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/********************************************************************** |
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rotor.cpp - Rotate dihedral angles according to rotor rules. |
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|
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Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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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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|
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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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|
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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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|
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#include "mol.hpp" |
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#include "rotor.hpp" |
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#include "torlib.hpp" |
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|
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using namespace std; |
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namespace OpenBabel |
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{ |
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|
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#define OB_DEFAULT_DELTA 10.0 |
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static bool GetDFFVector(OBMol&,vector<int>&,OBBitVec&); |
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static bool CompareRotor(const pair<OBBond*,int>&,const pair<OBBond*,int>&); |
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|
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|
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//************************************** |
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//**** OBRotorList Member Functions **** |
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//************************************** |
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|
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bool OBRotorList::Setup(OBMol &mol) |
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{ |
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Clear(); |
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FindRotors(mol); |
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if (!Size()) |
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return(false); |
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|
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SetEvalAtoms(mol); |
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AssignTorVals(mol); |
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|
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OBRotor *rotor; |
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vector<OBRotor*>::iterator i; |
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for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i)) |
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if (!rotor->Size()) |
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{ |
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int ref[4]; |
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rotor->GetDihedralAtoms(ref); |
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char buffer[BUFF_SIZE]; |
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sprintf(buffer,"The rotor has no associated torsion values -> %d %d %d %d",ref[0],ref[1],ref[2],ref[3]); |
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|
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obErrorLog.ThrowError(__FUNCTION__, buffer, obDebug); |
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} |
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|
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return(true); |
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} |
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|
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bool OBRotorList::FindRotors(OBMol &mol) |
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{ |
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mol.FindRingAtomsAndBonds(); |
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vector<int> gtd; |
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mol.GetGTDVector(gtd); |
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|
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obErrorLog.ThrowError(__FUNCTION__, |
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"Ran OpenBabel::FindRotors", obAuditMsg); |
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|
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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vector<pair<OBBond*,int> > vtmp; |
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|
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int score; |
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for (bond = mol.BeginBond(i);bond;bond = mol.NextBond(i)) |
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if (bond->IsRotor()) |
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{ |
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if (HasFixedAtoms() && IsFixedBond(bond)) |
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continue; |
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score = gtd[bond->GetBeginAtomIdx()-1] + |
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gtd[bond->GetEndAtomIdx()-1]; |
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vtmp.push_back(pair<OBBond*,int> (bond,score)); |
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} |
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|
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sort(vtmp.begin(),vtmp.end(),CompareRotor); |
