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/*******************************************************************************
* *
* Viewmol *
* *
* B U I L D . C *
* *
* Copyright (c) Joerg-R. Hill, October 2003 *
* *
********************************************************************************
*
* $Id: build.c,v 1.4 2003/11/07 10:58:28 jrh Exp $
* $Log: build.c,v $
* Revision 1.4 2003/11/07 10:58:28 jrh
* Release 2.4
*
* Revision 1.3 2000/12/10 15:02:33 jrh
* Release 2.3
*
* Revision 1.2 1999/05/24 01:24:52 jrh
* Release 2.2.1
*
* Revision 1.1 1999/02/07 21:45:03 jrh
* Initial revision
*
*
*/
#include<math.h>
#include<stdio.h>
#include<string.h>
#include<Xm/Xm.h>
#include "viewmol.h"
void buildMolecule(struct MOLECULE *, int, int, int);
void replaceAtom(struct MOLECULE *, int);
void addAtom(struct MOLECULE *, int, int);
void changeCoordination(struct MOLECULE *);
extern int makeConnectivity(struct MOLECULE *, int, int);
extern double centerMolecule(struct MOLECULE *);
extern void setWindowSize(double);
extern int findBondPartners(int *, int, int);
extern int findAttachedAtoms(int *, int, int);
extern void changeBondLength(int, int, int *, double);
extern int changeAngle(int, int, int *, double);
extern void vectorProduct(double *, double *, double *);
extern void *getmem(size_t, size_t);
extern void fremem(void **);
extern void *expmem(void *, size_t, size_t);
extern double bondAngle(struct ATOM *, int, int, int);
extern void clearGeometry(Widget, caddr_t, XmAnyCallbackStruct *);
extern void addUndo(struct MOLECULE *);
extern struct WINDOW windows[];
extern struct MOLECULE *molecules;
extern struct ELEMENT *elements;
extern double torsionDefault;
extern int element, bondType, localGeometry;
void buildMolecule(struct MOLECULE *mol, int picked, int operation, int setWindow)
{
int which, *list;
register int i, j, k;
/* Save coordinates before any change */
if (mol->na > 0) addUndo(mol);
if (mol->internals == NULL)
mol->internals=(struct INTERNAL *)getmem((size_t)1, sizeof(struct INTERNAL));
else
mol->internals=(struct INTERNAL *)expmem((void *)mol->internals,
(size_t)mol->ninternal+1, sizeof(struct INTERNAL));
switch (operation)
{
case DELETE_ATOM: mol->na--;
for (i=picked; i<mol->na; i++)
{
mol->atoms[i].x=mol->atoms[i+1].x;
mol->atoms[i].y=mol->atoms[i+1].y;
mol->atoms[i].z=mol->atoms[i+1].z;
mol->atoms[i].rad=mol->atoms[i+1].rad;
mol->atoms[i].radScale=mol->atoms[i+1].radScale;
mol->atoms[i].mass=mol->atoms[i+1].mass;
mol->atoms[i].neutronScatterfac=mol->atoms[i+1].neutronScatterfac;
mol->atoms[i].nbonds=mol->atoms[i+1].nbonds;
mol->atoms[i].nelectrons=mol->atoms[i+1].nelectrons;
mol->atoms[i].ref=mol->atoms[i+1].ref;
mol->atoms[i].flags=mol->atoms[i+1].flags;
mol->atoms[i].element=mol->atoms[i+1].element;
mol->atoms[i].basis=mol->atoms[i+1].basis;
strcpy(mol->atoms[i].name, mol->atoms[i+1].name);
strcpy(mol->atoms[i].basisname, mol->atoms[i+1].basisname);
}
