mirror of
https://github.com/rdkit/rdkit.git
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590 lines
24 KiB
C++
Executable File
590 lines
24 KiB
C++
Executable File
// $Id$
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//
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// Copyright (C) 2003-2010 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 "RDKitBase.h"
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#include <list>
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#include "QueryAtom.h"
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#include "QueryOps.h"
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#include <Geometry/Transform3D.h>
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#include <Geometry/point.h>
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namespace RDKit{
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// Local utility functionality:
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namespace {
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Atom *getAtomNeighborNot(ROMol *mol,const Atom *atom,const Atom *other){
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PRECONDITION(mol,"bad molecule");
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PRECONDITION(atom,"bad atom");
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PRECONDITION(atom->getDegree()>1,"bad degree");
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PRECONDITION(other,"bad atom");
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Atom *res=0;
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ROMol::ADJ_ITER nbrIdx,endNbrs;
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boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(atom);
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while(nbrIdx!=endNbrs){
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if(*nbrIdx != other->getIdx()){
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res = mol->getAtomWithIdx(*nbrIdx);
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break;
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}
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nbrIdx++;
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}
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POSTCONDITION(res,"no neighbor found");
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return res;
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}
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void setHydrogenCoords(ROMol *mol,unsigned int hydIdx,unsigned int heavyIdx){
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// we will loop over all the coordinates
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PRECONDITION(mol,"bad molecule");
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PRECONDITION(heavyIdx!=hydIdx,"degenerate atoms");
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Atom *hydAtom = mol->getAtomWithIdx(hydIdx);
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PRECONDITION(mol->getAtomDegree(hydAtom)==1,"bad atom degree");
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const Bond *bond=mol->getBondBetweenAtoms(heavyIdx,hydIdx);
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PRECONDITION(bond,"no bond between atoms");
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const Atom *heavyAtom = mol->getAtomWithIdx(heavyIdx);
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double bondLength = PeriodicTable::getTable()->getRb0(1) +
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PeriodicTable::getTable()->getRb0(heavyAtom->getAtomicNum());
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RDGeom::Point3D dirVect(0,0,0);
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RDGeom::Point3D perpVect,rotnAxis,nbrPerp;
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RDGeom::Point3D nbr1Vect,nbr2Vect,nbr3Vect;
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RDGeom::Transform3D tform;
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RDGeom::Point3D heavyPos, hydPos;
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const Atom *nbr1=0,*nbr2=0,*nbr3=0;
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const Bond *nbrBond;
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ROMol::ADJ_ITER nbrIdx,endNbrs;
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switch(heavyAtom->getDegree()){
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case 1:
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// --------------------------------------------------------------------------
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// No other atoms present:
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// --------------------------------------------------------------------------
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dirVect.z = 1;
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// loop over the conformations and set the coordinates
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for (ROMol::ConformerIterator cfi = mol->beginConformers();
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cfi != mol->endConformers(); cfi++) {
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heavyPos = (*cfi)->getAtomPos(heavyIdx);
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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}
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break;
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case 2:
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// --------------------------------------------------------------------------
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// One other neighbor:
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// --------------------------------------------------------------------------
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nbr1=getAtomNeighborNot(mol,heavyAtom,hydAtom);
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for (ROMol::ConformerIterator cfi = mol->beginConformers();
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cfi != mol->endConformers(); cfi++) {
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heavyPos = (*cfi)->getAtomPos(heavyIdx);
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RDGeom::Point3D nbr1Pos = (*cfi)->getAtomPos(nbr1->getIdx());
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// get a normalized vector pointing away from the neighbor:
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nbr1Vect = heavyPos.directionVector(nbr1Pos);
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nbr1Vect *= -1;
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// ok, nbr1Vect points away from the other atom, figure out where
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// this H goes:
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switch(heavyAtom->getHybridization()){
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case Atom::SP3:
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// get a perpendicular to nbr1Vect:
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perpVect=nbr1Vect.getPerpendicular();
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// and move off it:
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tform.SetRotation((180-109.471)*M_PI/180.,perpVect);
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dirVect = tform*nbr1Vect;
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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break;
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case Atom::SP2:
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// default position is to just take an arbitrary perpendicular:
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perpVect = nbr1Vect.getPerpendicular();
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if(nbr1->getDegree()>1){
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// can we use the neighboring atom to establish a perpendicular?