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|
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OBRotor *rotor; |
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int count; |
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vector<pair<OBBond*,int> >::iterator j; |
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for (j = vtmp.begin(),count=0;j != vtmp.end();j++,count++) |
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{ |
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rotor = new OBRotor; |
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rotor->SetBond((*j).first); |
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rotor->SetIdx(count); |
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rotor->SetNumCoords(mol.NumAtoms()*3); |
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_rotor.push_back(rotor); |
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} |
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|
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return(true); |
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} |
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|
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bool OBRotorList::IsFixedBond(OBBond *bond) |
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{ |
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OBAtom *a1,*a2,*a3; |
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vector<OBEdgeBase*>::iterator i; |
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|
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a1 = bond->GetBeginAtom(); |
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a2 = bond->GetEndAtom(); |
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if (!_fix[a1->GetIdx()] || !_fix[a2->GetIdx()]) |
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return(false); |
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|
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bool isfixed=false; |
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for (a3 = a1->BeginNbrAtom(i);a3;a3 = a1->NextNbrAtom(i)) |
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if (a3 != a2 && _fix[a3->GetIdx()]) |
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{ |
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isfixed = true; |
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break; |
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} |
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|
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if (!isfixed) |
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return(false); |
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|
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isfixed = false; |
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for (a3 = a2->BeginNbrAtom(i);a3;a3 = a2->NextNbrAtom(i)) |
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if (a3 != a1 && _fix[a3->GetIdx()]) |
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{ |
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isfixed = true; |
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break; |
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} |
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|
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return(isfixed); |
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} |
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|
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bool GetDFFVector(OBMol &mol,vector<int> &dffv,OBBitVec &bv) |
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{ |
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dffv.clear(); |
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dffv.resize(mol.NumAtoms()); |
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|
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int dffcount,natom; |
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OBBitVec used,curr,next; |
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OBAtom *atom,*atom1; |
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OBBond *bond; |
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vector<OBNodeBase*>::iterator i; |
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vector<OBEdgeBase*>::iterator j; |
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|
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next.Clear(); |
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|
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for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
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{ |
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if (bv[atom->GetIdx()]) |
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{ |
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dffv[atom->GetIdx()-1] = 0; |
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continue; |
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} |
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|
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dffcount = 0; |
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used.Clear(); |
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curr.Clear(); |
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used.SetBitOn(atom->GetIdx()); |
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curr.SetBitOn(atom->GetIdx()); |
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|
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while (!curr.IsEmpty() && (bv&curr).Empty()) |
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{ |
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next.Clear(); |
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for (natom = curr.NextBit(-1);natom != curr.EndBit();natom = curr.NextBit(natom)) |
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{ |
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atom1 = mol.GetAtom(natom); |
