src/openbabel/rotor.cpp

/**********************************************************************
rotor.cpp - Rotate dihedral angles according to rotor rules.
 
Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#include "mol.hpp"
#include "rotor.hpp"
#include "torlib.hpp"

using namespace std;
namespace OpenBabel
{

#define OB_DEFAULT_DELTA 10.0
static bool GetDFFVector(OBMol&,vector<int>&,OBBitVec&);
static bool CompareRotor(const pair<OBBond*,int>&,const pair<OBBond*,int>&);


//**************************************
//**** OBRotorList Member Functions ****
//**************************************

bool OBRotorList::Setup(OBMol &mol)
{
    Clear();
    FindRotors(mol);
    if (!Size())
        return(false);

    SetEvalAtoms(mol);
    AssignTorVals(mol);

    OBRotor *rotor;
    vector<OBRotor*>::iterator i;
    for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i))
        if (!rotor->Size())
        {
            int ref[4];
            rotor->GetDihedralAtoms(ref);
            char buffer[BUFF_SIZE];
            sprintf(buffer,"The rotor has no associated torsion values -> %d %d %d %d",ref[0],ref[1],ref[2],ref[3]);

            obErrorLog.ThrowError(__func__, buffer, obDebug);
        }

    return(true);
}

bool OBRotorList::FindRotors(OBMol &mol)
{
    mol.FindRingAtomsAndBonds();
    vector<int> gtd;
    mol.GetGTDVector(gtd);

    obErrorLog.ThrowError(__func__,
                          "Ran OpenBabel::FindRotors", obAuditMsg);

    OBBond *bond;
    vector<OBEdgeBase*>::iterator i;
    vector<pair<OBBond*,int> > vtmp;

    int score;
    for (bond = mol.BeginBond(i);bond;bond = mol.NextBond(i))
        if (bond->IsRotor())
        {
            if (HasFixedAtoms() && IsFixedBond(bond))
                continue;
            score = gtd[bond->GetBeginAtomIdx()-1] +
                    gtd[bond->GetEndAtomIdx()-1];
            vtmp.push_back(pair<OBBond*,int> (bond,score));
        }

    sort(vtmp.begin(),vtmp.end(),CompareRotor);

    OBRotor *rotor;
    int count;
    vector<pair<OBBond*,int> >::iterator j;
    for (j = vtmp.begin(),count=0;j != vtmp.end();j++,count++)
    {
        rotor = new OBRotor;
        rotor->SetBond((*j).first);
        rotor->SetIdx(count);
        rotor->SetNumCoords(mol.NumAtoms()*3);
        _rotor.push_back(rotor);
    }

    return(true);
}

bool OBRotorList::IsFixedBond(OBBond *bond)
{
    OBAtom *a1,*a2,*a3;
    vector<OBEdgeBase*>::iterator i;

    a1 = bond->GetBeginAtom();
    a2 = bond->GetEndAtom();
    if (!_fix[a1->GetIdx()] || !_fix[a2->GetIdx()])
        return(false);

    bool isfixed=false;
    for (a3 = a1->BeginNbrAtom(i);a3;a3 = a1->NextNbrAtom(i))
        if (a3 != a2 && _fix[a3->GetIdx()])
        {
            isfixed = true;
            break;
        }

    if (!isfixed)
        return(false);

    isfixed = false;
    for (a3 = a2->BeginNbrAtom(i);a3;a3 = a2->NextNbrAtom(i))
        if (a3 != a1 && _fix[a3->GetIdx()])
        {
            isfixed = true;
            break;
        }

    return(isfixed);
}

bool GetDFFVector(OBMol &mol,vector<int> &dffv,OBBitVec &bv)
{
    dffv.clear();
    dffv.resize(mol.NumAtoms());

    int dffcount,natom;
    OBBitVec used,curr,next;
    OBAtom *atom,*atom1;
    OBBond *bond;
    vector<OBNodeBase*>::iterator i;
    vector<OBEdgeBase*>::iterator j;

    next.Clear();

    for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
    {
        if (bv[atom->GetIdx()])
        {
            dffv[atom->GetIdx()-1] = 0;
            continue;
        }

        dffcount = 0;
        used.Clear();
        curr.Clear();
        used.SetBitOn(atom->GetIdx());
        curr.SetBitOn(atom->GetIdx());

        while (!curr.IsEmpty() && (bv&curr).Empty())
        {
            next.Clear();
            for (natom = curr.NextBit(-1);natom != curr.EndBit();natom = curr.NextBit(natom))
            {
                atom1 = mol.GetAtom(natom);
                for (bond = atom1->BeginBond(j);bond;bond = atom1->NextBond(j))
                    if (!used.BitIsOn(bond->GetNbrAtomIdx(atom1)) &&
                            !curr.BitIsOn(bond->GetNbrAtomIdx(atom1)))
                        if (!(bond->GetNbrAtom(atom1))->IsHydrogen())
                            next.SetBitOn(bond->GetNbrAtomIdx(atom1));
            }

            used |= next;
            curr = next;
            dffcount++;
        }

        dffv[atom->GetIdx()-1] = dffcount;
    }

    return(true);
}


static double MinimumPairRMS(OBMol&,double*,double*,bool &);

