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254 lines
8.1 KiB
C++
Executable File
254 lines
8.1 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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// our stuff
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include "RWMol.h"
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#include "Atom.h"
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#include "Bond.h"
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#include "BondIterators.h"
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namespace RDKit{
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void RWMol::destroy() {
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ROMol::destroy();
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d_partialBonds.clear();
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d_partialBonds.resize(0);
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};
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void RWMol::insertMol(const ROMol &other)
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{
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GRAPH_MOL_ATOM_PMAP::const_type atom_pMap = other.getAtomPMap();
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int activeAtomIdx = getActiveAtom()->getIdx();
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VERTEX_ITER firstA,lastA;
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boost::tie(firstA,lastA) = boost::vertices(other.d_graph);
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while(firstA!=lastA){
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GRAPH_NODE_TYPE newAt_sp = atom_pMap[*firstA];
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// adding the atom copies the existing Atom, so we'll need to reacquire
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// a pointer to id after addition
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int newIdx = addAtom(newAt_sp,false);
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newAt_sp = getAtomWithIdx(newIdx);
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// set a bookmark for this atom's original index so we can update bonds
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setAtomBookmark(newAt_sp,ci_ATOM_HOLDER + *firstA);
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firstA++;
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}
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GRAPH_MOL_BOND_PMAP::const_type bond_pMap = other.getBondPMap();
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EDGE_ITER firstB,lastB;
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boost::tie(firstB,lastB) = boost::edges(other.d_graph);
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while(firstB != lastB){
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GRAPH_EDGE_TYPE bond_p = bond_pMap[*firstB]->copy();
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int idx1,idx2;
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idx1 = getAtomWithBookmark(ci_ATOM_HOLDER + bond_p->getBeginAtomIdx())->getIdx();
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idx2 = getAtomWithBookmark(ci_ATOM_HOLDER + bond_p->getEndAtomIdx())->getIdx();
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bond_p->setOwningMol(this);
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bond_p->setBeginAtomIdx(idx1);
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bond_p->setEndAtomIdx(idx2);
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addBond(bond_p,true);
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firstB++;
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}
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// blow out those bookmarks we set
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boost::tie(firstA,lastA) = boost::vertices(other.d_graph);
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while(firstA!=lastA){
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clearAtomBookmark(ci_ATOM_HOLDER + *firstA);
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firstA++;
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}
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}
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unsigned int RWMol::addAtom(bool updateLabel){
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Atom *atom_p = new Atom();
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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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return which;
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}
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void RWMol::replaceAtom(unsigned int idx,Atom *atom_pin,bool updateLabel){
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PRECONDITION(atom_pin,"bad atom passed to replaceAtom");
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RANGE_CHECK(0,idx,getNumAtoms()-1);
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Atom *atom_p = atom_pin->copy();
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atom_p->setOwningMol(this);
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atom_p->setIdx(idx);
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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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Atom *oldAtom = pMap[vd];
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pMap[vd] = atom_p;
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delete oldAtom;
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// FIX: do something about bookmarks
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};
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RWMol::GRAPH_NODE_TYPE RWMol::getActiveAtom() {
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if(hasAtomBookmark(ci_RIGHTMOST_ATOM)) return getAtomWithBookmark(ci_RIGHTMOST_ATOM);
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else return getLastAtom();
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};
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void RWMol::setActiveAtom(Atom *at) {
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if(hasAtomBookmark(ci_RIGHTMOST_ATOM)) clearAtomBookmark(ci_RIGHTMOST_ATOM);
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setAtomBookmark(at,ci_RIGHTMOST_ATOM);
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};
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void RWMol::setActiveAtom(unsigned int idx) {
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setActiveAtom(getAtomWithIdx(idx));
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};
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void RWMol::removeAtom(unsigned int idx) {
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Atom *oatom = getAtomWithIdx(idx);
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// remove any bookmarks which point to this atom:
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ATOM_BOOKMARK_MAP *marks = getAtomBookmarks();
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ATOM_BOOKMARK_MAP::iterator markI=marks->begin();
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while(markI != marks->end()){
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ATOM_PTR_LIST &atoms=markI->second;
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// we need to copy the iterator then increment it, because the
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// deletion we're going to do in clearAtomBookmark will invalidate
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// it.