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for (bond = atom1->BeginBond(j);bond;bond = atom1->NextBond(j)) |
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if (!used.BitIsOn(bond->GetNbrAtomIdx(atom1)) && |
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!curr.BitIsOn(bond->GetNbrAtomIdx(atom1))) |
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if (!(bond->GetNbrAtom(atom1))->IsHydrogen()) |
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next.SetBitOn(bond->GetNbrAtomIdx(atom1)); |
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} |
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|
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used |= next; |
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curr = next; |
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dffcount++; |
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} |
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|
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dffv[atom->GetIdx()-1] = dffcount; |
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} |
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|
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return(true); |
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} |
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|
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|
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static double MinimumPairRMS(OBMol&,double*,double*,bool &); |
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|
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//! Rotates each bond to zero and 180 degrees and tests |
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//! if the 2 conformers are duplicates. if so - the symmetric torsion |
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//! values are removed from consideration during a search |
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void OBRotorList::RemoveSymVals(OBMol &mol) |
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{ |
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double *c,*c1,*c2; |
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c1 = new double [mol.NumAtoms()*3]; |
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c2 = new double [mol.NumAtoms()*3]; |
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c = mol.GetCoordinates(); |
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bool one2one; |
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double cutoff = 0.20; |
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|
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OBRotor *rotor; |
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vector<OBRotor*>::iterator i; |
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for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i)) |
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{ |
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//look for 2-fold symmetry about a bond |
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memcpy(c1,c,sizeof(double)*mol.NumAtoms()*3); |
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memcpy(c2,c,sizeof(double)*mol.NumAtoms()*3); |
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rotor->SetToAngle(c1,(double)(0.0*DEG_TO_RAD)); |
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rotor->SetToAngle(c2,(double)(180.0*DEG_TO_RAD)); |
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|
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if (MinimumPairRMS(mol,c1,c2,one2one) <cutoff && !one2one) |
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{ |
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rotor->RemoveSymTorsionValues(2); |
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OBBond *bond = rotor->GetBond(); |
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|
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if (!_quiet) |
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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 << "symmetry found = " << ' '; |
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errorMsg << bond->GetBeginAtomIdx() << ' ' << bond->GetEndAtomIdx() << ' ' ; |
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errorMsg << "rms = " << ' '; |
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errorMsg << MinimumPairRMS(mol,c1,c2,one2one) << endl; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obDebug); |
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} |
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continue; |
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} |
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|
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//look for 3-fold symmetry about a bond |
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memcpy(c1,c,sizeof(double)*mol.NumAtoms()*3); |
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memcpy(c2,c,sizeof(double)*mol.NumAtoms()*3); |
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rotor->SetToAngle(c1,(double)(0.0*DEG_TO_RAD)); |
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rotor->SetToAngle(c2,(double)(120.0*DEG_TO_RAD)); |
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|
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if (MinimumPairRMS(mol,c1,c2,one2one) <cutoff && !one2one) |
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{ |
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rotor->RemoveSymTorsionValues(3); |
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OBBond *bond = rotor->GetBond(); |
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|
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if (!_quiet) |
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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 << "3-fold symmetry found = " << ' '; |
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errorMsg << bond->GetBeginAtomIdx() << ' ' << bond->GetEndAtomIdx() << ' ' ; |