//! Rotates each bond to zero and 180 degrees and tests
//! if the 2 conformers are duplicates.  if so - the symmetric torsion
//! values are removed from consideration during a search
void OBRotorList::RemoveSymVals(OBMol &mol)
{
    double *c,*c1,*c2;
    c1 = new double [mol.NumAtoms()*3];
    c2 = new double [mol.NumAtoms()*3];
    c = mol.GetCoordinates();
    bool one2one;
    double cutoff = 0.20;

    OBRotor *rotor;
    vector<OBRotor*>::iterator i;
    for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i))
    {
        //look for 2-fold symmetry about a bond
        memcpy(c1,c,sizeof(double)*mol.NumAtoms()*3);
        memcpy(c2,c,sizeof(double)*mol.NumAtoms()*3);
        rotor->SetToAngle(c1,(double)(0.0*DEG_TO_RAD));
        rotor->SetToAngle(c2,(double)(180.0*DEG_TO_RAD));

        if (MinimumPairRMS(mol,c1,c2,one2one) <cutoff && !one2one)
        {
            rotor->RemoveSymTorsionValues(2);
            OBBond *bond = rotor->GetBond();

            if (!_quiet)
            {
#ifdef HAVE_SSTREAM
              stringstream errorMsg;
#else
              strstream errorMsg;
#endif
              errorMsg << "symmetry found = " << ' ';
              errorMsg << bond->GetBeginAtomIdx() << ' ' << bond->GetEndAtomIdx() << ' ' ;
              errorMsg << "rms = " << ' ';
              errorMsg << MinimumPairRMS(mol,c1,c2,one2one) << endl;
              obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug);
            }
            continue;
        }

        //look for 3-fold symmetry about a bond
        memcpy(c1,c,sizeof(double)*mol.NumAtoms()*3);
        memcpy(c2,c,sizeof(double)*mol.NumAtoms()*3);
        rotor->SetToAngle(c1,(double)(0.0*DEG_TO_RAD));
        rotor->SetToAngle(c2,(double)(120.0*DEG_TO_RAD));

        if (MinimumPairRMS(mol,c1,c2,one2one) <cutoff && !one2one)
        {
            rotor->RemoveSymTorsionValues(3);
            OBBond *bond = rotor->GetBond();

            if (!_quiet)
            {
#ifdef HAVE_SSTREAM
              stringstream errorMsg;
#else
              strstream errorMsg;
#endif
              errorMsg << "3-fold symmetry found = " << ' ';
              errorMsg << bond->GetBeginAtomIdx() << ' ' << bond->GetEndAtomIdx() << ' ' ;
              errorMsg << "rms = " << ' ';
              errorMsg << MinimumPairRMS(mol,c1,c2,one2one) << endl;
              obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug);
            }
        }
    }

    delete [] c1;
    delete [] c2;

    //pattern based duplicate removal
    int ref[4];
    vector<vector<int> > mlist;
    vector<vector<int> >::iterator k;
    vector<pair<OBSmartsPattern*,pair<int,int> > >::iterator j;
    for (j = _vsym2.begin();j != _vsym2.end();j++)
        if (j->first->Match(mol))
        {
            mlist = j->first->GetUMapList();

            for (k = mlist.begin();k != mlist.end();k++)
                for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i))
                {
                    rotor->GetDihedralAtoms(ref);
                    if (((*k)[j->second.first] == ref[1] && (*k)[j->second.second] == ref[2]) ||
                            ((*k)[j->second.first] == ref[2] && (*k)[j->second.second] == ref[1]))
                    {
                        rotor->RemoveSymTorsionValues(2);
                        if (!_quiet)
                        {
#ifdef HAVE_SSTREAM
              stringstream errorMsg;
#else
              strstream errorMsg;
#endif
              errorMsg << "2-fold pattern-based symmetry found = " << ' ';
              errorMsg << ref[1] << ' ' << ref[2] << endl;
              obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug);
                        }
                    }
                }
        }

    for (j = _vsym3.begin();j != _vsym3.end();j++)
        if (j->first->Match(mol))
        {
            mlist = j->first->GetUMapList();

