bool EEMCharges::ComputeCharges(OBMol &mol)
{
mol.SetPartialChargesPerceived();
if(_parameters.empty())
_loadParameters();
// Copied from spectrophore.cpp
// CHI and ETA
unsigned int _nAtoms = mol.NumAtoms();
unsigned int dim(_nAtoms + 1);
std::vector<double> CHI(dim);
double** ETA = new double*[dim];
for (unsigned int i = 0; i < dim; ++i)
{
ETA[i] = new double[dim];
}
double totalCharge(0.0);
unsigned int i(0);
double hardness;
double electronegativity;
for (OpenBabel::OBMolAtomIter atom(mol); atom; atom++, i++) {
int n = atom->GetAtomicNum();
int b = atom->HighestBondOrder();
// Search for parameters for a particular atom type
bool found = false;
for(unsigned int j = 0; j < _parameters.size(); j++) {
if((_parameters[j].Z == n && _parameters[j].bond_order == b) ||
(_parameters[j].Z == n && _parameters[j].bond_order == - 1) ||
(_parameters[j].Z == -1 && _parameters[j].bond_order == -1)) {
electronegativity = _parameters[j].A;
hardness = _parameters[j].B;
found = true;
break;
}
}
if(!found) {
std::stringstream ss;
ss << "No parameters found for: " << etab.GetSymbol(n) << " " << b
<< ". EEM charges were not calculated for the molecule." << std::endl;
obErrorLog.ThrowError(__FUNCTION__, ss.str(), obError);
return false;
}
CHI[i] = -electronegativity;
ETA[i][i] = hardness;
// Adjust the total molecular charge
totalCharge += atom->GetFormalCharge();
}
// Complete CHI
CHI[_nAtoms] = totalCharge;
// Complete ETA
OBAtom *rAtom, *cAtom;
for (unsigned int r = 0; r < _nAtoms; ++r)
{
rAtom = mol.GetAtom(r+1); // Atom index
for (unsigned int c = r + 1; c < _nAtoms; ++c)
{
cAtom = mol.GetAtom(c+1); // Atom index
ETA[r][c] = _kappa / cAtom->GetDistance(rAtom);
ETA[c][r] = ETA[r][c];
}
}
for (unsigned int i = 0; i < dim; ++i)
{
ETA[i][_nAtoms] = -1.0;
ETA[_nAtoms][i] = +1.0;
}
ETA[_nAtoms][_nAtoms] = 0.0;
// Solve the matrix equation
_solveMatrix(ETA, &(CHI[0]), dim); // CHI will contain the values
OBAtom *atom;
for (unsigned int i = 0; i < _nAtoms; ++i)
{
atom = mol.GetAtom(i+1); // atom index issue
atom->SetPartialCharge(CHI[i]);
}
OBChargeModel::FillChargeVectors(mol);
// Cleanup
for(unsigned int i = 0; i < dim; i++)
delete [] ETA[i];
delete [] ETA;
return true;
}
CPS_START_NAMESPACE
/*! \file
\brief Routine used internally in the DiracOpWilson class.
$Id: wilson_mdag.C,v 1.2 2011-02-26 00:19:27 chulwoo Exp $
*/
//--------------------------------------------------------------------
// CVS keywords
//
// $Author: chulwoo $
// $Date: 2011-02-26 00:19:27 $
// $Header: /home/chulwoo/CPS/repo/CVS/cps_only/cps_pp/src/util/dirac_op/d_op_wilson/sse/wilson_mdag.C,v 1.2 2011-02-26 00:19:27 chulwoo Exp $
// $Id: wilson_mdag.C,v 1.2 2011-02-26 00:19:27 chulwoo Exp $
// $Name: not supported by cvs2svn $
// $Locker: $
// $Revision: 1.2 $
// $Source: /home/chulwoo/CPS/repo/CVS/cps_only/cps_pp/src/util/dirac_op/d_op_wilson/sse/wilson_mdag.C,v $
// $State: Exp $
//
//--------------------------------------------------------------------
CPS_END_NAMESPACE
#include <util/data_types.h>
#include <util/wilson.h>
#include <util/dirac_op.h>
CPS_START_NAMESPACE
//! Access to the elements of the \e SU(3) matrix
/*!
Gets the element of the \e SU(3) matrix \e u with row \e row,
column \e col and complex component \e d
*/
#define U(r,row,col,d,n,cb) *(u+(r+2*(row+3*(col+3*(d+4*(n+vol[0]*(cb)))))))
//! Access to the elements of a spinor vector.
/*!