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errorMsg << "rms = " << ' '; |
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errorMsg << MinimumPairRMS(mol,c1,c2,one2one) << endl; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obDebug); |
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} |
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} |
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} |
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|
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delete [] c1; |
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delete [] c2; |
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|
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//pattern based duplicate removal |
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int ref[4]; |
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vector<vector<int> > mlist; |
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vector<vector<int> >::iterator k; |
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vector<pair<OBSmartsPattern*,pair<int,int> > >::iterator j; |
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for (j = _vsym2.begin();j != _vsym2.end();j++) |
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if (j->first->Match(mol)) |
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{ |
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mlist = j->first->GetUMapList(); |
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|
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for (k = mlist.begin();k != mlist.end();k++) |
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for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i)) |
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{ |
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rotor->GetDihedralAtoms(ref); |
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if (((*k)[j->second.first] == ref[1] && (*k)[j->second.second] == ref[2]) || |
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((*k)[j->second.first] == ref[2] && (*k)[j->second.second] == ref[1])) |
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{ |
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rotor->RemoveSymTorsionValues(2); |
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if (!_quiet) |
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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 |
289 |
errorMsg << "2-fold pattern-based symmetry found = " << ' '; |
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errorMsg << ref[1] << ' ' << ref[2] << endl; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obDebug); |
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} |
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} |
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} |
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} |
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|
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for (j = _vsym3.begin();j != _vsym3.end();j++) |
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if (j->first->Match(mol)) |
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{ |
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mlist = j->first->GetUMapList(); |
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|
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for (k = mlist.begin();k != mlist.end();k++) |
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for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i)) |
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{ |
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rotor->GetDihedralAtoms(ref); |
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if (((*k)[j->second.first] == ref[1] && (*k)[j->second.second] == ref[2]) || |
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((*k)[j->second.first] == ref[2] && (*k)[j->second.second] == ref[1])) |
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{ |
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rotor->RemoveSymTorsionValues(3); |
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if (!_quiet) |
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{ |
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#ifdef HAVE_SSTREAM |
313 |
stringstream errorMsg; |
314 |
#else |
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strstream errorMsg; |
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#endif |
317 |
errorMsg << "3-fold pattern-based symmetry found = " << ' '; |
318 |
errorMsg << ref[1] << ' ' << ref[2] << endl; |
319 |
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obDebug); |
320 |
} |
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} |
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} |
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} |
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} |
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|
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static double MinimumPairRMS(OBMol &mol,double *a,double *b,bool &one2one) |
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{ |
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int i,j,k=0; |
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double min,tmp,d_2 = 0.0; |
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OBBitVec bset; |
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one2one = true; |
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vector<OBNodeBase*> _atom; |
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_atom.resize(mol.NumAtoms()); |
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for (i = 0;i < (signed)mol.NumAtoms();i++) |
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_atom[i] = mol.GetAtom(i+1); |
336 |
|
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for (i = 0;i < (signed)mol.NumAtoms();i++) |
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{ |
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min = 10E10; |
