given bookmark
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ROMol::GRAPH_NODE_TYPE ROMol::getAtomWithBookmark(const int mark) {
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PRECONDITION(d_atomBookmarks.count(mark) != 0,"atom bookmark not found");
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PRECONDITION(d_atomBookmarks[mark].begin() != d_atomBookmarks[mark].end(),"atom bookmark not found");
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return *(d_atomBookmarks[mark].begin());
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};
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// returns all atoms with the given bookmark
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ROMol::ATOM_PTR_LIST &ROMol::getAllAtomsWithBookmark(const int mark) {
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PRECONDITION(d_atomBookmarks.count(mark) != 0,"atom bookmark not found");
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return d_atomBookmarks[mark];
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};
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// returns the first inserted bond with the given bookmark
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ROMol::GRAPH_EDGE_TYPE ROMol::getBondWithBookmark(const int mark) {
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PRECONDITION(d_bondBookmarks.count(mark) != 0,"bond bookmark not found");
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PRECONDITION(d_bondBookmarks[mark].begin() != d_bondBookmarks[mark].end(),"bond bookmark not found");
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return *(d_bondBookmarks[mark].begin());
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};
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// returns all bonds with the given bookmark
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ROMol::BOND_PTR_LIST &ROMol::getAllBondsWithBookmark(const int mark) {
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PRECONDITION(d_bondBookmarks.count(mark) != 0,"bond bookmark not found");
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return d_bondBookmarks[mark];
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};
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void ROMol::clearAtomBookmark(const int mark){
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d_atomBookmarks.erase(mark);
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}
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void ROMol::clearAtomBookmark(const int mark,const Atom *atom){
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if(d_atomBookmarks.count(mark) != 0){
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ATOM_PTR_LIST *entry=&d_atomBookmarks[mark];
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ATOM_PTR_LIST::iterator i;
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int tgtIdx=atom->getIdx();
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for(i=entry->begin();i!=entry->end();i++){
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if((*i)->getIdx()==tgtIdx){
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entry->erase(i);
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break;
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}
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}
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if(entry->begin() == entry->end()){
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d_atomBookmarks.erase(mark);
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}
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}
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}
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void ROMol::clearBondBookmark(const int mark){
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d_bondBookmarks.erase(mark);
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}
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void ROMol::clearBondBookmark(const int mark,const Bond *bond){
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if(d_bondBookmarks.count(mark) != 0){
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BOND_PTR_LIST *entry=&d_bondBookmarks[mark];
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BOND_PTR_LIST::iterator i;
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int tgtIdx=bond->getIdx();
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for(i=entry->begin();i!=entry->end();i++){
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if((*i)->getIdx()==tgtIdx){
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entry->erase(i);
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break;
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}
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}
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if(entry->begin() == entry->end()){
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d_bondBookmarks.erase(mark);
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}
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}
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}
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unsigned int ROMol::getNumBonds(bool onlyHeavy) const {
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// By default resturn the bonds that connect only the heavy atoms
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// hydrogen connecting bonds are ignores
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int res = boost::num_edges(d_graph);
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if (!onlyHeavy) {
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// If we need hydrogen connecting bonds add them up
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ConstAtomIterator ai;
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for (ai = beginAtoms(); ai != endAtoms(); ai++) {
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res += (*ai)->getTotalNumHs();
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}
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}
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return res;
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}
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ROMol::GRAPH_EDGE_TYPE ROMol::getBondWithIdx(unsigned int idx){