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nbrBond=mol->getBondBetweenAtoms(heavyIdx,nbr1->getIdx());
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if(nbrBond->getIsAromatic() || nbrBond->getBondType()==Bond::DOUBLE){
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nbr2=getAtomNeighborNot(mol,nbr1,heavyAtom);
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nbr2Vect=nbr1Pos.directionVector((*cfi)->getAtomPos(nbr2->getIdx()));
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perpVect = nbr2Vect.crossProduct(nbr1Vect);
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}
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}
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perpVect.normalize();
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// rotate the nbr1Vect 60 degrees about perpVect and we're done:
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tform.SetRotation(60.*M_PI/180.,perpVect);
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dirVect = tform*nbr1Vect;
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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break;
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case Atom::SP:
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// just lay the H along the vector:
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dirVect=nbr1Vect;
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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break;
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default:
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// FIX: handle other hybridizations
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// for now, just lay the H along the vector:
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dirVect=nbr1Vect;
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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}
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}
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break;
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case 3:
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// --------------------------------------------------------------------------
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// Two other neighbors:
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// --------------------------------------------------------------------------
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boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(heavyAtom);
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while(nbrIdx!=endNbrs){
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if(*nbrIdx != hydIdx){
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if(!nbr1) nbr1 = mol->getAtomWithIdx(*nbrIdx);
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else nbr2 = mol->getAtomWithIdx(*nbrIdx);
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}
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nbrIdx++;
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}
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TEST_ASSERT(nbr1);
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TEST_ASSERT(nbr2);
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for (ROMol::ConformerIterator cfi = mol->beginConformers();
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cfi != mol->endConformers(); cfi++) {
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// start along the average of the two vectors:
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heavyPos = (*cfi)->getAtomPos(heavyIdx);
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nbr1Vect = (*cfi)->getAtomPos(nbr1->getIdx()).directionVector(heavyPos);
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nbr2Vect = (*cfi)->getAtomPos(nbr2->getIdx()).directionVector(heavyPos);
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dirVect = nbr1Vect+nbr2Vect;
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dirVect.normalize();
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switch(heavyAtom->getHybridization()){
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case Atom::SP3:
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// get the perpendicular to the neighbors:
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nbrPerp = nbr1Vect.crossProduct(nbr2Vect);
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// and the perpendicular to that:
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rotnAxis = nbrPerp.crossProduct(dirVect);
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// and then rotate about that:
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rotnAxis.normalize();
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tform.SetRotation((109.471/2)*M_PI/180.,rotnAxis);
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dirVect = tform*dirVect;
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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break;
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case Atom::SP2:
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// don't need to do anything here, the H atom goes right on the
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// direction vector
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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break;
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default:
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// FIX: handle other hybridizations
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// for now, just lay the H along the neighbor vector;
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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break;
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}
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}
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break;
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case 4:
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// --------------------------------------------------------------------------
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// Three other neighbors:
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// --------------------------------------------------------------------------
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boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(heavyAtom);
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while(nbrIdx!=endNbrs){
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if(*nbrIdx != hydIdx){
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if(!nbr1) nbr1 = mol->getAtomWithIdx(*nbrIdx);
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else if(!nbr2) nbr2 = mol->getAtomWithIdx(*nbrIdx);
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else nbr3 = mol->getAtomWithIdx(*nbrIdx);
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}
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nbrIdx++;
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}
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TEST_ASSERT(nbr1);
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TEST_ASSERT(nbr2);
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TEST_ASSERT(nbr3);
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for (ROMol::ConformerIterator cfi = mol->beginConformers();
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cfi != mol->endConformers(); cfi++) {
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// use the average of the three vectors:
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heavyPos = (*cfi)->getAtomPos(heavyIdx);
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nbr1Vect = (*cfi)->getAtomPos(nbr1->getIdx()).directionVector(heavyPos);
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nbr2Vect = (*cfi)->getAtomPos(nbr2->getIdx()).directionVector(heavyPos);
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nbr3Vect = (*cfi)->getAtomPos(nbr3->getIdx()).directionVector(heavyPos);
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// if three neighboring atoms are more or less planar, this
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// is going to be in a quasi-random (but wrong) direction...