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for (j = 0;j < (signed)mol.NumAtoms();j++) |
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if ((_atom[i])->GetAtomicNum() == (_atom[j])->GetAtomicNum() && |
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(_atom[i])->GetHyb() == (_atom[j])->GetHyb()) |
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if (!bset[j]) |
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{ |
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tmp = SQUARE(a[3*i]-b[3*j]) + |
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SQUARE(a[3*i+1]-b[3*j+1]) + |
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SQUARE(a[3*i+2]-b[3*j+2]); |
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if (tmp < min) |
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{ |
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k = j; |
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min = tmp; |
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} |
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} |
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|
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if (i != j) |
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one2one = false; |
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bset.SetBitOn(k); |
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d_2 += min; |
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} |
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|
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d_2 /= (double)mol.NumAtoms(); |
362 |
|
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return(sqrt(d_2)); |
364 |
} |
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|
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//! Determines which atoms the internal energy should be calculated |
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//! if a the dihedral angle of the rotor is modified |
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bool OBRotorList::SetEvalAtoms(OBMol &mol) |
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{ |
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int j; |
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OBBond *bond; |
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OBAtom *a1,*a2; |
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OBRotor *rotor; |
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vector<OBRotor*>::iterator i; |
375 |
OBBitVec eval,curr,next; |
376 |
vector<OBEdgeBase*>::iterator k; |
377 |
|
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for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i)) |
379 |
{ |
380 |
bond = rotor->GetBond(); |
381 |
curr.Clear(); |
382 |
eval.Clear(); |
383 |
curr.SetBitOn(bond->GetBeginAtomIdx()); |
384 |
curr.SetBitOn(bond->GetEndAtomIdx()); |
385 |
eval |= curr; |
386 |
|
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//follow all non-rotor bonds and add atoms to eval list |
388 |
for (;!curr.Empty();) |
389 |
{ |
390 |
next.Clear(); |
391 |
for (j = curr.NextBit(0);j != curr.EndBit();j = curr.NextBit(j)) |
392 |
{ |
393 |
a1 = mol.GetAtom(j); |
394 |
for (a2 = a1->BeginNbrAtom(k);a2;a2 = a1->NextNbrAtom(k)) |
395 |
if (!eval[a2->GetIdx()]) |
396 |
if (!((OBBond*)*k)->IsRotor()||(HasFixedAtoms()&&IsFixedBond((OBBond*)*k))) |
397 |
{ |
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next.SetBitOn(a2->GetIdx()); |
399 |
eval.SetBitOn(a2->GetIdx()); |
400 |
} |
401 |
} |
402 |
curr = next; |
403 |
} |
404 |
|
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//add atoms alpha to eval list |
406 |
next.Clear(); |
407 |
for (j = eval.NextBit(0);j != eval.EndBit();j = eval.NextBit(j)) |
408 |
{ |
409 |
a1 = mol.GetAtom(j); |
410 |
for (a2 = a1->BeginNbrAtom(k);a2;a2 = a1->NextNbrAtom(k)) |
411 |
next.SetBitOn(a2->GetIdx()); |
412 |
} |
413 |
eval |= next; |
414 |
rotor->SetEvalAtoms(eval); |
415 |
} |
416 |
|
417 |
return(true); |
418 |
} |
419 |
|
420 |
bool OBRotorList::AssignTorVals(OBMol &mol) |
421 |
{ |
422 |
OBBond *bond; |
423 |
OBRotor *rotor; |
424 |
vector<OBRotor*>::iterator i; |
425 |
|
426 |
int ref[4]; |
427 |
double delta; |
428 |
vector<double> res; |
429 |
vector<int> itmp1; |
430 |
vector<int>::iterator j; |
431 |
for (i = _rotor.begin();i != _rotor.end();i++) |
432 |
{ |
433 |
rotor=*i; |
434 |
bond = rotor->GetBond(); |
435 |
_rr.GetRotorIncrements(mol,bond,ref,res,delta); |
436 |
rotor->SetTorsionValues(res); |
437 |
rotor->SetDelta(delta); |
438 |
|
439 |
mol.FindChildren(itmp1,ref[1],ref[2]); |
440 |
if (itmp1.size()+1 > mol.NumAtoms()/2) |
441 |
{ |
442 |
itmp1.clear(); |
443 |
mol.FindChildren(itmp1,ref[2],ref[1]); |
444 |
swap(ref[0],ref[3]); |
445 |
swap(ref[1],ref[2]); |
446 |
} |
447 |
|
448 |
for (j = itmp1.begin();j != itmp1.end();j++) |
449 |
*j = ((*j)-1)*3; |
450 |
rotor->SetRotAtoms(itmp1); |
451 |
rotor->SetDihedralAtoms(ref); |
452 |
} |
453 |
|
454 |
return(true); |
455 |
} |
456 |
|
457 |
bool OBRotorList::SetRotAtoms(OBMol &mol) |
458 |
{ |
459 |
OBRotor *rotor; |
460 |
vector<int> rotatoms,dihed; |
461 |
vector<OBRotor*>::iterator i; |
462 |
|
463 |
int ref[4]; |
464 |
vector<int>::iterator j; |
465 |
for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i)) |
466 |
{ |
467 |
dihed = rotor->GetDihedralAtoms(); |
468 |
ref[0] = dihed[0]/3+1; |
469 |
ref[1] = dihed[1]/3+1; |
470 |
ref[2] = dihed[2]/3+1; |
471 |
ref[3] = dihed[3]/3+1; |
472 |
|
473 |
mol.FindChildren(rotatoms,ref[1],ref[2]); |
474 |
if (rotatoms.size()+1 > mol.NumAtoms()/2) |
475 |
{ |
476 |
rotatoms.clear(); |
477 |
mol.FindChildren(rotatoms,ref[2],ref[1]); |
478 |
swap(ref[0],ref[3]); |
479 |
swap(ref[1],ref[2]); |
480 |
} |
481 |
|
482 |
for (j = rotatoms.begin();j != rotatoms.end();j++) |
483 |
*j = ((*j)-1)*3; |
484 |
rotor->SetRotAtoms(rotatoms); |
485 |
rotor->SetDihedralAtoms(ref); |
486 |
} |
487 |
|
488 |
return(true); |
489 |
} |
490 |
|
491 |
void OBRotorList::SetRotAtomsByFix(OBMol &mol) |