mol->atoms=(struct ATOM *)expmem((void *)mol->atoms,
(size_t)mol->na, sizeof(struct ATOM));
/* Scan through list of internal coordinates and delete all
which contain deleted atom */
for (i=0; i<mol->ninternal; i++)
{
if (mol->internals[i].atoms[0] == picked ||
mol->internals[i].atoms[1] == picked ||
mol->internals[i].atoms[2] == picked ||
mol->internals[i].atoms[3] == picked)
clearGeometry((Widget)0, (caddr_t)i, (XmAnyCallbackStruct *)0);
}
/* Scan through lists of bonds added or deleted by user
and change numbering of bonded atoms */
for (i=0; i<mol->nbAdded; i++)
{
if (mol->addedBonds[3*i] > picked) mol->addedBonds[3*i]--;
if (mol->addedBonds[3*i+1] > picked) mol->addedBonds[3*i+1]--;
}
for (i=0; i<mol->nbDeleted; i++)
{
if (mol->deletedBonds[2*i] > picked) mol->deletedBonds[2*i]--;
if (mol->deletedBonds[2*i+1] > picked) mol->deletedBonds[2*i+1]--;
}
/* Change coordination at atoms bond to deleted atom if
user desires so */
if (localGeometry)
{
list=(int *)getmem((size_t)mol->nb, sizeof(int));
j=0;
for (i=0; i<mol->nb; i++)
{
if (mol->bonds[i].first == picked || mol->bonds[i].second == picked)
{
list[j++]=i;
mol->bonds[i].order=(-1); /* mark bond as hydrogen bond to ex- */
} /* clude it from findBondPartners */
if (mol->bonds[i].first > picked) mol->bonds[i].first--;
if (mol->bonds[i].second > picked) mol->bonds[i].second--;
}
for (i=0; i<j; i++)
{
k=list[i];
if (mol->bonds[k].first == picked)
mol->internals[mol->ninternal].atoms[1]=mol->bonds[k].second;
else if (mol->bonds[k].second == picked)
mol->internals[mol->ninternal].atoms[1]=mol->bonds[k].first;
changeCoordination(mol);
}
fremem((void **)&list);
}
makeConnectivity(mol, FALSE, FALSE);
break;
case REPLACE_ATOM: replaceAtom(mol, picked);
break;
case ADD_ATOM: which=mol->na++;
mol->atoms=(struct ATOM *)expmem((void *)mol->atoms,
(size_t)mol->na, sizeof(struct ATOM));
replaceAtom(mol, which);
if (mol->unitcell) makeConnectivity(mol, FALSE, TRUE);
addAtom(mol, which, picked);
break;
}
if (mol->ninternal == 0)
fremem((void **)&(mol->internals));
else
mol->internals=(struct INTERNAL *)expmem((void *)mol->internals,
(size_t)mol->ninternal, sizeof(struct INTERNAL));
}
void replaceAtom(struct MOLECULE *mol, int which)
{
#include "isotopes.h"
int *move, nmove;
register int i;
mol->atoms[which].rad=elements[element].rad;
mol->atoms[which].radScale=elements[element].radScale;
mol->atoms[which].element=&elements[element];
mol->atoms[which].neutronScatterfac=0.0;
mol->atoms[which].basis=(struct BASISSET *)NULL;
strcpy(mol->atoms[which].name, elements[element].symbol);
strcpy(mol->atoms[which].basisname, "");
for (i=0; i<LASTELEMENT; i++)
{
if (!strncmp(mol->atoms[which].name, pse[i], 2))
{
mol->atoms[which].mass=isotope[i][0];
mol->atoms[which].nelectrons=electrons[i];
}
}
/* Adjust bond lengths */
move=(int *)getmem((size_t)mol->na, sizeof(int));
for (i=0; i<mol->nb; i++)
{
if (mol->bonds[i].first == which || mol->bonds[i].second == which)
{