            for (k = mlist.begin();k != mlist.end();k++)
                for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i))
                {
                    rotor->GetDihedralAtoms(ref);
                    if (((*k)[j->second.first] == ref[1] && (*k)[j->second.second] == ref[2]) ||
                            ((*k)[j->second.first] == ref[2] && (*k)[j->second.second] == ref[1]))
                    {
                        rotor->RemoveSymTorsionValues(3);
                        if (!_quiet)
                        {
#ifdef HAVE_SSTREAM
                          stringstream errorMsg;
#else
                          strstream errorMsg;
#endif
                          errorMsg << "3-fold pattern-based symmetry found = " << ' ';
                          errorMsg << ref[1] << ' ' << ref[2] << endl;
                          obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug);
                        }
                    }
                }
        }
}

static double MinimumPairRMS(OBMol &mol,double *a,double *b,bool &one2one)
{
    int i,j,k=0;
    double min,tmp,d_2 = 0.0;
    OBBitVec bset;
    one2one = true;
    vector<OBNodeBase*> _atom;
    _atom.resize(mol.NumAtoms());
    for (i = 0;i < (signed)mol.NumAtoms();i++)
        _atom[i] = mol.GetAtom(i+1);

    for (i = 0;i < (signed)mol.NumAtoms();i++)
    {
        min = 10E10;
        for (j = 0;j < (signed)mol.NumAtoms();j++)
            if ((_atom[i])->GetAtomicNum() == (_atom[j])->GetAtomicNum() &&
                    (_atom[i])->GetHyb()       == (_atom[j])->GetHyb())
                if (!bset[j])
                {
                    tmp = SQUARE(a[3*i]-b[3*j]) +
                          SQUARE(a[3*i+1]-b[3*j+1]) +
                          SQUARE(a[3*i+2]-b[3*j+2]);
                    if (tmp < min)
                    {
                        k = j;
                        min = tmp;
                    }
                }

        if (i != j)
            one2one = false;
        bset.SetBitOn(k);
        d_2 += min;
    }

    d_2 /= (double)mol.NumAtoms();

    return(sqrt(d_2));
}

//! Determines which atoms the internal energy should be calculated
//! if a the dihedral angle of the rotor is modified
bool OBRotorList::SetEvalAtoms(OBMol &mol)
{
    int j;
    OBBond *bond;
    OBAtom *a1,*a2;
    OBRotor *rotor;
    vector<OBRotor*>::iterator i;
    OBBitVec eval,curr,next;
    vector<OBEdgeBase*>::iterator k;

    for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i))
    {
        bond = rotor->GetBond();
        curr.Clear();
        eval.Clear();
        curr.SetBitOn(bond->GetBeginAtomIdx());
        curr.SetBitOn(bond->GetEndAtomIdx());
        eval |= curr;

        //follow all non-rotor bonds and add atoms to eval list
        for (;!curr.Empty();)
        {
            next.Clear();
            for (j = curr.NextBit(0);j != curr.EndBit();j = curr.NextBit(j))
            {
                a1 = mol.GetAtom(j);
                for (a2 = a1->BeginNbrAtom(k);a2;a2 = a1->NextNbrAtom(k))
                    if (!eval[a2->GetIdx()])
                        if (!((OBBond*)*k)->IsRotor()||(HasFixedAtoms()&&IsFixedBond((OBBond*)*k)))
                        {
                            next.SetBitOn(a2->GetIdx());
                            eval.SetBitOn(a2->GetIdx());
                        }
            }
            curr = next;
        }

        //add atoms alpha to eval list
        next.Clear();
        for (j = eval.NextBit(0);j != eval.EndBit();j = eval.NextBit(j))
        {
            a1 = mol.GetAtom(j);
            for (a2 = a1->BeginNbrAtom(k);a2;a2 = a1->NextNbrAtom(k))
                next.SetBitOn(a2->GetIdx());
        }
        eval |= next;
        rotor->SetEvalAtoms(eval);
    }

    return(true);
}

bool OBRotorList::AssignTorVals(OBMol &mol)
{
    OBBond *bond;
    OBRotor *rotor;
    vector<OBRotor*>::iterator i;

    int ref[4];
    double delta;
    vector<double> res;
    vector<int> itmp1;
    vector<int>::iterator j;
    for (i = _rotor.begin();i != _rotor.end();i++)
    {
        rotor=*i;
        bond = rotor->GetBond();
        _rr.GetRotorIncrements(mol,bond,ref,res,delta);
        rotor->SetTorsionValues(res);
        rotor->SetDelta(delta);

        mol.FindChildren(itmp1,ref[1],ref[2]);
        if (itmp1.size()+1 > mol.NumAtoms()/2)
        {
            itmp1.clear();
            mol.FindChildren(itmp1,ref[2],ref[1]);
            swap(ref[0],ref[3]);
            swap(ref[1],ref[2]);
        }