492 |
{ |
493 |
int ref[4]; |
494 |
OBRotor *rotor; |
495 |
vector<int> rotatoms,dihed; |
496 |
vector<int>::iterator j; |
497 |
vector<OBRotor*>::iterator i; |
498 |
|
499 |
GetDFFVector(mol,_dffv,_fix); |
500 |
|
501 |
for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i)) |
502 |
{ |
503 |
rotatoms.clear(); |
504 |
dihed = rotor->GetDihedralAtoms(); |
505 |
ref[0] = dihed[0]/3+1; |
506 |
ref[1] = dihed[1]/3+1; |
507 |
ref[2] = dihed[2]/3+1; |
508 |
ref[3] = dihed[3]/3+1; |
509 |
|
510 |
if (_fix[ref[1]] && _fix[ref[2]]) |
511 |
{ |
512 |
if (!_fix[ref[0]]) |
513 |
{ |
514 |
swap(ref[0],ref[3]); |
515 |
swap(ref[1],ref[2]); |
516 |
mol.FindChildren(rotatoms,ref[1],ref[2]); |
517 |
for (j = rotatoms.begin();j != rotatoms.end();j++) |
518 |
*j = ((*j)-1)*3; |
519 |
rotor->SetRotAtoms(rotatoms); |
520 |
rotor->SetDihedralAtoms(ref); |
521 |
} |
522 |
} |
523 |
else |
524 |
if (_dffv[ref[1]-1] > _dffv[ref[2]-1]) |
525 |
{ |
526 |
swap(ref[0],ref[3]); |
527 |
swap(ref[1],ref[2]); |
528 |
mol.FindChildren(rotatoms,ref[1],ref[2]); |
529 |
for (j = rotatoms.begin();j != rotatoms.end();j++) |
530 |
*j = ((*j)-1)*3; |
531 |
rotor->SetRotAtoms(rotatoms); |
532 |
rotor->SetDihedralAtoms(ref); |
533 |
} |
534 |
} |
535 |
} |
536 |
|
537 |
OBRotorList::OBRotorList() |
538 |
{ |
539 |
_rotor.clear(); |
540 |
_quiet=false; |
541 |
_removesym=true; |
542 |
|
543 |
//para-disub benzene |
544 |
OBSmartsPattern *sp; |
545 |
sp = new OBSmartsPattern; |
546 |
sp->Init("*c1[cD2][cD2]c(*)[cD2][cD2]1"); |
547 |
_vsym2.push_back(pair<OBSmartsPattern*,pair<int,int> > (sp,pair<int,int> (0,1))); |
548 |
|
549 |
//piperidine amide |
550 |
sp = new OBSmartsPattern; |
551 |
sp->Init("O=CN1[CD2][CD2][CD2][CD2][CD2]1"); |
552 |
_vsym2.push_back(pair<OBSmartsPattern*,pair<int,int> > (sp,pair<int,int> (1,2))); |
553 |
|
554 |
//terminal phosphate |
555 |
sp = new OBSmartsPattern; |
556 |
sp->Init("[#8D2][#15,#16](~[#8D1])(~[#8D1])~[#8D1]"); |
557 |
_vsym3.push_back(pair<OBSmartsPattern*,pair<int,int> > (sp,pair<int,int> (0,1))); |
558 |
|
559 |
} |
560 |
|
561 |
OBRotorList::~OBRotorList() |
562 |
{ |
563 |
vector<OBRotor*>::iterator i; |
564 |
for (i = _rotor.begin();i != _rotor.end();i++) |
565 |
delete *i; |
566 |
|
567 |
vector<pair<OBSmartsPattern*,pair<int,int> > >::iterator j; |
568 |
for (j = _vsym2.begin();j != _vsym2.end();j++) |
569 |
delete j->first; |
570 |
|
571 |
for (j = _vsym3.begin();j != _vsym3.end();j++) |
572 |
delete j->first; |
573 |
} |
574 |
|
575 |
void OBRotorList::Clear() |
576 |
{ |
577 |
vector<OBRotor*>::iterator i; |
578 |
for (i = _rotor.begin();i != _rotor.end();i++) |
579 |
delete *i; |
580 |
_rotor.clear(); |
581 |
_fix.Clear(); |
582 |
} |
583 |
|
584 |
bool CompareRotor(const pair<OBBond*,int> &a,const pair<OBBond*,int> &b) |
585 |
{ |
586 |
//return(a.second > b.second); //outside->in |
587 |
return(a.second < b.second); //inside->out |
588 |
} |
589 |
|
590 |
//********************************** |
591 |
//**** OBRotor Member Functions **** |
592 |
//********************************** |
593 |
|
594 |
OBRotor::OBRotor() |
595 |
{ |
596 |
_delta = 10.0; |
597 |
_rotatoms = NULL; |
598 |
} |
599 |
|
600 |
double OBRotor::CalcTorsion(double *c) |
601 |
{ |
602 |
double v1x,v1y,v1z,v2x,v2y,v2z,v3x,v3y,v3z; |
603 |
double c1x,c1y,c1z,c2x,c2y,c2z,c3x,c3y,c3z; |
604 |
double c1mag,c2mag,ang,costheta; |
605 |
|
606 |
// |
607 |
//calculate the torsion angle |
608 |
// |
609 |
v1x = c[_torsion[0]] - c[_torsion[1]]; |
610 |
v1y = c[_torsion[0]+1] - c[_torsion[1]+1]; |
611 |
v1z = c[_torsion[0]+2] - c[_torsion[1]+2]; |
612 |
v2x = c[_torsion[1]] - c[_torsion[2]]; |
613 |
v2y = c[_torsion[1]+1] - c[_torsion[2]+1]; |
614 |
v2z = c[_torsion[1]+2] - c[_torsion[2]+2]; |
615 |
v3x = c[_torsion[2]] - c[_torsion[3]]; |
616 |
v3y = c[_torsion[2]+1] - c[_torsion[3]+1]; |
617 |
v3z = c[_torsion[2]+2] - c[_torsion[3]+2]; |
618 |
|
619 |
c1x = v1y*v2z - v1z*v2y; |
620 |
c2x = v2y*v3z - v2z*v3y; |
621 |
c1y = -v1x*v2z + v1z*v2x; |
622 |
c2y = -v2x*v3z + v2z*v3x; |
623 |
c1z = v1x*v2y - v1y*v2x; |
624 |
c2z = v2x*v3y - v2y*v3x; |
625 |
c3x = c1y*c2z - c1z*c2y; |
626 |
c3y = -c1x*c2z + c1z*c2x; |
627 |
c3z = c1x*c2y - c1y*c2x; |
628 |
|
629 |
c1mag = SQUARE(c1x)+SQUARE(c1y)+SQUARE(c1z); |
630 |
c2mag = SQUARE(c2x)+SQUARE(c2y)+SQUARE(c2z); |
631 |
if (c1mag*c2mag < 0.01) |
632 |
costheta = 1.0; //avoid div by zero error |
633 |
else |
634 |
costheta = (c1x*c2x + c1y*c2y + c1z*c2z)/(sqrt(c1mag*c2mag)); |
635 |
|
636 |
if (costheta < -0.9999999) |
637 |
costheta = -0.9999999; |
638 |
if (costheta > 0.9999999) |
639 |
costheta = 0.9999999; |
640 |
|
641 |
if ((v2x*c3x + v2y*c3y + v2z*c3z) > 0.0) |
642 |
ang = -acos(costheta); |
643 |
else |
644 |
ang = acos(costheta); |
645 |
|
646 |
return(ang); |
647 |
} |
648 |
|
649 |
double OBRotor::CalcBondLength(double *c) |
650 |
{ |
651 |
double dx,dy,dz; |
652 |
|
653 |
dx = c[_torsion[1]] - c[_torsion[2]]; |
654 |
dy = c[_torsion[1]+1] - c[_torsion[2]+1]; |
655 |
dz = c[_torsion[1]+2] - c[_torsion[2]+2]; |
656 |
return(sqrt(SQUARE(dx)+SQUARE(dy)+SQUARE(dz))); |
657 |
} |
658 |
|
659 |
void OBRotor::Precalc(vector<double*> &cv) |
660 |
{ |
661 |
double *c,ang; |
662 |
vector<double*>::iterator i; |
663 |
vector<double>::iterator j; |
664 |
vector<double> cs,sn,t; |
665 |
for (i = cv.begin();i != cv.end();i++) |
666 |
{ |
667 |
c = *i; |
668 |
cs.clear(); |
669 |
sn.clear(); |
670 |
t.clear(); |
671 |
ang = CalcTorsion(c); |
672 |
|
673 |
for (j = _res.begin();j != _res.end();j++) |
674 |
{ |
675 |
cs.push_back(cos(*j-ang)); |
676 |
sn.push_back(sin(*j-ang)); |
677 |
t.push_back(1 - cos(*j-ang)); |
678 |
} |
679 |
|
680 |
_cs.push_back(cs); |
681 |
_sn.push_back(sn); |
682 |
_t.push_back(t); |
683 |
_invmag.push_back(1.0/CalcBondLength(c)); |
684 |
} |
685 |
} |
686 |
|
687 |
|
688 |
void OBRotor::SetRotor(double *c,int idx,int prev) |
689 |
{ |
690 |
double ang,sn,cs,t,dx,dy,dz,mag; |
691 |
|
692 |
if (prev == -1) |
693 |
ang = _res[idx] - CalcTorsion(c); |
694 |
else |