mol->internals[mol->ninternal].atoms[0]=mol->bonds[i].first;
mol->internals[mol->ninternal].atoms[1]=mol->bonds[i].second;
mol->internals[mol->ninternal].type=BONDLENGTH;
move[0]=mol->bonds[i].first == which ? mol->bonds[i].second : mol->bonds[i].first;
if ((nmove=findAttachedAtoms(move, 1, which)) > 0)
changeBondLength(mol->ninternal, nmove, move,
0.9*(mol->atoms[mol->bonds[i].first].rad
+mol->atoms[mol->bonds[i].second].rad));
}
}
fremem((void *)&move);
}
void addAtom(struct MOLECULE *mol, int which, int picked)
{
mol->atoms[which].flags=ORIGINAL;
mol->atoms[which].nbonds=0;
if (picked == -1) /* if atom is not attached to another atom */
{
mol->atoms[which].x=0.0;
mol->atoms[which].y=0.0;
mol->atoms[which].z=0.0;
return;
}
else
{
mol->atoms[which].x=mol->atoms[picked].x+1.0;
mol->atoms[which].y=mol->atoms[picked].y;
mol->atoms[which].z=mol->atoms[picked].z;
}
mol->nb++;
mol->bonds=(struct BOND *)expmem((void *)mol->bonds, (size_t)mol->nb,
sizeof(struct BOND));
mol->bonds[mol->nb-1].first=picked;
mol->bonds[mol->nb-1].second=which;
mol->bonds[mol->nb-1].order=1;
mol->bonds[mol->nb-1].frac=mol->atoms[picked].rad/(mol->atoms[picked].rad+mol->atoms[which].rad);
mol->internals[mol->ninternal].atoms[0]=which;
mol->internals[mol->ninternal].atoms[1]=picked;
mol->internals[mol->ninternal].type=BONDLENGTH;
changeBondLength(mol->ninternal, 1, &which,
0.9*(mol->atoms[which].rad+mol->atoms[picked].rad));
changeCoordination(mol);
setWindowSize(centerMolecule(mol));
}
void changeCoordination(struct MOLECULE *mol)
{
double v1[3], v2[3], v3[3], t=torsionDefault, angle, sign;
int *bondPartners, *nbonds, max, imax, picked, added=FALSE;
int linear=FALSE, useDummy=FALSE;
register int i, j, n;
bondPartners=(int *)getmem((size_t)mol->na, sizeof(int));
picked=mol->internals[mol->ninternal].atoms[1];
bondPartners[0]=picked;
n=findBondPartners(bondPartners, 1, -1);
if (n < 3) return;
bondPartners=(int *)expmem((void *)bondPartners, (size_t)((n+2)*mol->na),
sizeof(int));
nbonds=(int *)getmem((size_t)n, sizeof(int));
max=0;
imax=0;
for (i=1; i<n; i++)
{
bondPartners[i*mol->na]=bondPartners[i];
if (abs(nbonds[i]=findAttachedAtoms(&bondPartners[i*mol->na], 1,
picked)) > max)
{
max=abs(nbonds[i]);
imax=i;
}
}
mol->internals[mol->ninternal].atoms[3]=bondPartners[imax*mol->na+1];
angle=180.;
sign=1.0;
for (i=1; i<n; i++)
{
if (nbonds[i] < 0) continue;
if (i != imax && (nbonds[i] != mol->na-2 || mol->na < 4))
{
mol->internals[mol->ninternal].atoms[0]=bondPartners[i];
mol->internals[mol->ninternal].atoms[2]=bondPartners[imax];
if (n > 4 && max <= 1)
mol->internals[mol->ninternal].atoms[3]=(-1);
else
{
if (bondAngle(mol->atoms, bondPartners[i],
picked, bondPartners[imax]) < 179.9)
linear=FALSE;
else
{
if (nbonds[imax] > 1)
{
for (j=0; j<nbonds[imax]; j++)
{
if (bondAngle(mol->atoms, bondPartners[i], picked,
bondPartners[imax*mol->na+j]) < 179.9)
{
mol->internals[mol->ninternal].atoms[3]=bondPartners[imax*mol->na+j];
break;
}