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// correct for this case:
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if(fabs(nbr3Vect.dotProduct(nbr1Vect.crossProduct(nbr2Vect)))<0.1){
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dirVect = nbr1Vect.crossProduct(nbr2Vect);
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// FIX: check chiral volume
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} else {
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dirVect = nbr1Vect+nbr2Vect+nbr3Vect;
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dirVect.normalize();
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}
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hydPos = heavyPos + dirVect*bondLength;
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(*cfi)->setAtomPos(hydIdx, hydPos);
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}
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break;
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default:
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// --------------------------------------------------------------------------
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// FIX: figure out what to do here
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// --------------------------------------------------------------------------
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hydPos = heavyPos + dirVect*bondLength;
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for (ROMol::ConformerIterator cfi = mol->beginConformers();
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cfi != mol->endConformers(); cfi++) {
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(*cfi)->setAtomPos(hydIdx, hydPos);
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}
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break;
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}
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}
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} // end of unnamed namespace
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namespace MolOps {
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// NOTE that in most cases we do not need to check for chiral
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// atoms when adding Hs because the bond order goes from hydrogen
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// implicitly first to hydrogen explicitly last. This is a cyclic
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// permutation, so it doesn't affect the chirality. (Of course
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// there can only be one H on the atom... otherwise it wouldn't be
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// chiral!)
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// The exception to this rule is when the central atom has no
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// preceding bond in the molecule; in that case the implicit H
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// is the first bond and the permutation is no longer cyclic.
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// This includes situations like [C@H](C)(Cl)F, which needs to
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// go to [C@@](C)(Cl)(F)[H]
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ROMol *addHs(const ROMol &mol,bool explicitOnly,bool addCoords){
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RWMol *res = new RWMol(mol);
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// when we hit each atom, clear its computed properties
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// NOTE: it is essential that we not clear the ring info in the
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// molecule's computed properties. We don't want to have to
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// regenerate that. This caused Issue210 and Issue212:
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res->clearComputedProps(false);
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// precompute the number of hydrogens we are going to add so that we can
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// pre-allocate the necessary space on the conformations of the molecule
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// for their coordinates
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unsigned int numAddHyds = 0;
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for(ROMol::ConstAtomIterator at=mol.beginAtoms();at!=mol.endAtoms();++at){
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numAddHyds += (*at)->getNumExplicitHs();
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if (!explicitOnly) {
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numAddHyds += (*at)->getNumImplicitHs();
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}
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}
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unsigned int nSize = mol.getNumAtoms() + numAddHyds;
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// loop over the conformations of the molecule and allocate new space
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// for the H locations (need to do this even if we aren't adding coords so
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// that the conformers have the correct number of atoms).
