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/*******************************************************************************
* *
* Viewmol *
* *
* B O N D O R D E R . C *
* *
* Copyright (c) Joerg-R. Hill, October 2003 *
* *
********************************************************************************
*
* $Id: bondorder.c,v 1.5 2003/11/07 10:58:19 jrh Exp $
* $Log: bondorder.c,v $
* Revision 1.5 2003/11/07 10:58:19 jrh
* Release 2.4
*
* Revision 1.4 2000/12/10 15:02:22 jrh
* Release 2.3
*
* Revision 1.3 1999/05/24 01:24:49 jrh
* Release 2.2.1
*
* Revision 1.2 1999/02/07 21:44:46 jrh
* Release 2.2
*
* Revision 1.1 1998/01/26 00:34:45 jrh
* Initial revision
*
*/
#include<math.h>
#include<stdlib.h>
#include<string.h>
#include "viewmol.h"
extern struct MOLECULE *molecules;
extern void *getmem(size_t, size_t);
void calculateShift(struct MOLECULE *, struct BOND *, int *, int, int, int);
void findConjugation(struct MOLECULE *, struct BOND *, int *, int, int);
void vectorProduct(double *, double *, double *);
double scalarProduct(double *, double *);
void bondOrder(struct MOLECULE *mol, struct BOND *bond, int *connectivity,
int maxBondsPerAtom)
{
int i, j, ni, nj, bo=1;
/* Assign bond orders by counting electrons. If the number of electrons
for an atom is set to -1 assign only single bonds. */
i=bond->first;
if (mol->atoms[i].nelectrons == (-1))
{
bond->order=1;
return;
}
j=bond->second;
if (mol->atoms[j].nelectrons == (-1))
{
bond->order=1;
return;
}
/* Compare number of electrons with number of atoms atom is bound to
and deduce bond order */
do
{
if (mol->atoms[i].nelectrons > 4)
ni=8-mol->atoms[i].nelectrons;
else
ni=mol->atoms[i].nelectrons;
if (mol->atoms[j].nelectrons > 4)
nj=8-mol->atoms[j].nelectrons;
else
nj=mol->atoms[j].nelectrons;
ni-=mol->atoms[i].nbonds-mol->atoms[i].hbonds;
nj-=mol->atoms[j].nbonds-mol->atoms[j].hbonds;
if (ni < 0)
ni=mol->atoms[i].nelectrons-mol->atoms[i].nbonds+mol->atoms[i].hbonds;
if (nj < 0)
nj=mol->atoms[j].nelectrons-mol->atoms[j].nbonds+mol->atoms[j].hbonds;
if (ni > 0 && nj > 0)
{
mol->atoms[i].nbonds++;
mol->atoms[j].nbonds++;
bo++;
}
else
break;
} while (bo <= 4);
bond->order=bo;
/* Bond order has been found, calculate shift vector to draw multiple bonds. */
if (bo > 1) calculateShift(mol, bond, connectivity, maxBondsPerAtom, i, j);
}
void calculateShift(struct MOLECULE *mol, struct BOND *bond, int *connectivity,
int maxBondsPerAtom, int i, int j)
{
double v1[3], v2[3], v3[3];
int ni, nj, bo, kh=(-1);
register double r1, r2;
register int k, l;
/* Rules for multiple bonds: Shall be in the same plane as other bond framework,
but do not use hydrogens to determine this plane
unless impossible otherwise. */
bo=abs(bond->order);
ni=(mol->atoms[i].nbonds >= mol->atoms[j].nbonds ? i : j);
nj=(ni == i ? j : i);
l=0;
do
{