        for (j = itmp1.begin();j != itmp1.end();j++)
            *j = ((*j)-1)*3;
        rotor->SetRotAtoms(itmp1);
        rotor->SetDihedralAtoms(ref);
    }

    return(true);
}

bool OBRotorList::SetRotAtoms(OBMol &mol)
{
    OBRotor *rotor;
    vector<int> rotatoms,dihed;
    vector<OBRotor*>::iterator i;

    int ref[4];
    vector<int>::iterator j;
    for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i))
    {
        dihed = rotor->GetDihedralAtoms();
        ref[0] = dihed[0]/3+1;
        ref[1] = dihed[1]/3+1;
        ref[2] = dihed[2]/3+1;
        ref[3] = dihed[3]/3+1;

        mol.FindChildren(rotatoms,ref[1],ref[2]);
        if (rotatoms.size()+1 > mol.NumAtoms()/2)
        {
            rotatoms.clear();
            mol.FindChildren(rotatoms,ref[2],ref[1]);
            swap(ref[0],ref[3]);
            swap(ref[1],ref[2]);
        }

        for (j = rotatoms.begin();j != rotatoms.end();j++)
            *j = ((*j)-1)*3;
        rotor->SetRotAtoms(rotatoms);
        rotor->SetDihedralAtoms(ref);
    }

    return(true);
}

void OBRotorList::SetRotAtomsByFix(OBMol &mol)
{
    int ref[4];
    OBRotor *rotor;
    vector<int> rotatoms,dihed;
    vector<int>::iterator j;
    vector<OBRotor*>::iterator i;

    GetDFFVector(mol,_dffv,_fix);

    for (rotor = BeginRotor(i);rotor;rotor = NextRotor(i))
    {
        rotatoms.clear();
        dihed = rotor->GetDihedralAtoms();
        ref[0] = dihed[0]/3+1;
        ref[1] = dihed[1]/3+1;
        ref[2] = dihed[2]/3+1;
        ref[3] = dihed[3]/3+1;

        if (_fix[ref[1]] && _fix[ref[2]])
        {
            if (!_fix[ref[0]])
            {
                swap(ref[0],ref[3]);
                swap(ref[1],ref[2]);
                mol.FindChildren(rotatoms,ref[1],ref[2]);
                for (j = rotatoms.begin();j != rotatoms.end();j++)
                    *j = ((*j)-1)*3;
                rotor->SetRotAtoms(rotatoms);
                rotor->SetDihedralAtoms(ref);
            }
        }
        else
            if (_dffv[ref[1]-1] > _dffv[ref[2]-1])
            {
                swap(ref[0],ref[3]);
                swap(ref[1],ref[2]);
                mol.FindChildren(rotatoms,ref[1],ref[2]);
                for (j = rotatoms.begin();j != rotatoms.end();j++)
                    *j = ((*j)-1)*3;
                rotor->SetRotAtoms(rotatoms);
                rotor->SetDihedralAtoms(ref);
            }
    }
}

OBRotorList::OBRotorList()
{
    _rotor.clear();
    _quiet=false;
    _removesym=true;

    //para-disub benzene
    OBSmartsPattern *sp;
    sp = new OBSmartsPattern;
    sp->Init("*c1[cD2][cD2]c(*)[cD2][cD2]1");
    _vsym2.push_back(pair<OBSmartsPattern*,pair<int,int> > (sp,pair<int,int> (0,1)));

    //piperidine amide
    sp = new OBSmartsPattern;
    sp->Init("O=CN1[CD2][CD2][CD2][CD2][CD2]1");
    _vsym2.push_back(pair<OBSmartsPattern*,pair<int,int> > (sp,pair<int,int> (1,2)));

    //terminal phosphate
    sp = new OBSmartsPattern;
    sp->Init("[#8D2][#15,#16](~[#8D1])(~[#8D1])~[#8D1]");
    _vsym3.push_back(pair<OBSmartsPattern*,pair<int,int> > (sp,pair<int,int> (0,1)));

}

OBRotorList::~OBRotorList()
{
    vector<OBRotor*>::iterator i;
    for (i = _rotor.begin();i != _rotor.end();i++)
        delete *i;

    vector<pair<OBSmartsPattern*,pair<int,int> > >::iterator j;
    for (j = _vsym2.begin();j != _vsym2.end();j++)
        delete j->first;

    for (j = _vsym3.begin();j != _vsym3.end();j++)
        delete j->first;
}

void OBRotorList::Clear()
{
    vector<OBRotor*>::iterator i;
    for (i = _rotor.begin();i != _rotor.end();i++)
        delete *i;
    _rotor.clear();
    _fix.Clear();
}

bool CompareRotor(const pair<OBBond*,int> &a,const pair<OBBond*,int> &b)
{
    //return(a.second > b.second); //outside->in
    return(a.second < b.second);   //inside->out
}