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RANGE_CHECK(0,idx,getNumBonds()-1);
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GRAPH_MOL_BOND_PMAP::type bondMap = getBondPMap();
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BOND_ITER_PAIR bIter = getEdges();
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for(unsigned int i=0;i<idx;i++) bIter.first++;
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ROMol::GRAPH_EDGE_TYPE res = bondMap[*(bIter.first)];
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POSTCONDITION(res!=0,"Invalid bond requested");
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return res;
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}
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ROMol::GRAPH_EDGE_CONST_TYPE ROMol::getBondWithIdx(unsigned int idx) const {
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RANGE_CHECK(0,idx,getNumBonds()-1);
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GRAPH_MOL_BOND_PMAP::const_type bondMap = getBondPMap();
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BOND_ITER_PAIR bIter = getEdges();
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for(unsigned int i=0;i<idx;i++) bIter.first++;
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return bondMap[*(bIter.first)];
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}
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ROMol::GRAPH_EDGE_TYPE ROMol::getBondBetweenAtoms(unsigned int idx1,unsigned int idx2){
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RANGE_CHECK(0,idx1,getNumAtoms()-1);
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RANGE_CHECK(0,idx2,getNumAtoms()-1);
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GRAPH_EDGE_TYPE res;
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GRAPH_MOL_TRAITS::edge_descriptor edge;
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bool found;
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boost::tie(edge,found) = boost::edge(boost::vertex(idx1,d_graph),
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boost::vertex(idx2,d_graph),
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d_graph);
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if(!found){
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res = static_cast<GRAPH_EDGE_TYPE>(0);
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} else {
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res = getBondPMap()[edge];
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}
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return res;
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}
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ROMol::GRAPH_EDGE_CONST_TYPE ROMol::getBondBetweenAtoms(unsigned int idx1,unsigned int idx2) const{
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RANGE_CHECK(0,idx1,getNumAtoms()-1);
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RANGE_CHECK(0,idx2,getNumAtoms()-1);
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GRAPH_EDGE_TYPE res;
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GRAPH_MOL_TRAITS::edge_descriptor edge;
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bool found;
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boost::tie(edge,found) = boost::edge(boost::vertex(idx1,d_graph),
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boost::vertex(idx2,d_graph),
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d_graph);
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if(!found){
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res = static_cast<GRAPH_EDGE_TYPE>(0);
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} else {
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res = getBondPMap()[edge];
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}
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return res;
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}
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ROMol::ADJ_ITER_PAIR ROMol::getAtomNeighbors(Atom const *at) const {
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return boost::adjacent_vertices(at->getIdx(),d_graph);
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};
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ROMol::ADJ_ITER_PAIR ROMol::getAtomNeighbors(Atom::ATOM_SPTR at) const {
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return boost::adjacent_vertices(at->getIdx(),d_graph);
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};
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ROMol::OBOND_ITER_PAIR ROMol::getAtomBonds(Atom const *at) const {
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return boost::out_edges(at->getIdx(),d_graph);
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}
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ROMol::GRAPH_MOL_ATOM_PMAP::type ROMol::getAtomPMap() {
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return boost::get(vertex_atom_t(),d_graph);
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}
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ROMol::GRAPH_MOL_BOND_PMAP::type ROMol::getBondPMap() {
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return boost::get(edge_bond_t(),d_graph);
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}
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ROMol::GRAPH_MOL_ATOM_PMAP::const_type ROMol::getAtomPMap() const {
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return boost::get(vertex_atom_t(),d_graph);
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}
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ROMol::GRAPH_MOL_BOND_PMAP::const_type ROMol::getBondPMap() const{
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return boost::get(edge_bond_t(),d_graph);
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}
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ROMol::ATOM_ITER_PAIR ROMol::getVertices() { return boost::vertices(d_graph);}
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ROMol::BOND_ITER_PAIR ROMol::getEdges() {return boost::edges(d_graph);}
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ROMol::ATOM_ITER_PAIR ROMol::getVertices() const { return boost::vertices(d_graph);}
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ROMol::BOND_ITER_PAIR ROMol::getEdges() const {return boost::edges(d_graph);}
