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tim |
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chiral.cpp - Detect chiral atoms and molecules. |
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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#include <list> |
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#include "mol.hpp" |
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#include "obutil.hpp" |
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#include "matrix.hpp" |
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#include "chiral.hpp" |
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#include "matrix3x3.hpp" |
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using namespace std; |
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namespace OpenBabel |
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{ |
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//! Sets atom->IsChiral() to true for chiral atoms |
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void OBMol::FindChiralCenters() |
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{ |
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if (HasChiralityPerceived()) |
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return; |
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SetChiralityPerceived(); |
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obErrorLog.ThrowError(__FUNCTION__, |
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"Ran OpenBabel::FindChiralCenters", obAuditMsg); |
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//do quick test to see if there are any possible chiral centers |
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bool mayHaveChiralCenter=false; |
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OBAtom *atom,*nbr; |
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vector<OBNodeBase*>::iterator i; |
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for (atom = BeginAtom(i);atom;atom = NextAtom(i)) |
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if (atom->GetHyb() == 3 && atom->GetHvyValence() >= 3) |
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{ |
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mayHaveChiralCenter=true; |
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break; |
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} |
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if (!mayHaveChiralCenter) |
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return; |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator j; |
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for (bond = BeginBond(j);bond;bond = NextBond(j)) |
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if (bond->IsWedge() || bond->IsHash()) |
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(bond->GetBeginAtom())->SetChiral(); |
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#define INTMETHOD |
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#ifdef INTMETHOD |
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vector<unsigned int> vgid; |
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GetGIDVector(vgid); |
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vector<unsigned int> tlist; |
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vector<unsigned int>::iterator k; |
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#else //use Golender floating point method |
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vector<double> gp; |
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GraphPotentials(*this,gp); |
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vector<double> tlist; |
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vector<double>::iterator k; |
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#endif |
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bool ischiral; |
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for (atom = BeginAtom(i);atom;atom = NextAtom(i)) |
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if (atom->GetHyb() == 3 && atom->GetHvyValence() >= 3 && !atom->IsChiral()) |
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{ |
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tlist.clear(); |
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ischiral = true; |
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for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j)) |
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{ |
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for (k = tlist.begin();k != tlist.end();k++) |
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#ifdef INTMETHOD |
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if (vgid[nbr->GetIdx()-1] == *k) |
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#else |
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if (fabs(gp[nbr->GetIdx()]-*k) < 0.001) |
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#endif |
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ischiral = false; |
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#ifdef INTMETHOD |
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if (ischiral) |
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tlist.push_back(vgid[nbr->GetIdx()-1]); |
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#else |
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if (ischiral) |
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tlist.push_back(gp[nbr->GetIdx()]); |
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#endif |
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else |
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break; |
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} |
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if (ischiral) |
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atom->SetChiral(); |
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} |
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} |
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// Seems to make a vector chirality become filled with array of +/- 1 for chiral atoms. |
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void GetChirality(OBMol &mol, std::vector<int> &chirality) |
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{ |
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chirality.resize(mol.NumAtoms()+1); |
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fill(chirality.begin(),chirality.end(),0); |
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OBAtom *atom; |
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vector<OBNodeBase*>::iterator i; |
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for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
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if (atom->IsChiral()) |
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{ |
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if (!atom->HasChiralVolume()) |