Gets the element of the spinor \e psi with spin \e s,
colour \e c and complex component \e r
*/
#define PSI(r,c,s,n) *(psi+(r+2*(c+3*(s+4*(n)))))
//! As above, but the vector is called chi
#define CHI(r,c,s,n) *(chi+(r+2*(c+3*(s+4*(n)))))
#define TMP1(r,c,s,n) *(tmp1+(r+2*(c+3*(s+4*(n)))))
void wilson_mdag(IFloat *chi_f,
IFloat *u_f,
IFloat *psi_f,
IFloat kappa_f,
Wilson *wilson_p)
{
IFloat *tmp1_f;
int vol;
int r, c, s, n;
/*--------------------------------------------------------------------------*/
/* Initializations */
/*--------------------------------------------------------------------------*/
vol = wilson_p->vol[0];
tmp1_f = wilson_p->af[0];
Float *chi = (Float *) chi_f;
Float *psi = (Float *) psi_f;
Float kappa = Float(kappa_f);
/*--------------------------------------------------------------------------*/
/* DslashDag_E0 */
/*--------------------------------------------------------------------------*/
wilson_dslash(tmp1_f, u_f, psi_f, 1, 1, wilson_p);
/*--------------------------------------------------------------------------*/
/* DslashDag_0E */
/*--------------------------------------------------------------------------*/
wilson_dslash(chi_f, u_f, tmp1_f, 0, 1, wilson_p);
/*--------------------------------------------------------------------------*/
/* [1_OO - kappa * DslashDag_0E * DslashDag_E0] ] */
/*--------------------------------------------------------------------------*/
for(n=0;n<vol;n++){
for(s=0;s<4;s++){
for(c=0;c<3;c++){
for(r=0;r<2;r++){
CHI(r,c,s,n) = ( PSI(r,c,s,n) - kappa*kappa * CHI(r,c,s,n));
}
}
}
}
DiracOp::CGflops += vol*24*2;
}
void
OBSpectrophore::_calculateProperties(OpenBabel::OBMol* mol)
{
//
// PROPERTY 1: ATOMIC PARTIAL CHARGES [0]
//
// CHI and ETA
unsigned int dim(_nAtoms + 1);
std::vector<double> CHI(dim);
double** ETA = new double*[dim];
double** ETA2 = new double*[dim]; // A copy for the electrophilicity later on
for (unsigned int i = 0; i < dim; ++i)
{
ETA[i] = new double[dim];
ETA2[i] = new double[dim];
}
double totalCharge(0.0);
unsigned int i(0);
unsigned int n;
double hardness;
double electronegativity;
for (OpenBabel::OBMolAtomIter atom(mol); atom; ++atom)
{
n = (unsigned int) atom->GetAtomicNum();
switch (n)
{
case 1: // H
hardness = 0.65971;
electronegativity = 0.20606;
break;
case 3: // Li
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 5: // B
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 6: // C
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 7: // N
hardness = 0.34519;
electronegativity = 0.49279;
break;
case 8: // O
hardness = 0.54428;
electronegativity = 0.73013;
break;
case 9: // F
hardness = 0.72664;
electronegativity = 0.72052;
break;
case 11: // Na
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 12: // Mg
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 14: // Si
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 15: // P
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 16: // S
hardness = 0.20640;
electronegativity = 0.62020;
break;
case 17: // Cl
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 19: // K
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 20: // Ca
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 26: // Fe
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 29: // Cu
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 30: // Zn
hardness = 0.32966;
electronegativity = 0.36237;
break;
case 35: // Br
hardness = 0.54554;
electronegativity = 0.70052;
break;
case 53: // I
hardness = 0.30664;
electronegativity = 0.68052;
break;
default:
hardness = 0.65971;
electronegativity = 0.20606;
break;
}
CHI[i] = -electronegativity;
ETA[i][i] = 2.0 * hardness;