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unsigned int ROMol::addAtom(Atom *atom_pin,bool updateLabel,bool takeOwnership){
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PRECONDITION(atom_pin,"null atom passed in");
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Atom *atom_p;
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if(!takeOwnership) atom_p = atom_pin->copy();
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else atom_p = atom_pin;
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atom_p->setOwningMol(this);
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int which = boost::add_vertex(AtomProperty(atom_p),d_graph);
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atom_p->setIdx(which);
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if(updateLabel){
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if(hasAtomBookmark(ci_RIGHTMOST_ATOM)) clearAtomBookmark(ci_RIGHTMOST_ATOM);
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setAtomBookmark(atom_p,ci_RIGHTMOST_ATOM);
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}
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ConformerIterator cfi;
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// EFF: I think this is going to cause a lot of re-allocation when
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// building molecules from SMILES
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for (cfi = this->beginConformers(); cfi != this->endConformers(); cfi++) {
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(*cfi)->setAtomPos(which, RDGeom::Point3D(0.0, 0.0, 0.0));
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}
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return which;
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};
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unsigned int ROMol::addAtom(Atom::ATOM_SPTR atom_sp,bool updateLabel)
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{
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return addAtom(atom_sp.get(),updateLabel,false);
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}
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unsigned int ROMol::addBond(Bond *bond_pin,bool takeOwnership){
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PRECONDITION(bond_pin,"null bond passed in");
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RANGE_CHECK(0,bond_pin->getBeginAtomIdx(),getNumAtoms()-1);
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RANGE_CHECK(0,bond_pin->getEndAtomIdx(),getNumAtoms()-1);
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Bond *bond_p;
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if(!takeOwnership) bond_p = bond_pin->copy();
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else bond_p = bond_pin;
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bond_p->setOwningMol(this);
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boost::add_edge(bond_p->getBeginAtomIdx(),bond_p->getEndAtomIdx(),
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BondProperty(bond_p,BondWeight(1.0)),d_graph);
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int res = boost::num_edges(d_graph);
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bond_p->setIdx(res-1);
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return res;
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}
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unsigned int ROMol::addBond(Bond::BOND_SPTR bsp){
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return addBond(bsp.get());
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}
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void ROMol::debugMol(std::ostream &str) const{
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ATOM_ITER_PAIR atItP = getVertices();
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GRAPH_MOL_ATOM_PMAP::const_type atMap = getAtomPMap();
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BOND_ITER_PAIR bondItP = getEdges();
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GRAPH_MOL_BOND_PMAP::const_type bondMap = getBondPMap();
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str << "Atoms:" << std::endl;
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while(atItP.first != atItP.second ){
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str << "\t" << *atMap[*(atItP.first++)] << std::endl;
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}
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str << "Bonds:" << std::endl;
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while(bondItP.first != bondItP.second ){
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str << "\t" << *bondMap[*(bondItP.first++)] << std::endl;
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}
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}
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// --------------------------------------------
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//
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// Iterators
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//
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// --------------------------------------------
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ROMol::AtomIterator ROMol::beginAtoms() {
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return AtomIterator(this);
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}
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ROMol::ConstAtomIterator ROMol::beginAtoms() const {
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return ConstAtomIterator(this);
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}
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ROMol::AtomIterator ROMol::endAtoms(){
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return AtomIterator(this,getNumAtoms());
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}
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ROMol::ConstAtomIterator ROMol::endAtoms() const{
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return ConstAtomIterator(this,getNumAtoms());
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}
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ROMol::AromaticAtomIterator ROMol::beginAromaticAtoms(){