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{ |
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double sv = CalcSignedVolume(mol,atom); |
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if (sv < 0.0) |
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{ |
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chirality[atom->GetIdx()-1] = -1; |
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atom->SetNegativeStereo(); |
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} |
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else if (sv > 0.0) |
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{ |
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chirality[atom->GetIdx()-1] = 1; |
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atom->SetPositiveStereo(); |
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} |
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} |
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else // already calculated signed volume (e.g., imported from somewhere) |
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{ |
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if (atom ->IsPositiveStereo()) |
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chirality[atom->GetIdx()-1] = 1; |
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else |
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chirality[atom->GetIdx()-1] = -1; |
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} |
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} |
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} |
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int GetParity4Ref(vector<unsigned int> pref) |
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{ |
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if(pref.size()!=4)return(-1); // should be given a vector of size 4. |
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int parity=0; |
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for (int i=0;i<3;i++) // do the bubble sort this many times |
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{ |
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for(int j=0;j<3;j++) // iterate across the array 4th element has no |
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{ // right hand neighbour so no need to sort |
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if (pref[j+1] < pref[j]) // compare the two neighbors |
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{ |
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unsigned int tmp = pref[j]; // swap a[j] and a[j+1] |
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pref[j] = pref[j+1]; |
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pref[j+1] = tmp; |
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parity++; // parity odd will invert stereochem |
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} |
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} |
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} // End Bubble Sort |
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return(parity%2); |
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} |
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bool CorrectChirality(OBMol &mol, OBAtom *atm, atomreftype i, atomreftype o) |
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{ |
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if (!atm->HasChiralitySpecified()) // if no chirality defined can't do any more for 0D |
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return(false); |
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int parityI=0,parityO=0; |
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OBChiralData* cd=(OBChiralData*)atm->GetData(OBGenericDataType::ChiralData); |
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if ((cd->GetAtom4Refs(input)).size()!=4)return(false); // must have 4 refs |
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parityI=GetParity4Ref(cd->GetAtom4Refs(i)); // Gets Atom4Refs used to define the chirality |
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parityO=GetParity4Ref(cd->GetAtom4Refs(o));//GetsOutput parity. |
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/* switch (CHTYPE) |
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{ |
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case SMILES: // SMILES always uses 1234 atom refs |
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parityO=0; // if parityO==parityI then clockwise in input = clockwise in output |
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break; |
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case MOLV3000: // MOLV3000 uses 1234 unless an H then 123H |
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if (atm->GetHvyValence()==3) |
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{ |
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OBAtom *nbr; |
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int Hid=1000;// max Atom ID +1 should be used here |
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vector<int> nbr_atms; |
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vector<OBEdgeBase*>::iterator i; |
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for (nbr = atm->BeginNbrAtom(i);nbr;nbr = atm->NextNbrAtom(i)) |
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{ |
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if (nbr->IsHydrogen()){Hid=nbr->GetIdx();continue;} |
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nbr_atms.push_back(nbr->GetIdx()); |
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} |
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sort(nbr_atms.begin(),nbr_atms.end()); |
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nbr_atms.push_back(Hid); |
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int tmp[4]; |
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for(int i=0;i<4;i++){tmp[i]=nbr_atms[i];} |
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parityO=GetParity4Ref(tmp); |
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} |
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else if (atm->GetHvyValence()==4) |
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parityO=0; |
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break; |
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default: |
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parityO=0; |
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}*/ |
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if (parityO==parityI) |
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{//cout << "Parity is the same"<<endl; |
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return(true); |
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} |
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else if(parityO!=parityI) // Need to invert the Chirality which has been set |