//**********************************
//**** OBRotor Member Functions ****
//**********************************

OBRotor::OBRotor()
{
    _delta = 10.0;
    _rotatoms = NULL;
}

double OBRotor::CalcTorsion(double *c)
{
    double v1x,v1y,v1z,v2x,v2y,v2z,v3x,v3y,v3z;
    double c1x,c1y,c1z,c2x,c2y,c2z,c3x,c3y,c3z;
    double c1mag,c2mag,ang,costheta;

    //
    //calculate the torsion angle
    //
    v1x = c[_torsion[0]] -  c[_torsion[1]];
    v1y = c[_torsion[0]+1] - c[_torsion[1]+1];
    v1z = c[_torsion[0]+2] - c[_torsion[1]+2];
    v2x = c[_torsion[1]] - c[_torsion[2]];
    v2y = c[_torsion[1]+1] - c[_torsion[2]+1];
    v2z = c[_torsion[1]+2] - c[_torsion[2]+2];
    v3x = c[_torsion[2]]   - c[_torsion[3]];
    v3y = c[_torsion[2]+1] - c[_torsion[3]+1];
    v3z = c[_torsion[2]+2] - c[_torsion[3]+2];

    c1x = v1y*v2z - v1z*v2y;
    c2x = v2y*v3z - v2z*v3y;
    c1y = -v1x*v2z + v1z*v2x;
    c2y = -v2x*v3z + v2z*v3x;
    c1z = v1x*v2y - v1y*v2x;
    c2z = v2x*v3y - v2y*v3x;
    c3x = c1y*c2z - c1z*c2y;
    c3y = -c1x*c2z + c1z*c2x;
    c3z = c1x*c2y - c1y*c2x;

    c1mag = SQUARE(c1x)+SQUARE(c1y)+SQUARE(c1z);
    c2mag = SQUARE(c2x)+SQUARE(c2y)+SQUARE(c2z);
    if (c1mag*c2mag < 0.01)
        costheta = 1.0; //avoid div by zero error
    else
        costheta = (c1x*c2x + c1y*c2y + c1z*c2z)/(sqrt(c1mag*c2mag));

    if (costheta < -0.9999999)
        costheta = -0.9999999;
    if (costheta >  0.9999999)
        costheta =  0.9999999;

    if ((v2x*c3x + v2y*c3y + v2z*c3z) > 0.0)
        ang = -acos(costheta);
    else
        ang = acos(costheta);

    return(ang);
}

double OBRotor::CalcBondLength(double *c)
{
    double dx,dy,dz;

    dx = c[_torsion[1]] - c[_torsion[2]];
    dy = c[_torsion[1]+1] - c[_torsion[2]+1];
    dz = c[_torsion[1]+2] - c[_torsion[2]+2];
    return(sqrt(SQUARE(dx)+SQUARE(dy)+SQUARE(dz)));
}

void OBRotor::Precalc(vector<double*> &cv)
{
    double *c,ang;
    vector<double*>::iterator i;
    vector<double>::iterator j;
    vector<double> cs,sn,t;
    for (i = cv.begin();i != cv.end();i++)
    {
        c = *i;
        cs.clear();
        sn.clear();
        t.clear();
        ang = CalcTorsion(c);

        for (j = _res.begin();j != _res.end();j++)
        {
            cs.push_back(cos(*j-ang));
            sn.push_back(sin(*j-ang));
            t.push_back(1 - cos(*j-ang));
        }

        _cs.push_back(cs);
        _sn.push_back(sn);
        _t.push_back(t);
        _invmag.push_back(1.0/CalcBondLength(c));
    }
}


void OBRotor::SetRotor(double *c,int idx,int prev)
{
    double ang,sn,cs,t,dx,dy,dz,mag;

    if (prev == -1)
        ang = _res[idx] - CalcTorsion(c);
    else
        ang = _res[idx] - _res[prev];

    sn = sin(ang);
    cs = cos(ang);
    t = 1 - cs;

    dx = c[_torsion[1]]   - c[_torsion[2]];
    dy = c[_torsion[1]+1] - c[_torsion[2]+1];
    dz = c[_torsion[1]+2] - c[_torsion[2]+2];
    mag = sqrt(SQUARE(dx) + SQUARE(dy) + SQUARE(dz));