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ATOM_BOOKMARK_MAP::iterator tmpI=markI;
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markI++;
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if(std::find(atoms.begin(),atoms.end(),oatom)!=atoms.end()){
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clearAtomBookmark(tmpI->first,oatom);
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}
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}
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// remove bonds attached to the atom
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ADJ_ITER b1,b2;
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boost::tie(b1,b2)=getAtomNeighbors(oatom);
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while(b1!=b2){
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removeBond(oatom->getIdx(),*b1);
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b1++;
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}
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// loop over all atoms with higher indices and update their indices
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for(unsigned int i=idx+1;i<getNumAtoms();i++){
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Atom *atom = getAtomWithIdx(i);
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atom->setIdx(i-1);
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}
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// do the same with the coordinates in the conformations
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CONF_SPTR_LIST_I ci;
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for (ci = d_confs.begin(); ci != d_confs.end(); ci++) {
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POINT3D_VECT &positions = (*ci)->getPositions();
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POINT3D_VECT_I pi = positions.begin();
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for (unsigned int i = 0; i < getNumAtoms()-1;i++) {
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pi++;
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if (i >= idx) {
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positions[i] = positions[i+1];
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}
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}
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positions.erase(pi);
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}
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// now deal with bonds:
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// their end indices may need to be decremented and their
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// indices will need to be handled
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BondIterator bondIt;
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unsigned int nBonds=0;
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for(bondIt=beginBonds();bondIt!=endBonds();bondIt++){
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Bond *bond = *bondIt;
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unsigned int tmpIdx = bond->getBeginAtomIdx();
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if( tmpIdx > idx) bond->setBeginAtomIdx(tmpIdx-1);
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tmpIdx = bond->getEndAtomIdx();
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if( tmpIdx > idx) bond->setEndAtomIdx(tmpIdx-1);
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bond->setIdx(nBonds++);
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}
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// remove all connections to the atom:
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boost::clear_vertex(idx,d_graph);
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delete oatom;
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// finally remove the vertex itself
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boost::remove_vertex(idx,d_graph);
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}
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void RWMol::removeAtom(Atom *atom) {
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removeAtom(atom->getIdx());
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}
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unsigned int RWMol::addBond(unsigned int atomIdx1,unsigned int atomIdx2,
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Bond::BondType bondType){
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RANGE_CHECK(0,atomIdx1,getNumAtoms()-1);
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RANGE_CHECK(0,atomIdx2,getNumAtoms()-1);
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Bond *b = new Bond(bondType);
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b->setOwningMol(this);
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if(bondType==Bond::AROMATIC){
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b->setIsAromatic(1);
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//
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// assume that aromatic bonds connect aromatic atoms
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// This is relevant for file formats like MOL, where there
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// is no such thing as an aromatic atom, but bonds can be
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// marked aromatic.
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//
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getAtomWithIdx(atomIdx1)->setIsAromatic(1);
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getAtomWithIdx(atomIdx2)->setIsAromatic(1);
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}
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Bond *bsp = b;
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boost::add_edge(atomIdx1,atomIdx2,BondProperty(bsp,BondWeight(1.0)),d_graph);
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unsigned int res = boost::num_edges(d_graph);
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b->setIdx(res-1);
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b->setBeginAtomIdx(atomIdx1);
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b->setEndAtomIdx(atomIdx2);
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return res;
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}
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unsigned int RWMol::addBond(Atom *atom1,Atom *atom2,
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Bond::BondType bondType){
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return addBond(atom1->getIdx(),atom2->getIdx(),bondType);
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}
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unsigned int RWMol::addBond(Atom::ATOM_SPTR atom1,Atom::ATOM_SPTR atom2,
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Bond::BondType bondType){
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return addBond(atom1->getIdx(),atom2->getIdx(),bondType);
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}
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void RWMol::removeBond(unsigned int aid1, unsigned int aid2) {
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RANGE_CHECK(0,aid1,getNumAtoms()-1);
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RANGE_CHECK(0,aid2,getNumAtoms()-1);
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Bond *bnd = getBondBetweenAtoms(aid1, aid2);
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// remove any bookmarks which point to this bond:
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BOND_BOOKMARK_MAP *marks = getBondBookmarks();
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BOND_BOOKMARK_MAP::iterator markI=marks->begin();
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while(markI != marks->end()){
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BOND_PTR_LIST &bonds=markI->second;
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// we need to copy the iterator then increment it, because the
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// deletion we're going to do in clearBondBookmark will invalidate
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// it.
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BOND_BOOKMARK_MAP::iterator tmpI=markI;
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markI++;
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if(std::find(bonds.begin(),bonds.end(),bnd)!=bonds.end()){
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clearBondBookmark(tmpI->first,bnd);
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}
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}
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boost::remove_edge(aid1, aid2, d_graph);
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delete bnd;
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}
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Bond *RWMol::createPartialBond(unsigned int atomIdx1,Bond::BondType bondType){
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RANGE_CHECK(0,atomIdx1,getNumAtoms()-1);
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Bond *b = new Bond(bondType);
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b->setOwningMol(this);
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b->setBeginAtomIdx(atomIdx1);
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return b;
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}
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unsigned int RWMol::finishPartialBond(unsigned int atomIdx2,int bondBookmark,
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Bond::BondType bondType){
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PRECONDITION(hasBondBookmark(bondBookmark),"no such partial bond");
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RANGE_CHECK(0,atomIdx2,getNumAtoms()-1);
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GRAPH_EDGE_TYPE bsp = getBondWithBookmark(bondBookmark);
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if(bondType==Bond::UNSPECIFIED){
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bondType = bsp->getBondType();
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}
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return addBond(bsp->getBeginAtomIdx(),atomIdx2,bondType);
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}
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} // end o' namespace
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