// Adjust the total molecular charge
totalCharge += atom->GetFormalCharge();
// Increment
++i;
}
// Complete CHI
CHI[_nAtoms] = totalCharge;
// Complete ETA
double d;
for (unsigned int r = 0; r < _nAtoms; ++r)
{
for (unsigned int c = r + 1; c < _nAtoms; ++c)
{
d = (_oricoor[r][0] - _oricoor[c][0]) * (_oricoor[r][0] - _oricoor[c][0]);
d += (_oricoor[r][1] - _oricoor[c][1]) * (_oricoor[r][1] - _oricoor[c][1]);
d += (_oricoor[r][2] - _oricoor[c][2]) * (_oricoor[r][2] - _oricoor[c][2]);
ETA[r][c] = 0.529176 / sqrt(d); // 0.529176: Angstrom to au
ETA[c][r] = ETA[r][c];
}
}
for (unsigned int i = 0; i < dim; ++i)
{
ETA[i][_nAtoms] = -1.0;
ETA[_nAtoms][i] = +1.0;
}
ETA[_nAtoms][_nAtoms] = 0.0;
// Make ETA2 a copy of ETA
for (unsigned int r(0); r < dim; ++r)
{
for (unsigned int c(0); c < dim; ++c)
{
ETA2[r][c] = ETA[r][c];
}
}
// Solve the matrix equation
_solveMatrix(ETA, &(CHI[0]), dim); // CHI will contain the values
// Add values to property matrix
for (unsigned int i = 0; i < _nAtoms; ++i)
{
_property[i][0] = CHI[i];
}
double CHIeq2 = CHI[dim - 1] * CHI[dim - 1]; // For electrophilicity later on
// Clean
for (unsigned int i = 0; i < dim; ++i)
{
delete[] ETA[i];
ETA[i] = NULL;
}
delete[] ETA;
ETA = NULL;
//
// PROPERTY 2: ATOMIC LIPOPHILICITY VALUES [1]
//
unsigned int a(0);
for (OpenBabel::OBMolAtomIter atom(mol); atom; ++atom)
{
n = (unsigned int) atom->GetAtomicNum();
switch (n)
{
case 1: // H
if (atom->GetValence())
{
if (atom->IsNonPolarHydrogen())
// Non-polar H
{
_property[a][1] = -0.018;
}
else
// Polar H
{
_property[a][1] = -0.374;
}
}
else
{
_property[a][1] = -0.175;
}
break;
case 6: // C
_property[a][1] = 0.271;
break;
case 7: // N
_property[a][1] = -0.137;
break;
case 8: // O
_property[a][1] = -0.321;
break;
case 9: // F
_property[a][1] = 0.217;
break;
case 16: // S
_property[a][1] = 0.385;
break;
case 17: // Cl
_property[a][1] = 0.632;
break;
case 35: // Br
_property[a][1] = 0.815;
break;
case 53: // I
_property[a][1] = 0.198;
break;
default: // The rest
_property[a][1] = -0.175;
break;
}
// Increment
++a;
}
//
// PROPERTY 3: ATOMIC SHAPE DEVIATIONS [2]
//
for (unsigned int a(0); a < _nAtoms; ++a)
{
for (unsigned int c(0); c < 3; ++c)
{
_coor[a][c] = _oricoor[a][c];
}
}
double COG[3]; // Center of geometry
for (unsigned int c(0); c < 3; ++c)
{
COG[c] = _coor[0][c];
for (unsigned int a(1); a < _nAtoms; ++a)
{
COG[c] += _coor[a][c];
}
COG[c] /= _nAtoms;
}
// Shift molecules to COG and calculate individual distances
std::vector<double> distance(_nAtoms);
double averageDistance(0.0);
for (unsigned int a(0); a < _nAtoms; ++a)
{
distance[a] = 0.0;
for (unsigned int c(0); c < 3; ++c)
{
_coor[a][c] -= COG[c];
distance[a] += _coor[a][c] * _coor[a][c];
}
distance[a] = sqrt(distance[a]);
averageDistance += distance[a];
}
averageDistance /= _nAtoms;
// Set relative to average distance
for (unsigned int a(0); a < _nAtoms; ++a)
{
distance[a] -= averageDistance;
distance[a] *= averageDistance;
}
// Add property
for (unsigned int a(0); a < _nAtoms; ++a)
{
_property[a][2] = distance[a];
}
//
// PROPERTY 4: ATOMIC ELECTROPHILICITY [3]
//
// CHI and ETA2
for (unsigned int i(0); i < dim; ++i)
{
CHI[i] = 1.0;
}
CHI[_nAtoms] = 0.0;
// Complete ETA2
for (unsigned int i = 0; i < dim; ++i)
{
ETA2[i][_nAtoms] = 0.0;
ETA2[_nAtoms][i] = 1.0;
}
ETA2[_nAtoms][_nAtoms] = -1.0;
// Solve the matrix equation
_solveMatrix(ETA2, &(CHI[0]), dim); // CHI will contain the values
// Add values to property matrix
for (unsigned int i = 0; i < _nAtoms; ++i)
{
_property[i][3] = CHI[i] * CHIeq2;
}
// Clean
for (unsigned int i = 0; i < dim; ++i)
{
delete[] ETA2[i];
ETA2[i] = NULL;
}
delete[] ETA2;
ETA2 = NULL;
//
// Return
//
return;
}