    Set(c,sn,cs,t,1.0/mag);
}

void OBRotor::Precompute(double *c)
{
    double dx,dy,dz;
    dx = c[_torsion[1]]   - c[_torsion[2]];
    dy = c[_torsion[1]+1] - c[_torsion[2]+1];
    dz = c[_torsion[1]+2] - c[_torsion[2]+2];
    _imag = 1.0/sqrt(SQUARE(dx) + SQUARE(dy) + SQUARE(dz));

    _refang = CalcTorsion(c);
}

void OBRotor::Set(double *c,int idx)
{
    double ang,sn,cs,t;

    ang = _res[idx] - _refang;
    sn = sin(ang);
    cs = cos(ang);
    t = 1-cs;

    double x,y,z,tx,ty,tz,m[9];

    x = c[_torsion[1]]   - c[_torsion[2]];
    y = c[_torsion[1]+1] - c[_torsion[2]+1];
    z = c[_torsion[1]+2] - c[_torsion[2]+2];

    x *= _imag;
    y *= _imag;
    z *= _imag; //normalize the rotation vector

    //set up the rotation matrix
    tx = t*x;
    ty = t*y;
    tz = t*z;
    m[0]= tx*x + cs;
    m[1] = tx*y + sn*z;
    m[2] = tx*z - sn*y;
    m[3] = tx*y - sn*z;
    m[4] = ty*y + cs;
    m[5] = ty*z + sn*x;
    m[6] = tx*z + sn*y;
    m[7] = ty*z - sn*x;
    m[8] = tz*z + cs;

    //
    //now the matrix is set - time to rotate the atoms
    //
    tx = c[_torsion[1]];
    ty = c[_torsion[1]+1];
    tz = c[_torsion[1]+2];
    int i,j;
    for (i = 0;i < _size;i++)
    {
        j = _rotatoms[i];
        c[j] -= tx;
        c[j+1] -= ty;
        c[j+2]-= tz;
        x = c[j]*m[0] + c[j+1]*m[1] + c[j+2]*m[2];
        y = c[j]*m[3] + c[j+1]*m[4] + c[j+2]*m[5];
        z = c[j]*m[6] + c[j+1]*m[7] + c[j+2]*m[8];
        c[j] = x+tx;
        c[j+1] = y+ty;
        c[j+2] = z+tz;
    }
}

void OBRotor::Set(double *c,double sn,double cs,double t,double invmag)
{
    double x,y,z,tx,ty,tz,m[9];

    x = c[_torsion[1]]   - c[_torsion[2]];
    y = c[_torsion[1]+1] - c[_torsion[2]+1];
    z = c[_torsion[1]+2] - c[_torsion[2]+2];

    //normalize the rotation vector

    x *= invmag;
    y *= invmag;
    z *= invmag;

    //set up the rotation matrix
    tx = t*x;
    ty = t*y;
    tz = t*z;
    m[0]= tx*x + cs;
    m[1] = tx*y + sn*z;
    m[2] = tx*z - sn*y;
    m[3] = tx*y - sn*z;
    m[4] = ty*y + cs;
    m[5] = ty*z + sn*x;
    m[6] = tx*z + sn*y;
    m[7] = ty*z - sn*x;
    m[8] = tz*z + cs;

    //
    //now the matrix is set - time to rotate the atoms
    //
    tx = c[_torsion[1]];
    ty = c[_torsion[1]+1];
    tz = c[_torsion[1]+2];
    int i,j;
    for (i = 0;i < _size;i++)
    {
        j = _rotatoms[i];
        c[j] -= tx;
        c[j+1] -= ty;
        c[j+2]-= tz;
        x = c[j]*m[0] + c[j+1]*m[1] + c[j+2]*m[2];
        y = c[j]*m[3] + c[j+1]*m[4] + c[j+2]*m[5];
        z = c[j]*m[6] + c[j+1]*m[7] + c[j+2]*m[8];
        c[j] = x+tx;
        c[j+1] = y+ty;
        c[j+2] = z+tz;
    }
}

void OBRotor::RemoveSymTorsionValues(int fold)
{
    vector<double>::iterator i;
    vector<double> tv;
    if (_res.size() == 1)
        return;

    for (i = _res.begin();i != _res.end();i++)
        if (*i >= 0.0)
        {
            if (fold == 2 && *i < DEG_TO_RAD*180.0)
                tv.push_back(*i);
            if (fold == 3 && *i < DEG_TO_RAD*120.0)
                tv.push_back(*i);
        }

    if (tv.empty())
        return;
    _res = tv;
}

void OBRotor::SetDihedralAtoms(int ref[4])
{
    for (int i = 0;i < 4;i++)
        _ref[i] = ref[i];
    _torsion.resize(4);
    _torsion[0] = (ref[0]-1)*3;
    _torsion[1] = (ref[1]-1)*3;
    _torsion[2] = (ref[2]-1)*3;
    _torsion[3] = (ref[3]-1)*3;
}

void OBRotor::SetRotAtoms(vector<int> &vi)
{
    if (_rotatoms)
        delete [] _rotatoms;
    _rotatoms = new int [vi.size()];
    copy(vi.begin(),vi.end(),_rotatoms);
    _size = vi.size();
}