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return AromaticAtomIterator(this);
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}
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ROMol::ConstAromaticAtomIterator ROMol::beginAromaticAtoms() const{
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return ConstAromaticAtomIterator(this);
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}
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ROMol::AromaticAtomIterator ROMol::endAromaticAtoms(){
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return AromaticAtomIterator(this,getNumAtoms());
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}
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ROMol::ConstAromaticAtomIterator ROMol::endAromaticAtoms() const{
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return ConstAromaticAtomIterator(this,getNumAtoms());
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}
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ROMol::HeteroatomIterator ROMol::beginHeteros(){
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return HeteroatomIterator(this);
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}
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ROMol::ConstHeteroatomIterator ROMol::beginHeteros() const{
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return ConstHeteroatomIterator(this);
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}
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ROMol::HeteroatomIterator ROMol::endHeteros(){
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return HeteroatomIterator(this,getNumAtoms());
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}
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ROMol::ConstHeteroatomIterator ROMol::endHeteros() const{
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return ConstHeteroatomIterator(this,getNumAtoms());
|
|
}
|
|
|
|
ROMol::QueryAtomIterator ROMol::beginQueryAtoms(QueryAtom const *what) {
|
|
return QueryAtomIterator(this,what);
|
|
}
|
|
ROMol::ConstQueryAtomIterator ROMol::beginQueryAtoms(QueryAtom const *what) const {
|
|
return ConstQueryAtomIterator(this,what);
|
|
}
|
|
ROMol::QueryAtomIterator ROMol::endQueryAtoms(){
|
|
return QueryAtomIterator(this,getNumAtoms());
|
|
}
|
|
ROMol::ConstQueryAtomIterator ROMol::endQueryAtoms() const{
|
|
return ConstQueryAtomIterator(this,getNumAtoms());
|
|
}
|
|
|
|
ROMol::BondIterator ROMol::beginBonds(){
|
|
return BondIterator(this);
|
|
}
|
|
ROMol::ConstBondIterator ROMol::beginBonds() const {
|
|
return ConstBondIterator(this);
|
|
}
|
|
ROMol::BondIterator ROMol::endBonds(){
|
|
EDGE_ITER beg,end;
|
|
boost::tie(beg,end)=getEdges();
|
|
return BondIterator(this,end);
|
|
}
|
|
ROMol::ConstBondIterator ROMol::endBonds() const{
|
|
EDGE_ITER beg,end;
|
|
boost::tie(beg,end)=getEdges();
|
|
return ConstBondIterator(this,end);
|
|
}
|
|
|
|
|
|
void ROMol::clearComputedProps(bool includeRings) const {
|
|
// the SSSR information:
|
|
if(includeRings) this->dp_ringInfo->reset();
|
|
|
|
STR_VECT compLst;
|
|
getProp("computedProps", compLst);
|
|
STR_VECT_CI svi;
|
|
for (svi = compLst.begin(); svi != compLst.end(); svi++) {
|
|
dp_props->clearVal(*svi);
|
|
}
|
|
compLst.clear();
|
|
dp_props->setVal("computedProps", compLst);
|
|
for(ConstAtomIterator atomIt=this->beginAtoms();
|
|
atomIt!=this->endAtoms();
|
|
atomIt++){
|
|
(*atomIt)->clearComputedProps();
|
|
}
|
|
for(ConstBondIterator bondIt=this->beginBonds();
|
|
bondIt!=this->endBonds();
|
|
bondIt++){
|
|
(*bondIt)->clearComputedProps();
|
|
}
|
|
}
|
|
|
|
void ROMol::updatePropertyCache(bool strict) {
|
|
for(AtomIterator atomIt=this->beginAtoms();
|
|
atomIt!=this->endAtoms();
|
|
atomIt++){
|
|
(*atomIt)->updatePropertyCache(strict);
|
|
}
|
|
for(BondIterator bondIt=this->beginBonds();
|
|
bondIt!=this->endBonds();
|
|
bondIt++){
|
|
(*bondIt)->updatePropertyCache(strict);
|
|
}
|
|
}
|
|
|
|
const Conformer &ROMol::getConformer(int id) const {
|
|
// make sure we have more than one conformation
|
|
if (d_confs.size() == 0) {
|
|
throw ConformerException("No conformations available on the molecule");
|
|
}
|
|
|
|
ConstConformerIterator ci;
|
|
if (id < 0) {
|
|
return *(d_confs.front());
|
|
}
|
|
unsigned int cid = (unsigned int)id;
|
|
for (ci = this->beginConformers(); ci != this->endConformers(); ci++) {
|
|
if ((*ci)->getId() == cid) {
|
|
return *(*ci);
|
|
}
|
|
}
|
|
// we did not find a coformation with the specified ID
|
|
std::string mesg = "Can't find conformation with ID: ";
|
|
mesg += id;
|
|
throw ConformerException(mesg);
|
|
}
|
|
|
|
Conformer &ROMol::getConformer(int id) {
|
|
// make sure we have more than one conformation
|
|
if (d_confs.size() == 0) {
|
|
throw ConformerException("No conformations available on the molecule");
|
|
}
|
|
|
|
if (id < 0) {
|
|
return *(d_confs.front());
|
|
}
|
|
ConformerIterator ci;
|
|
unsigned int cid = (unsigned int)id;
|
|
for (ci = this->beginConformers(); ci != this->endConformers(); ci++) {
|
|
if ((*ci)->getId() == cid) {
|
|
return *(*ci);
|
|
}
|
|
}
|
|
// we did not find a coformation with the specified ID
|
|
std::string mesg = "Can't find conformation with ID: ";
|
|
mesg += id;
|
|
throw ConformerException(mesg);
|
|
}
|
|
|
|
void ROMol::removeConformer(unsigned int id) {
|
|
CONF_SPTR_LIST_I ci;
|
|
for (ci = d_confs.begin(); ci != d_confs.end(); ci++) {
|
|
if ((*ci)->getId() == id) {
|
|
d_confs.erase(ci);
|
|
return;
|
|
}
|
|
}
|
|
}
|
|
|
|
unsigned int ROMol::addConformer(Conformer * conf, bool assignId) {
|
|
PRECONDITION(conf->getNumAtoms() == this->getNumAtoms(), "Number of atom mismatch")
|
|
if (assignId) {
|
|
int maxId = -1;
|
|
CONF_SPTR_LIST_I ci;
|
|
for (ci = d_confs.begin(); ci != d_confs.end(); ci++) {
|
|
if ((int)(*ci)->getId() > maxId) {
|
|
maxId = (int)(*ci)->getId();
|
|
}
|
|
}
|
|
maxId++;
|
|
conf->setId((unsigned int)maxId);
|
|
}
|
|
conf->setOwningMol(this);
|
|
CONFORMER_SPTR nConf(conf);
|
|
d_confs.push_back(nConf);
|
|
return conf->getId();
|
|
}
|
|
|
|
|
|
#if 0
|
|
ROMol::AtomIterator ai;
|
|
ROMol::ConstAtomIterator cai;
|
|
ROMol::HeteroatomIterator hi;
|
|
ROMol::ConstHeteroatomIterator chi;
|
|
ROMol::QueryAtomIterator qi;
|
|
ROMol::ConstQueryAtomIterator cqi;
|
|
BondIterator bi;
|
|
ConstBondIterator cbi;
|
|
#endif
|
|
|
|
|
|
} // end o' namespace
|