695 |
ang = _res[idx] - _res[prev]; |
696 |
|
697 |
sn = sin(ang); |
698 |
cs = cos(ang); |
699 |
t = 1 - cs; |
700 |
|
701 |
dx = c[_torsion[1]] - c[_torsion[2]]; |
702 |
dy = c[_torsion[1]+1] - c[_torsion[2]+1]; |
703 |
dz = c[_torsion[1]+2] - c[_torsion[2]+2]; |
704 |
mag = sqrt(SQUARE(dx) + SQUARE(dy) + SQUARE(dz)); |
705 |
|
706 |
Set(c,sn,cs,t,1.0/mag); |
707 |
} |
708 |
|
709 |
void OBRotor::Precompute(double *c) |
710 |
{ |
711 |
double dx,dy,dz; |
712 |
dx = c[_torsion[1]] - c[_torsion[2]]; |
713 |
dy = c[_torsion[1]+1] - c[_torsion[2]+1]; |
714 |
dz = c[_torsion[1]+2] - c[_torsion[2]+2]; |
715 |
_imag = 1.0/sqrt(SQUARE(dx) + SQUARE(dy) + SQUARE(dz)); |
716 |
|
717 |
_refang = CalcTorsion(c); |
718 |
} |
719 |
|
720 |
void OBRotor::Set(double *c,int idx) |
721 |
{ |
722 |
double ang,sn,cs,t; |
723 |
|
724 |
ang = _res[idx] - _refang; |
725 |
sn = sin(ang); |
726 |
cs = cos(ang); |
727 |
t = 1-cs; |
728 |
|
729 |
double x,y,z,tx,ty,tz,m[9]; |
730 |
|
731 |
x = c[_torsion[1]] - c[_torsion[2]]; |
732 |
y = c[_torsion[1]+1] - c[_torsion[2]+1]; |
733 |
z = c[_torsion[1]+2] - c[_torsion[2]+2]; |
734 |
|
735 |
x *= _imag; |
736 |
y *= _imag; |
737 |
z *= _imag; //normalize the rotation vector |
738 |
|
739 |
//set up the rotation matrix |
740 |
tx = t*x; |
741 |
ty = t*y; |
742 |
tz = t*z; |
743 |
m[0]= tx*x + cs; |
744 |
m[1] = tx*y + sn*z; |
745 |
m[2] = tx*z - sn*y; |
746 |
m[3] = tx*y - sn*z; |
747 |
m[4] = ty*y + cs; |
748 |
m[5] = ty*z + sn*x; |
749 |
m[6] = tx*z + sn*y; |
750 |
m[7] = ty*z - sn*x; |
751 |
m[8] = tz*z + cs; |
752 |
|
753 |
// |
754 |
//now the matrix is set - time to rotate the atoms |
755 |
// |
756 |
tx = c[_torsion[1]]; |
757 |
ty = c[_torsion[1]+1]; |
758 |
tz = c[_torsion[1]+2]; |
759 |
int i,j; |
760 |
for (i = 0;i < _size;i++) |
761 |
{ |
762 |
j = _rotatoms[i]; |
763 |
c[j] -= tx; |
764 |
c[j+1] -= ty; |
765 |
c[j+2]-= tz; |
766 |
x = c[j]*m[0] + c[j+1]*m[1] + c[j+2]*m[2]; |
767 |
y = c[j]*m[3] + c[j+1]*m[4] + c[j+2]*m[5]; |
768 |
z = c[j]*m[6] + c[j+1]*m[7] + c[j+2]*m[8]; |
769 |
c[j] = x+tx; |
770 |
c[j+1] = y+ty; |
771 |
c[j+2] = z+tz; |
772 |
} |
773 |
} |
774 |
|
775 |
void OBRotor::Set(double *c,double sn,double cs,double t,double invmag) |
776 |
{ |
777 |
double x,y,z,tx,ty,tz,m[9]; |
778 |
|
779 |
x = c[_torsion[1]] - c[_torsion[2]]; |
780 |
y = c[_torsion[1]+1] - c[_torsion[2]+1]; |
781 |
z = c[_torsion[1]+2] - c[_torsion[2]+2]; |
782 |
|
783 |
//normalize the rotation vector |
784 |
|
785 |
x *= invmag; |
786 |
y *= invmag; |
787 |
z *= invmag; |
788 |
|
789 |
//set up the rotation matrix |
790 |
tx = t*x; |
791 |
ty = t*y; |
792 |
tz = t*z; |
793 |
m[0]= tx*x + cs; |
794 |
m[1] = tx*y + sn*z; |
795 |
m[2] = tx*z - sn*y; |
796 |
m[3] = tx*y - sn*z; |
797 |
m[4] = ty*y + cs; |
798 |
m[5] = ty*z + sn*x; |
799 |
m[6] = tx*z + sn*y; |
800 |
m[7] = ty*z - sn*x; |
801 |
m[8] = tz*z + cs; |
802 |
|
803 |
// |
804 |
//now the matrix is set - time to rotate the atoms |
805 |
// |
806 |
tx = c[_torsion[1]]; |
807 |
ty = c[_torsion[1]+1]; |
808 |
tz = c[_torsion[1]+2]; |
809 |
int i,j; |
810 |
for (i = 0;i < _size;i++) |
811 |
{ |
812 |
j = _rotatoms[i]; |
813 |
c[j] -= tx; |
814 |
c[j+1] -= ty; |
815 |
c[j+2]-= tz; |
816 |
x = c[j]*m[0] + c[j+1]*m[1] + c[j+2]*m[2]; |
817 |
y = c[j]*m[3] + c[j+1]*m[4] + c[j+2]*m[5]; |
818 |
z = c[j]*m[6] + c[j+1]*m[7] + c[j+2]*m[8]; |
819 |
c[j] = x+tx; |
820 |
c[j+1] = y+ty; |
821 |
c[j+2] = z+tz; |
822 |
} |
823 |
} |
824 |
|
825 |
void OBRotor::RemoveSymTorsionValues(int fold) |
826 |
{ |
827 |
vector<double>::iterator i; |
828 |
vector<double> tv; |
829 |
if (_res.size() == 1) |
830 |
return; |
831 |
|
832 |
for (i = _res.begin();i != _res.end();i++) |
833 |
if (*i >= 0.0) |
834 |
{ |
835 |
if (fold == 2 && *i < DEG_TO_RAD*180.0) |
836 |
tv.push_back(*i); |
837 |
if (fold == 3 && *i < DEG_TO_RAD*120.0) |
838 |
tv.push_back(*i); |
839 |
} |
840 |
|
841 |
if (tv.empty()) |
842 |
return; |
843 |
_res = tv; |
844 |
} |
845 |
|
846 |
void OBRotor::SetDihedralAtoms(int ref[4]) |
847 |
{ |
848 |
for (int i = 0;i < 4;i++) |
849 |
_ref[i] = ref[i]; |
850 |
_torsion.resize(4); |
851 |
_torsion[0] = (ref[0]-1)*3; |
852 |
_torsion[1] = (ref[1]-1)*3; |
853 |
_torsion[2] = (ref[2]-1)*3; |
854 |
_torsion[3] = (ref[3]-1)*3; |
855 |
} |
856 |
|
857 |
void OBRotor::SetRotAtoms(vector<int> &vi) |
858 |
{ |
859 |
if (_rotatoms) |
860 |
delete [] _rotatoms; |
861 |
_rotatoms = new int [vi.size()]; |
862 |
copy(vi.begin(),vi.end(),_rotatoms); |
863 |
_size = vi.size(); |
864 |
} |
865 |
|
866 |
//*************************************** |
867 |
//**** OBRotorRules Member functions **** |
868 |
//*************************************** |
869 |
OBRotorRules::OBRotorRules() |
870 |
{ |
871 |
_quiet=false; |
872 |
_init = false; |
873 |
_dir = BABEL_DATADIR; |
874 |
_envvar = "BABEL_DATADIR"; |
875 |
_filename = "torlib.txt"; |
876 |
_subdir = "data"; |
877 |
_dataptr = TorsionDefaults; |
878 |
} |
879 |
|
880 |
void OBRotorRules::ParseLine(const char *buffer) |
881 |
{ |
882 |
int i; |
883 |
int ref[4]; |
884 |
double delta; |
885 |
vector<double> vals; |
886 |
vector<string> vs; |
887 |
vector<string>::iterator j; |
888 |
char temp_buffer[BUFF_SIZE]; |
889 |
|
890 |
if (buffer[0] == '#') |
891 |
return; |
892 |
tokenize(vs,buffer); |
893 |
if (vs.empty()) |
894 |
return; |
895 |
|
896 |
if (EQn(buffer,"SP3-SP3",7)) |
897 |
{ |
898 |
_sp3sp3.clear(); |
899 |
for (j = vs.begin(),j++;j != vs.end();j++) |
900 |
_sp3sp3.push_back(DEG_TO_RAD*atof(j->c_str())); |
901 |
return; |
902 |
} |
903 |
|
904 |
if (EQn(buffer,"SP3-SP2",7)) |
905 |
{ |
906 |
_sp3sp2.clear(); |
907 |
for (j = vs.begin(),j++;j != vs.end();j++) |
908 |
_sp3sp2.push_back(DEG_TO_RAD*atof(j->c_str())); |
909 |
return; |
910 |
} |
911 |
|
912 |
if (EQn(buffer,"SP2-SP2",7)) |
913 |
{ |
914 |
_sp2sp2.clear(); |
915 |
for (j = vs.begin(),j++;j != vs.end();j++) |
916 |
_sp2sp2.push_back(DEG_TO_RAD*atof(j->c_str())); |
917 |
return; |
918 |
} |
919 |
|
920 |
if (!vs.empty() && vs.size() > 5) |