//***************************************
//**** OBRotorRules Member functions ****
//***************************************
OBRotorRules::OBRotorRules()
{
    _quiet=false;
    _init = false;
    STR_DEFINE(_dir, FRC_PATH );
    _envvar = "FORCE_PARAM_PATH";
    _filename = "torlib.txt";
    _subdir = "data";
    _dataptr = TorsionDefaults;
}

void OBRotorRules::ParseLine(const char *buffer)
{
    int i;
    int ref[4];
    double delta;
    vector<double> vals;
    vector<string> vs;
    vector<string>::iterator j;
    char temp_buffer[BUFF_SIZE];

    if (buffer[0] == '#')
        return;
    tokenize(vs,buffer);
    if (vs.empty())
        return;

    if (EQn(buffer,"SP3-SP3",7))
    {
        _sp3sp3.clear();
        for (j = vs.begin(),j++;j != vs.end();j++)
            _sp3sp3.push_back(DEG_TO_RAD*atof(j->c_str()));
        return;
    }

    if (EQn(buffer,"SP3-SP2",7))
    {
        _sp3sp2.clear();
        for (j = vs.begin(),j++;j != vs.end();j++)
            _sp3sp2.push_back(DEG_TO_RAD*atof(j->c_str()));
        return;
    }

    if (EQn(buffer,"SP2-SP2",7))
    {
        _sp2sp2.clear();
        for (j = vs.begin(),j++;j != vs.end();j++)
            _sp2sp2.push_back(DEG_TO_RAD*atof(j->c_str()));
        return;
    }

    if (!vs.empty() && vs.size() > 5)
    {
        strncpy(temp_buffer,vs[0].c_str(), sizeof(temp_buffer) - 1);
        temp_buffer[sizeof(temp_buffer) - 1] = '\0';
        //reference atoms
        for (i = 0;i < 4;i++)
            ref[i] = atoi(vs[i+1].c_str())-1;
        //possible torsions
        vals.clear();
        delta = OB_DEFAULT_DELTA;
        for (i = 5;(unsigned)i < vs.size();i++)
        {
            if (i == (signed)(vs.size()-2) && vs[i] == "Delta")
            {
                delta = atof(vs[i+1].c_str());
                i += 2;
            }
            else
                vals.push_back(DEG_TO_RAD*atof(vs[i].c_str()));
        }

        if (vals.empty())
        {
            string err = "The following rule has no associated torsions: ";
            err += vs[0];
            obErrorLog.ThrowError(__func__, err, obDebug);
        }
        OBRotorRule *rr = new OBRotorRule (temp_buffer,ref,vals,delta);
        if (rr->IsValid())
            _vr.push_back(rr);
        else
            delete rr;
    }

}

void OBRotorRules::GetRotorIncrements(OBMol &mol,OBBond *bond,
                                      int ref[4],vector<double> &vals,double &delta)
{
    vals.clear();
    vector<pair<int,int> > vpr;
    vpr.push_back(pair<int,int> (0,bond->GetBeginAtomIdx()));
    vpr.push_back(pair<int,int> (0,bond->GetEndAtomIdx()));

    delta = OB_DEFAULT_DELTA;

    int j;
    OBSmartsPattern *sp;
    vector<vector<int> > map;
    vector<OBRotorRule*>::iterator i;
    for (i = _vr.begin();i != _vr.end();i++)
    {
        sp = (*i)->GetSmartsPattern();
        (*i)->GetReferenceAtoms(ref);
        vpr[0].first = ref[1];
        vpr[1].first = ref[2];

        if (!sp->RestrictedMatch(mol,vpr,true))
        {
            swap(vpr[0].first,vpr[1].first);
            if (!sp->RestrictedMatch(mol,vpr,true))
                continue;
        }

        map = sp->GetMapList();
        for (j = 0;j < 4;j++)
            ref[j] = map[0][ref[j]];
        vals = (*i)->GetTorsionVals();
        delta = (*i)->GetDelta();