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for (ROMol::ConformerIterator cfi = res->beginConformers();
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cfi != res->endConformers(); ++cfi) {
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(*cfi)->reserve(nSize);
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}
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for(ROMol::ConstAtomIterator at=mol.beginAtoms();at!=mol.endAtoms();++at){
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unsigned int newIdx;
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Atom *newAt=res->getAtomWithIdx((*at)->getIdx());
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// check the chirality special case:
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unsigned int nHere=(*at)->getNumExplicitHs()+(*at)->getNumImplicitHs();
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if(nHere==1 && ((*at)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW ||
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(*at)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW )) {
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bool hasTruePrecedingAtom=false;
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ROMol::OEDGE_ITER beg,end;
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boost::tie(beg,end) = mol.getAtomBonds(*at);
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while(beg!=end){
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unsigned int otherIdx=mol[*beg]->getOtherAtom(*at)->getIdx();
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if( otherIdx < (*at)->getIdx() &&
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mol[*beg]->getBeginAtomIdx()==otherIdx){
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hasTruePrecedingAtom=true;
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break;
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}
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++beg;
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}
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if(!hasTruePrecedingAtom){
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// this is the special case described above. switch the stereochem:
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if((*at)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW){
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newAt->setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
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} else {
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newAt->setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
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}
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}
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}
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newAt->clearComputedProps();
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// always convert explicit Hs
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for(unsigned int i=0;i<(*at)->getNumExplicitHs();i++){
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newIdx=res->addAtom(new Atom(1),false,true);
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res->addBond((*at)->getIdx(),newIdx,Bond::SINGLE);
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res->getAtomWithIdx(newIdx)->updatePropertyCache();
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if(addCoords) setHydrogenCoords(res,newIdx,(*at)->getIdx());
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}
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// clear the local property
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newAt->setNumExplicitHs(0);
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if(!explicitOnly){
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// take care of implicits
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for(unsigned int i=0;i<(*at)->getNumImplicitHs();i++){
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newIdx=res->addAtom(new Atom(1),false,true);
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res->addBond((*at)->getIdx(),newIdx,Bond::SINGLE);
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// set the isImplicit label so that we can strip these back
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// off later if need be.
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res->getAtomWithIdx(newIdx)->setProp("isImplicit",1, true);
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res->getAtomWithIdx(newIdx)->updatePropertyCache();
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if(addCoords) setHydrogenCoords(res,newIdx,(*at)->getIdx());
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}
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// be very clear about implicits not being allowed in this representation
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newAt->setProp("origNoImplicit",(*at)->getNoImplicit(), true);
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newAt->setNoImplicit(true);
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}
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// update the atom's derived properties (valence count, etc.)
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newAt->updatePropertyCache();
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}
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return static_cast<ROMol *>(res);
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};
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//
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// This routine removes hydrogens (and bonds to them) from the molecular graph.
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// Other Atom and bond indices may be affected by the removal.
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//
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// NOTES:
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// - Hydrogens which aren't connected to a heavy atom will not be
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// removed. This prevents molecules like "[H][H]" from having
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// all atoms removed.
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// - Labelled hydrogen (e.g. atoms with atomic number=1, but mass > 1),
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// will not be removed.
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//
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ROMol *removeHs(const ROMol &mol,bool implicitOnly,bool updateExplicitCount,bool sanitize){
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Atom *atom;
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unsigned int currIdx=0,origIdx=0;
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std::map<unsigned int,unsigned int> idxMap;
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RWMol *res = new RWMol(mol);
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while(currIdx < res->getNumAtoms()){
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atom = res->getAtomWithIdx(currIdx);
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idxMap[origIdx]=currIdx;
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origIdx++;
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if(atom->getAtomicNum()==1){
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bool removeIt=false;
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if(atom->hasProp("isImplicit")){
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removeIt=true;
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} else if(!implicitOnly && atom->getMass()<1.1){
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ROMol::ADJ_ITER begin,end;
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boost::tie(begin,end) = res->getAtomNeighbors(atom);
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while(begin!=end){
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if(res->getAtomWithIdx(*begin)->getAtomicNum() != 1){
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removeIt=true;
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break;
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}
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begin++;
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}
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}
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if(removeIt){
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ROMol::OEDGE_ITER beg,end;
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boost::tie(beg,end) = res->getAtomBonds(atom);
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// note the assumption that the H only has one neighbor... I
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// feel no need to handle the case of hypervalent hydrogen!