k=abs(connectivity[maxBondsPerAtom*ni+l]);
if (k != nj && strcmp(mol->atoms[k].element->symbol, "H")) break;
if (k != nj && !strcmp(mol->atoms[k].element->symbol, "H")) kh=k;
l++;
} while (l < maxBondsPerAtom);
/* No non-hydrogen atom found so we have to use a hydrogen atom */
if (l == maxBondsPerAtom && kh != (-1)) k=kh;
v1[0]=mol->atoms[k].x-mol->atoms[ni].x;
v1[1]=mol->atoms[k].y-mol->atoms[ni].y;
v1[2]=mol->atoms[k].z-mol->atoms[ni].z;
r1=scalarProduct(v1, v1);
v2[0]=mol->atoms[nj].x-mol->atoms[ni].x;
v2[1]=mol->atoms[nj].y-mol->atoms[ni].y;
v2[2]=mol->atoms[nj].z-mol->atoms[ni].z;
r2=scalarProduct(v2, v2);
if (r1 != 0.0 && r2 != 0.0)
r1=fabs(scalarProduct(v1, v2)/(sqrt(r1*r2))+1.0);
else
r1=0.0;
if (r1 > 1.0e-6)
{
vectorProduct(v1, v2, v3);
vectorProduct(v2, v3, v1);
r1=mol->bondShift/sqrt(scalarProduct(v1, v1));
if (bo == 2) r1*=0.5;
bond->x=v1[0]*r1;
bond->y=v1[1]*r1;
bond->z=v1[2]*r1;
}
else
{
v1[0]=1.0;
v1[1]=0.0;
v1[2]=0.0;
r1=scalarProduct(v1, v2)/sqrt(r2);
if (bo == 2) r2=0.5;
else r2=1.0;
bond->x=r2*mol->bondShift*sqrt(1.0-r1*r1);
bond->y=r2*mol->bondShift*r1;
bond->z=0.0;
}
/*v3[0]=0.5*(v1[0]-v2[0]);
v3[1]=0.5*(v1[1]-v2[1]);
v3[2]=0.5*(v1[2]-v2[2]);
r1=mol->bondShift/sqrt(scalarProduct(v3, v3));
if (bo == 2) r1*=0.5;
bond->x=v3[0]*r1;
bond->y=v3[1]*r1;
bond->z=v3[2]*r1; */
}
void findConjugation(struct MOLECULE *mol, struct BOND *bonds, int *connectivity,
int maxBondsPerAtom, int nb)
{
int atom1, atom2, conjugated;
register int i, j, k, l;
for (i=0; i<mol->nb; i++)
{
if (abs(mol->bonds[i].order) == 2)
{
atom1=mol->bonds[i].first;
while (TRUE)
{
for (j=0; j<mol->nb; j++)
{
if ((mol->bonds[j].first == atom1
|| mol->bonds[j].second == atom1)
&& mol->bonds[j].order == 1)
{
atom2=mol->bonds[j].first == atom1
? mol->bonds[j].second : mol->bonds[j].first;
for (k=0; k<mol->nb; k++)
{
if ((mol->bonds[k].first == atom2
|| mol->bonds[k].second == atom2)
&& abs(mol->bonds[k].order) == 2)
{
conjugated=TRUE;
for (l=0; l<mol->nb; l++)
{
if (l == i || l == j || l == k) continue;
if (mol->bonds[l].first != atom1
&& mol->bonds[l].second != atom1) continue;
if (mol->bonds[l].order != 1
&& mol->bonds[l].order != (-2))
{
conjugated=FALSE;
break;
}
}
if (conjugated)
{
mol->bonds[i].order=(-2);
mol->bonds[j].order=(-2);
mol->bonds[k].order=(-2);
/* calculate shift vector for bond j */
calculateShift(mol, &(mol->bonds[j]), connectivity,
maxBondsPerAtom, atom1, atom2);
break;
}
}
}
}
}
if (atom1 == mol->bonds[i].second) break;
atom1=mol->bonds[i].second;
}
}
}
}
void vectorProduct(double *v1, double *v2, double *v3)
{
v3[0]=v1[1]*v2[2]-v1[2]*v2[1];
v3[1]=v1[2]*v2[0]-v1[0]*v2[2];
v3[2]=v1[0]*v2[1]-v1[1]*v2[0];
}
double scalarProduct(double *v1, double *v2)
{
return(v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2]);
}
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