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{ //cout << "Parity is Opposite"<<endl; |
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if (atm->IsClockwise()) |
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{atm->UnsetStereo();atm->SetAntiClockwiseStereo();} |
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else if (atm->IsAntiClockwise()) |
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{atm->UnsetStereo();atm->SetClockwiseStereo();} |
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else |
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return(false); |
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return(true); |
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} |
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return false; |
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} |
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//! Calculate the signed volume for an atom. If the atom has a valence of 3 |
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//! the coordinates of an attached hydrogen are calculated |
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//! Puts attached Hydrogen last at the moment, like mol V3000 format. |
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double CalcSignedVolume(OBMol &mol,OBAtom *atm) |
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{ |
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vector3 tmp_crd; |
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vector<unsigned int> nbr_atms; |
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vector<vector3> nbr_crds; |
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bool use_central_atom = false,is2D=false; |
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double hbrad = etab.CorrectedBondRad(1,0); |
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if (!mol.Has3D()) //give peudo Z coords if mol is 2D |
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{ |
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vector3 v,vz(0.0,0.0,1.0); |
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is2D = true; |
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OBAtom *nbr; |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = atm->BeginBond(i);bond;bond = atm->NextBond(i)) |
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{ |
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nbr = bond->GetEndAtom(); |
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if (nbr != atm) |
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{ |
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v = nbr->GetVector(); |
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if (bond->IsWedge()) |
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v += vz; |
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else |
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if (bond->IsHash()) |
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v -= vz; |
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nbr->SetVector(v); |
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} |
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else |
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{ |
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nbr = bond->GetBeginAtom(); |
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v = nbr->GetVector(); |
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if (bond->IsWedge()) |
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v -= vz; |
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else |
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if (bond->IsHash()) |
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v += vz; |
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nbr->SetVector(v); |
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} |
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} |
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} |
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if (atm->GetHvyValence() < 3) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << "Cannot calculate a signed volume for an atom with a heavy atom valence of " << atm->GetHvyValence() << endl; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo); |
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return(0.0); |
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} |
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// Create a vector with the coordinates of the neighbor atoms |
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// Also make a vector with Atom IDs |
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OBAtom *nbr; |
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vector<OBEdgeBase*>::iterator bint; |
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for (nbr = atm->BeginNbrAtom(bint);nbr;nbr = atm->NextNbrAtom(bint)) |
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{ |
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nbr_atms.push_back(nbr->GetIdx()); |
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} |
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// sort the neighbor atoms to insure a consistent ordering |
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sort(nbr_atms.begin(),nbr_atms.end()); |
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for (unsigned int i = 0; i < nbr_atms.size(); i++) |
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{ |
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OBAtom *tmp_atm = mol.GetAtom(nbr_atms[i]); |
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nbr_crds.push_back(tmp_atm->GetVector()); |
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} |
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/* |
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// If we have three heavy atoms we need to calculate the position of the fourth |
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if (atm->GetHvyValence() == 3) |
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{ |
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double bondlen = hbrad+etab.CorrectedBondRad(atm->GetAtomicNum(),atm->GetHyb()); |
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atm->GetNewBondVector(tmp_crd,bondlen); |
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nbr_crds.push_back(tmp_crd); |
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} |
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*/ |
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for(int j=0;j < nbr_crds.size();j++) // Checks for a neighbour having 0 co-ords (added hydrogen etc) |
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{ |
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if (nbr_crds[j]==0 && use_central_atom==false)use_central_atom=true; |
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else if (nbr_crds[j]==0) |
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{ |