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// :-)
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const BOND_SPTR bond = (*res)[*beg];
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Atom *heavyAtom =bond->getOtherAtom(atom);
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// we'll update the atom's explicit H count if we were told to
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// *or* if the atom is chiral, in which case the H is needed
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// in order to complete the coordination
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// *or* if the atom has the noImplicit flag set:
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if( updateExplicitCount || heavyAtom->getNoImplicit() ||
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heavyAtom->getChiralTag()!=Atom::CHI_UNSPECIFIED ){
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heavyAtom->setNumExplicitHs(heavyAtom->getNumExplicitHs()+1);
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} else {
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// this is a special case related to Issue 228 and the
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// "disappearing Hydrogen" problem discussed in MolOps::adjustHs
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//
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// If we remove a hydrogen from an aromatic N, we need to
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// be *sure* to increment the explicit count, even if the
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// H itself isn't marked as explicit
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if(heavyAtom->getAtomicNum()==7 && heavyAtom->getIsAromatic()
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&& heavyAtom->getFormalCharge()==0){
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heavyAtom->setNumExplicitHs(heavyAtom->getNumExplicitHs()+1);
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}
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}
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// One other consequence of removing the H from the graph is
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// that we may change the ordering of the bonds about a
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// chiral center. This may change the chiral label at that
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// atom. We deal with that by explicitly checking here:
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if(heavyAtom->getChiralTag()!=Atom::CHI_UNSPECIFIED){
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INT_LIST neighborIndices;
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unsigned int atomsBeforeHeavy=0;
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boost::tie(beg,end) = res->getAtomBonds(heavyAtom);
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while(beg!=end){
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if((*res)[*beg]->getIdx()!=bond->getIdx()){
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neighborIndices.push_back((*res)[*beg]->getIdx());
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if((*res)[*beg]->getBeginAtomIdx()!=heavyAtom->getIdx() &&
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(*res)[*beg]->getOtherAtom(heavyAtom)->getIdx()<heavyAtom->getIdx() ){
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++atomsBeforeHeavy;
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}
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}
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++beg;
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}
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if(atomsBeforeHeavy){
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neighborIndices.insert(++neighborIndices.begin(),bond->getIdx());
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} else {
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neighborIndices.push_front(bond->getIdx());
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}
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int nSwaps = heavyAtom->getPerturbationOrder(neighborIndices);
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//std::cerr << " swaps: " << nSwaps << " " << atomsBeforeHeavy << std::endl;
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if(nSwaps%2){
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heavyAtom->invertChirality();
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}
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}
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res->removeAtom(atom);
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} else {
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// only increment the atom idx if we don't remove the atom
|
|
currIdx++;
|
|
}
|
|
} else {
|
|
// only increment the atom idx if we don't remove the atom
|
|
currIdx++;
|
|
if(atom->hasProp("origNoImplicit")){
|
|
// we'll get in here if we haven't already processed the atom's implicit
|
|
// hydrogens. (this is protection for the case that removeHs() is called
|
|
// multiple times on a single molecule without intervening addHs() calls)
|
|
bool tmpBool;
|
|
atom->getProp("origNoImplicit",tmpBool);
|
|
atom->setNoImplicit(tmpBool);
|
|
atom->clearProp("origNoImplicit");
|
|
}
|
|
}
|
|
}
|
|
//
|
|
// If we didn't only remove implicit Hs, which are guaranteed to
|
|
// be the highest numbered atoms, we may have altered atom indices.
|
|
// This can screw up derived properties (such as ring members), so
|
|
// do some checks:
|
|
//
|
|
if(!implicitOnly){
|
|
if(sanitize){
|
|
sanitizeMol(*res);
|
|
}
|
|
if(mol.hasProp("_StereochemDone")){
|
|
// stereochem had been perceived in the original molecule,
|
|
// loop over the bonds and fix their stereoAtoms fields:
|
|
for(ROMol::BondIterator bondIt=res->beginBonds();
|
|
bondIt!=res->endBonds();
|
|
++bondIt){
|
|
Bond *bond=*bondIt;
|
|
if( bond->getBondType()==Bond::DOUBLE &&
|
|
bond->getStereo()!=Bond::STEREONONE){
|
|
for(INT_VECT_I it=bond->getStereoAtoms().begin();it!=bond->getStereoAtoms().end();++it){
|
|
*it = idxMap[*it];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
return static_cast<ROMol *>(res);
|
|
};
|
|
|
|
//
|
|
// This routine removes explicit hydrogens (and bonds to them) from
|
|
// the molecular graph and adds them as queries to the heavy atoms
|
|
// to which they are bound. If the heavy atoms (or atom queries)
|
|
// already have hydrogen-count queries, they will be updated.