        OBAtom *a1,*a2,*a3,*a4,*r;
        a1 = mol.GetAtom(ref[0]);
        a4 = mol.GetAtom(ref[3]);
        if (a1->IsHydrogen() && a4->IsHydrogen())
            continue; //don't allow hydrogens at both ends
        if (a1->IsHydrogen() || a4->IsHydrogen()) //need a heavy atom reference - can use hydrogen
        {
            bool swapped = false;
            a2 = mol.GetAtom(ref[1]);
            a3 = mol.GetAtom(ref[2]);
            if (a4->IsHydrogen())
            {
                swap(a1,a4);
                swap(a2,a3);
                swapped = true;
            }

            vector<OBEdgeBase*>::iterator k;
            for (r = a2->BeginNbrAtom(k);r;r = a2->NextNbrAtom(k))
                if (!r->IsHydrogen() && r != a3)
                    break;

            if (!r)
                continue; //unable to find reference heavy atom
            //                  cerr << "r = " << r->GetIdx() << endl;

            double t1 = mol.GetTorsion(a1,a2,a3,a4);
            double t2 = mol.GetTorsion(r,a2,a3,a4);
            double diff = t2 - t1;
            if (diff > 180.0)
                diff -= 360.0;
            if (diff < -180.0)
                diff += 360.0;
            diff *= DEG_TO_RAD;

            vector<double>::iterator m;
            for (m = vals.begin();m != vals.end();m++)
            {
                *m += diff;
                if (*m < PI)
                    *m += 2.0*PI;
                if (*m > PI)
                    *m -= 2.0*PI;
            }

            if (swapped)
                ref[3] = r->GetIdx();
            else
                ref[0] = r->GetIdx();

            /*
                  mol.SetTorsion(r,a2,a3,a4,vals[0]);
                  cerr << "test = " << (vals[0]-diff)*RAD_TO_DEG << ' ';
                  cerr << mol.GetTorsion(a1,a2,a3,a4) <<  ' ';
                  cerr << mol.GetTorsion(r,a2,a3,a4) << endl;
                  */
        }

        char buffer[BUFF_SIZE];
        if (!_quiet)
        {
            snprintf(buffer, BUFF_SIZE, "%3d%3d%3d%3d %s",
                    ref[0],ref[1],ref[2],ref[3],
                    ((*i)->GetSmartsString()).c_str());
            obErrorLog.ThrowError(__func__, buffer, obDebug);
        }
        return;
    }

    //***didn't match any rules - assign based on hybridization***
    OBAtom *a1,*a2,*a3,*a4;
    a2 = bond->GetBeginAtom();
    a3 = bond->GetEndAtom();
    vector<OBEdgeBase*>::iterator k;

    for (a1 = a2->BeginNbrAtom(k);a1;a1 = a2->NextNbrAtom(k))
        if (!a1->IsHydrogen() && a1 != a3)
            break;
    for (a4 = a3->BeginNbrAtom(k);a4;a4 = a3->NextNbrAtom(k))
        if (!a4->IsHydrogen() && a4 != a2)
            break;

    ref[0] = a1->GetIdx();
    ref[1] = a2->GetIdx();
    ref[2] = a3->GetIdx();
    ref[3] = a4->GetIdx();

    if (a2->GetHyb() == 3 && a3->GetHyb() == 3) //sp3-sp3
    {
        vals = _sp3sp3;

        if (!_quiet)
        {
            char buffer[BUFF_SIZE];
            snprintf(buffer,BUFF_SIZE,"%3d%3d%3d%3d %s",
                    ref[0],ref[1],ref[2],ref[3],"sp3-sp3");
            obErrorLog.ThrowError(__func__, buffer, obDebug);
        }
    }
    else
        if (a2->GetHyb() == 2 && a3->GetHyb() == 2) //sp2-sp2
        {
            vals = _sp2sp2;

            if (!_quiet)
            {
                char buffer[BUFF_SIZE];
                snprintf(buffer,BUFF_SIZE,"%3d%3d%3d%3d %s",
                        ref[0],ref[1],ref[2],ref[3],"sp2-sp2");
                obErrorLog.ThrowError(__func__, buffer, obDebug);
            }
        }
        else //must be sp2-sp3
        {
            vals = _sp3sp2;

            if (!_quiet)
            {
                char buffer[BUFF_SIZE];
                snprintf(buffer,BUFF_SIZE,"%3d%3d%3d%3d %s",
                        ref[0],ref[1],ref[2],ref[3],"sp2-sp3");
                obErrorLog.ThrowError(__func__, buffer, obDebug);
            }
        }
}

OBRotorRules::~OBRotorRules()
{
    vector<OBRotorRule*>::iterator i;
    for (i = _vr.begin();i != _vr.end();i++)
        delete (*i);
}

#undef OB_DEFAULT_DELTA
}

//! \file rotor.cpp
//! \brief Rotate dihedral angles according to rotor rules.
Revision:	1081
Committed:	Thu Oct 19 20:49:05 2006 UTC (18 years, 6 months ago) by gezelter
File size:	31010 byte(s)
Log Message:	updated OpenBabel to version 2.0.2