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obErrorLog.ThrowError(__FUNCTION__, "More than 2 neighbours have 0 co-ords when attempting 3D chiral calculation", obInfo); |
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} |
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} |
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// If we have three heavy atoms we can use the chiral center atom itself for the fourth |
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// will always give same sign (for tetrahedron), magnitude will be smaller. |
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if(nbr_atms.size()==3 || use_central_atom==true) |
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{ |
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nbr_crds.push_back(atm->GetVector()); |
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nbr_atms.push_back(mol.NumAtoms()+1); // meed to add largest number on end to work |
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} |
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OBChiralData* cd=(OBChiralData*)atm->GetData(OBGenericDataType::ChiralData); //Set the output atom4refs to the ones used |
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if(cd==NULL) |
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{ |
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cd = new OBChiralData; |
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atm->SetData(cd); |
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} |
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cd->SetAtom4Refs(nbr_atms,calcvolume); |
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//re-zero psuedo-coords |
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if (is2D) |
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{ |
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vector3 v; |
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OBAtom *atom; |
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vector<OBNodeBase*>::iterator k; |
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for (atom = mol.BeginAtom(k);atom;atom = mol.NextAtom(k)) |
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{ |
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v = atom->GetVector(); |
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v.SetZ(0.0); |
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atom->SetVector(v); |
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} |
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} |
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return(signed_volume(nbr_crds[0],nbr_crds[1],nbr_crds[2],nbr_crds[3])); |
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} |
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//! Calculate a signed volume given a set of 4 coordinates |
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double signed_volume(const vector3 &a, const vector3 &b, const vector3 &c, const vector3 &d) |
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{ |
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vector3 A,B,C; |
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A = b-a; |
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B = c-a; |
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C = d-a; |
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matrix3x3 m(A,B,C); |
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return(m.determinant()); |
| 361 |
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} |
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//! \brief Calculate the Graph Potentials of a molecule |
| 364 |
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//! |
| 365 |
|
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//! based on |
| 366 |
|
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//! V.E. and Rozenblit, A.B. Golender |
| 367 |
|
|
//! <em>Logical and Combinatorial Algorithms for Drug Design</em>. \n |
| 368 |
|
|
//! For an example see: |
| 369 |
|
|
//! Walters, W. P., Yalkowsky, S. H., \em JCICS, 1996, 36(5), 1015-1017. |
| 370 |
|
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//! <a href="http://dx.doi.org/10.1021/ci950278o">DOI: 10.1021/ci950278o</a> |
| 371 |
|
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void GraphPotentials(OBMol &mol, std::vector<double> &pot) |
| 372 |
|
|
{ |
| 373 |
|
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double det; |
| 374 |
|
|
|
| 375 |
|
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vector<vector<double> > g,c,h; |
| 376 |
|
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construct_g_matrix(mol,g); |
| 377 |
|
|
invert_matrix(g,det); |
| 378 |
|
|
construct_c_matrix(mol,c); |
| 379 |
|
|
mult_matrix(h,g,c); |
| 380 |
|
|
pot.resize(mol.NumAtoms()+1); |
| 381 |
|
|
|
| 382 |
|
|
for (unsigned int i = 0; i < mol.NumAtoms();i++) |
| 383 |
|
|
pot[i+1] = h[i][0]; |
| 384 |
|
|
} |
| 385 |
|
|
|
| 386 |
|
|
|
| 387 |
|
|
//! Construct the matrix G, which puts each atoms valence+1 |
| 388 |
|
|
//! on the diagonal and and -1 on the off diagonal if two |
| 389 |
|
|
//! atoms are connected. |
| 390 |
|
|
void construct_g_matrix(OBMol &mol, std::vector<std::vector<double> > &m) |
| 391 |
|
|
{ |
| 392 |
|
|
unsigned int i,j; |
| 393 |
|
|
|
| 394 |
|
|
OBAtom *atm1,*atm2; |
| 395 |
|
|
vector<OBNodeBase*>::iterator aint,bint; |
| 396 |
|
|
|
| 397 |
|
|
m.resize(mol.NumAtoms()); |
| 398 |
|
|
for (i = 0; i < m.size(); i++) |
| 399 |
|
|
m[i].resize(mol.NumAtoms()); |
| 400 |
|
|
|
| 401 |
|
|
for (atm1 = mol.BeginAtom(aint),i=0;atm1;atm1 = mol.NextAtom(aint),i++) |
| 402 |
|
|
for (atm2 = mol.BeginAtom(bint),j=0;atm2;atm2 = mol.NextAtom(bint),j++) |
| 403 |
|
|
{ |
| 404 |
|
|
if (i == j) |
| 405 |
|
|
{ |
| 406 |
|
|
m[i][j] = atm1->GetValence() + 1; |
| 407 |
|
|
m[i][j] += (double)atm1->GetAtomicNum()/10.0; |
| 408 |
|
|
m[i][j] += (double)atm1->GetHyb()/100.0; |
| 409 |
|
|
} |
| 410 |
|
|
else |
| 411 |
|
|
{ |
| 412 |
|
|
if (atm1->IsConnected(atm2)) |
| 413 |
|
|
m[i][j] = -1; |
| 414 |
|
|
else |
| 415 |
|
|
m[i][j] = 0; |
| 416 |
|
|
} |
| 417 |
|
|
} |
| 418 |
|
|
} |
| 419 |
|
|
|
| 420 |
|
|
//! Construct the matrix C, which is simply a column vector |
| 421 |
|
|
//! consisting of the valence for each atom |
| 422 |
|
|
void construct_c_matrix(OBMol &mol,std::vector<std::vector<double > > &m) |
| 423 |
|
|
{ |
| 424 |
|
|
unsigned int i; |
| 425 |
|
|
OBAtom *atm1; |
| 426 |
|
|
vector<OBNodeBase*>::iterator aint; |
| 427 |
|
|
|
| 428 |
|
|
m.resize(mol.NumAtoms()); |
| 429 |
|
|
for (i = 0; i < m.size(); i++) |
| 430 |
|
|
m[i].resize(1); |
| 431 |
|
|
for (atm1 = mol.BeginAtom(aint),i=0;atm1;atm1 = mol.NextAtom(aint),i++) |
| 432 |
|
|
{ |
| 433 |
|
|
m[i][0] = atm1->GetValence(); |
| 434 |
|
|
} |
| 435 |
|
|
} |
| 436 |
|
|
|
| 437 |
|
|
} // namespace OpenBabel |
| 438 |
|
|
|
| 439 |
|
|
//! \file chiral.cpp |
| 440 |
|
|
//! \brief Detect chiral atoms and molecules. |