|
|
//
|
|
// NOTE:
|
|
// - Hydrogens which aren't connected to a heavy atom will not be
|
|
// removed. This prevents molecules like "[H][H]" from having
|
|
// all atoms removed.
|
|
//
|
|
ROMol *mergeQueryHs(const ROMol &mol){
|
|
unsigned int currIdx=0;
|
|
RWMol *res = new RWMol(mol);
|
|
while(currIdx < res->getNumAtoms()){
|
|
Atom *atom = res->getAtomWithIdx(currIdx);
|
|
if(atom->getAtomicNum()==1){
|
|
bool removeIt=false;
|
|
ROMol::ADJ_ITER begin,end;
|
|
boost::tie(begin,end) = res->getAtomNeighbors(atom);
|
|
while(begin!=end){
|
|
if(res->getAtomWithIdx(*begin)->getAtomicNum() > 1){
|
|
removeIt=true;
|
|
break;
|
|
}
|
|
begin++;
|
|
}
|
|
if(removeIt){
|
|
ROMol::ADJ_ITER begin,end;
|
|
boost::tie(begin,end) = res->getAtomNeighbors(atom);
|
|
Atom *nbr = res->getAtomWithIdx(*begin);
|
|
//
|
|
// We've found the neighbor.
|
|
// 1) If the neighbor has no H query already:
|
|
// - add a generic H query
|
|
// else:
|
|
// - do nothing
|
|
// 2) Remove the atom from the molecular graph
|
|
//
|
|
// Examples:
|
|
// C[H] -> [C;!H0]
|
|
// [C;H1][H] -> [C;H1]
|
|
// [C;H2][H] -> [C;H2]
|
|
//
|
|
// FIX: this is going to behave oddly in the case of a contradictory
|
|
// SMARTS like: [C;H0][H], where it will give the equivalent of:
|
|
// [C;H0] I think this is actually correct, but I can be persuaded
|
|
// otherwise.
|
|
//
|
|
// First we'll search for an H query:
|
|
bool hasHQuery=false;
|
|
if(nbr->hasQuery()){
|
|
std::list<QueryAtom::QUERYATOM_QUERY::CHILD_TYPE> childStack;
|
|
QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI child1;
|
|
for(child1=nbr->getQuery()->beginChildren();
|
|
child1!=nbr->getQuery()->endChildren();
|
|
child1++){
|
|
childStack.push_back(*child1);
|
|
}
|
|
while( !hasHQuery && childStack.size() ){
|
|
QueryAtom::QUERYATOM_QUERY::CHILD_TYPE query = childStack.front();
|
|
childStack.pop_front();
|
|
if(query->getDescription()=="AtomHCount"){
|
|
hasHQuery=true;
|
|
} else {
|
|
for(child1=query->beginChildren();
|
|
child1!=query->endChildren();
|
|
child1++){
|
|
childStack.push_back(*child1);
|
|
}
|
|
}
|
|
}
|
|
|
|
if(!hasHQuery){
|
|
ATOM_EQUALS_QUERY *tmp=makeAtomHCountQuery(0);
|
|
tmp->setNegation(true);
|
|
nbr->expandQuery(tmp);
|
|
}
|
|
} else {
|
|
// it wasn't a query atom, we need to replace it:
|
|
ATOM_EQUALS_QUERY *tmp=makeAtomHCountQuery(0);
|
|
tmp->setNegation(true);
|
|
QueryAtom *newAt = new QueryAtom;
|
|
newAt->setQuery(tmp);
|
|
res->replaceAtom(nbr->getIdx(),newAt);
|
|
delete newAt;
|
|
}
|
|
res->removeAtom(atom);
|
|
} else {
|
|
// only increment the atom idx if we don't remove the atom
|
|
currIdx++;
|
|
}
|
|
} else {
|
|
currIdx++;
|
|
}
|
|
}
|
|
return static_cast<ROMol *>(res);
|
|
};
|
|
}; // end of namespace MolOps
|
|
}; // end of namespace RDKit
|