}
}
else
mol->internals[mol->ninternal].atoms[3]=(-1);
linear=TRUE;
}
}
mol->internals[mol->ninternal].type=ANGLE;
if (n == 3 && mol->atoms[picked].nelectrons > 4)
{
n+=mol->atoms[picked].nelectrons-4;
added=TRUE;
}
switch (n)
{
case 3: (void)changeAngle(mol->ninternal, nbonds[i],
&bondPartners[i*mol->na], 180.);
break;
case 4: (void)changeAngle(mol->ninternal, nbonds[i],
&bondPartners[i*mol->na], sign*120.0);
if (linear) sign=(-1.0);
break;
case 5: (void)changeAngle(mol->ninternal, nbonds[i],
&bondPartners[i*mol->na], 109.47122);
break;
default: (void)changeAngle(mol->ninternal, nbonds[i],
&bondPartners[i*mol->na], angle);
angle=90.;
break;
}
if (added)
{
n-=mol->atoms[picked].nelectrons-4;
added=FALSE;
}
if (n > 3)
{
mol->internals[mol->ninternal].type=TORSION;
if (mol->internals[mol->ninternal].atoms[3] >= 0)
{
if (!changeAngle(mol->ninternal, nbonds[i], &bondPartners[i*mol->na], t))
{
useDummy=TRUE;
v1[0]=mol->atoms[bondPartners[i]].x-mol->atoms[picked].x;
v1[1]=mol->atoms[bondPartners[i]].y-mol->atoms[picked].y;
v1[2]=mol->atoms[bondPartners[i]].z-mol->atoms[picked].z;
v2[0]=mol->atoms[bondPartners[imax]].x-mol->atoms[picked].x;
v2[1]=mol->atoms[bondPartners[imax]].y-mol->atoms[picked].y;
v2[2]=mol->atoms[bondPartners[imax]].z-mol->atoms[picked].z;
vectorProduct(v1, v2, v3);
mol->atoms=(struct ATOM *)expmem((void *)mol->atoms, (size_t)(mol->na+1),
sizeof(struct ATOM));
mol->atoms[mol->na].x=mol->atoms[bondPartners[imax]].x+v3[0];
mol->atoms[mol->na].y=mol->atoms[bondPartners[imax]].y+v3[1];
mol->atoms[mol->na].z=mol->atoms[bondPartners[imax]].z+v3[2];
mol->internals[mol->ninternal].atoms[3]=mol->na;
(void)changeAngle(mol->ninternal, nbonds[i], &bondPartners[i*mol->na], t);
}
if (n > 5)
t+=360.0/(double)(n-3);
else
t+=360.0/(double)(n-2);
}
else
{
if (n > 4)
{
if (!useDummy)
{
useDummy=TRUE;
v1[0]=mol->atoms[bondPartners[i]].x-mol->atoms[picked].x;
v1[1]=mol->atoms[bondPartners[i]].y-mol->atoms[picked].y;
v1[2]=mol->atoms[bondPartners[i]].z-mol->atoms[picked].z;
v2[0]=mol->atoms[bondPartners[imax]].x-mol->atoms[picked].x;
v2[1]=mol->atoms[bondPartners[imax]].y-mol->atoms[picked].y;
v2[2]=mol->atoms[bondPartners[imax]].z-mol->atoms[picked].z;
vectorProduct(v1, v2, v3);
mol->atoms=(struct ATOM *)expmem((void *)mol->atoms, (size_t)(mol->na+1),
sizeof(struct ATOM));
mol->atoms[mol->na].x=mol->atoms[bondPartners[imax]].x+v3[0];
mol->atoms[mol->na].y=mol->atoms[bondPartners[imax]].y+v3[1];
mol->atoms[mol->na].z=mol->atoms[bondPartners[imax]].z+v3[2];
}
mol->internals[mol->ninternal].atoms[3]=mol->na;
(void)changeAngle(mol->ninternal, nbonds[i], &bondPartners[i*mol->na], t);
if (n > 5)
t+=360.0/(double)(n-3);
else
t+=360.0/(double)(n-2);
}
}
}
}
} /* end of for-loop */
fremem((void **)&bondPartners);
fremem((void **)&nbonds);
if (useDummy) mol->atoms=(struct ATOM *)expmem((void *)mol->atoms, (size_t)(mol->na),
sizeof(struct ATOM));
}
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