921 |
{ |
922 |
strcpy(temp_buffer,vs[0].c_str()); |
923 |
//reference atoms |
924 |
for (i = 0;i < 4;i++) |
925 |
ref[i] = atoi(vs[i+1].c_str())-1; |
926 |
//possible torsions |
927 |
vals.clear(); |
928 |
delta = OB_DEFAULT_DELTA; |
929 |
for (i = 5;(unsigned)i < vs.size();i++) |
930 |
{ |
931 |
if (i == (signed)(vs.size()-2) && vs[i] == "Delta") |
932 |
{ |
933 |
delta = atof(vs[i+1].c_str()); |
934 |
i += 2; |
935 |
} |
936 |
else |
937 |
vals.push_back(DEG_TO_RAD*atof(vs[i].c_str())); |
938 |
} |
939 |
|
940 |
if (vals.empty()) |
941 |
{ |
942 |
string err = "The following rule has no associated torsions: "; |
943 |
err += vs[0]; |
944 |
obErrorLog.ThrowError(__FUNCTION__, err, obDebug); |
945 |
} |
946 |
OBRotorRule *rr = new OBRotorRule (temp_buffer,ref,vals,delta); |
947 |
if (rr->IsValid()) |
948 |
_vr.push_back(rr); |
949 |
else |
950 |
delete rr; |
951 |
} |
952 |
|
953 |
} |
954 |
|
955 |
void OBRotorRules::GetRotorIncrements(OBMol &mol,OBBond *bond, |
956 |
int ref[4],vector<double> &vals,double &delta) |
957 |
{ |
958 |
vals.clear(); |
959 |
vector<pair<int,int> > vpr; |
960 |
vpr.push_back(pair<int,int> (0,bond->GetBeginAtomIdx())); |
961 |
vpr.push_back(pair<int,int> (0,bond->GetEndAtomIdx())); |
962 |
|
963 |
delta = OB_DEFAULT_DELTA; |
964 |
|
965 |
int j; |
966 |
OBSmartsPattern *sp; |
967 |
vector<vector<int> > map; |
968 |
vector<OBRotorRule*>::iterator i; |
969 |
for (i = _vr.begin();i != _vr.end();i++) |
970 |
{ |
971 |
sp = (*i)->GetSmartsPattern(); |
972 |
(*i)->GetReferenceAtoms(ref); |
973 |
vpr[0].first = ref[1]; |
974 |
vpr[1].first = ref[2]; |
975 |
|
976 |
if (!sp->RestrictedMatch(mol,vpr,true)) |
977 |
{ |
978 |
swap(vpr[0].first,vpr[1].first); |
979 |
if (!sp->RestrictedMatch(mol,vpr,true)) |
980 |
continue; |
981 |
} |
982 |
|
983 |
map = sp->GetMapList(); |
984 |
for (j = 0;j < 4;j++) |
985 |
ref[j] = map[0][ref[j]]; |
986 |
vals = (*i)->GetTorsionVals(); |
987 |
delta = (*i)->GetDelta(); |
988 |
|
989 |
OBAtom *a1,*a2,*a3,*a4,*r; |
990 |
a1 = mol.GetAtom(ref[0]); |
991 |
a4 = mol.GetAtom(ref[3]); |
992 |
if (a1->IsHydrogen() && a4->IsHydrogen()) |
993 |
continue; //don't allow hydrogens at both ends |
994 |
if (a1->IsHydrogen() || a4->IsHydrogen()) //need a heavy atom reference - can use hydrogen |
995 |
{ |
996 |
bool swapped = false; |
997 |
a2 = mol.GetAtom(ref[1]); |
998 |
a3 = mol.GetAtom(ref[2]); |
999 |
if (a4->IsHydrogen()) |
1000 |
{ |
1001 |
swap(a1,a4); |
1002 |
swap(a2,a3); |
1003 |
swapped = true; |
1004 |
} |
1005 |
|
1006 |
vector<OBEdgeBase*>::iterator k; |
1007 |
for (r = a2->BeginNbrAtom(k);r;r = a2->NextNbrAtom(k)) |
1008 |
if (!r->IsHydrogen() && r != a3) |
1009 |
break; |
1010 |
|
1011 |
if (!r) |
1012 |
continue; //unable to find reference heavy atom |
1013 |
// cerr << "r = " << r->GetIdx() << endl; |
1014 |
|
1015 |
double t1 = mol.GetTorsion(a1,a2,a3,a4); |
1016 |
double t2 = mol.GetTorsion(r,a2,a3,a4); |
1017 |
double diff = t2 - t1; |
1018 |
if (diff > 180.0) |
1019 |
diff -= 360.0; |
1020 |
if (diff < -180.0) |
1021 |
diff += 360.0; |
1022 |
diff *= DEG_TO_RAD; |
1023 |
|
1024 |
vector<double>::iterator m; |
1025 |
for (m = vals.begin();m != vals.end();m++) |
1026 |
{ |
1027 |
*m += diff; |
1028 |
if (*m < PI) |
1029 |
*m += 2.0*PI; |
1030 |
if (*m > PI) |
1031 |
*m -= 2.0*PI; |
1032 |
} |
1033 |
|
1034 |
if (swapped) |
1035 |
ref[3] = r->GetIdx(); |
1036 |
else |
1037 |
ref[0] = r->GetIdx(); |
1038 |
|
1039 |
/* |
1040 |
mol.SetTorsion(r,a2,a3,a4,vals[0]); |
1041 |
cerr << "test = " << (vals[0]-diff)*RAD_TO_DEG << ' '; |
1042 |
cerr << mol.GetTorsion(a1,a2,a3,a4) << ' '; |
1043 |
cerr << mol.GetTorsion(r,a2,a3,a4) << endl; |
1044 |
*/ |
1045 |
} |
1046 |
|
1047 |
char buffer[BUFF_SIZE]; |
1048 |
if (!_quiet) |
1049 |
{ |
1050 |
sprintf(buffer,"%3d%3d%3d%3d %s", |
1051 |
ref[0],ref[1],ref[2],ref[3], |
1052 |
((*i)->GetSmartsString()).c_str()); |
1053 |
obErrorLog.ThrowError(__FUNCTION__, buffer, obDebug); |
1054 |
} |
1055 |
return; |
1056 |
} |
1057 |
|
1058 |
//***didn't match any rules - assign based on hybridization*** |
1059 |
OBAtom *a1,*a2,*a3,*a4; |
1060 |
a2 = bond->GetBeginAtom(); |
1061 |
a3 = bond->GetEndAtom(); |
1062 |
vector<OBEdgeBase*>::iterator k; |
1063 |
|
1064 |
for (a1 = a2->BeginNbrAtom(k);a1;a1 = a2->NextNbrAtom(k)) |
1065 |
if (!a1->IsHydrogen() && a1 != a3) |
1066 |
break; |
1067 |
for (a4 = a3->BeginNbrAtom(k);a4;a4 = a3->NextNbrAtom(k)) |
1068 |
if (!a4->IsHydrogen() && a4 != a2) |
1069 |
break; |
1070 |
|
1071 |
ref[0] = a1->GetIdx(); |
1072 |
ref[1] = a2->GetIdx(); |
1073 |
ref[2] = a3->GetIdx(); |
1074 |
ref[3] = a4->GetIdx(); |
1075 |
|
1076 |
if (a2->GetHyb() == 3 && a3->GetHyb() == 3) //sp3-sp3 |
1077 |
{ |
1078 |
vals = _sp3sp3; |
1079 |
|
1080 |
if (!_quiet) |
1081 |
{ |
1082 |
char buffer[BUFF_SIZE]; |
1083 |
sprintf(buffer,"%3d%3d%3d%3d %s", |
1084 |
ref[0],ref[1],ref[2],ref[3],"sp3-sp3"); |
1085 |
obErrorLog.ThrowError(__FUNCTION__, buffer, obDebug); |
1086 |
} |
1087 |
} |
1088 |
else |
1089 |
if (a2->GetHyb() == 2 && a3->GetHyb() == 2) //sp2-sp2 |
1090 |
{ |
1091 |
vals = _sp2sp2; |
1092 |
|
1093 |
if (!_quiet) |
1094 |
{ |
1095 |
char buffer[BUFF_SIZE]; |
1096 |
sprintf(buffer,"%3d%3d%3d%3d %s", |
1097 |
ref[0],ref[1],ref[2],ref[3],"sp2-sp2"); |
1098 |
obErrorLog.ThrowError(__FUNCTION__, buffer, obDebug); |
1099 |
} |
1100 |
} |
1101 |
else //must be sp2-sp3 |
1102 |
{ |
1103 |
vals = _sp3sp2; |
1104 |
|
1105 |
if (!_quiet) |
1106 |
{ |
1107 |
char buffer[BUFF_SIZE]; |
1108 |
sprintf(buffer,"%3d%3d%3d%3d %s", |
1109 |
ref[0],ref[1],ref[2],ref[3],"sp2-sp3"); |
1110 |
obErrorLog.ThrowError(__FUNCTION__, buffer, obDebug); |
1111 |
} |
1112 |
} |
1113 |
} |
1114 |
|
1115 |
OBRotorRules::~OBRotorRules() |
1116 |
{ |
1117 |
vector<OBRotorRule*>::iterator i; |
1118 |
for (i = _vr.begin();i != _vr.end();i++) |
1119 |
delete (*i); |
1120 |
} |
1121 |
|
1122 |
#undef OB_DEFAULT_DELTA |
1123 |
} |
1124 |
|
1125 |
//! \file rotor.cpp |
1126 |
//! \brief Rotate dihedral angles according to rotor rules. |