translate_unit.c

Go to the documentation of this file.

// Function written by B. Lachele Foley, 2007
//#include "../inc/mylib.h"
//#include "../inc/molecules.h"

/****************** translate_molecule() *********************/
/* Translates the molecule so that the all coordinates are displaced
 * by the vector vec.  The source coordinates should be in cs and
 * the target coordinates go in ct (in either case, -1 means the
 * main coordinate location).
 */
/*
void translate_molecule(molecule *m,atype *ATYPE,int tw){
int ta=0,tuse=0,tsz=0,tbins=0;
double tmm=0; 

// calculate the molecular weight of residue 0 (the molecule, here) 
for(ta=0;ta<m[0].r[0].na;ta++){
        tmm+=ATYPE[m[0].r[0].a[ta].t].m;
        }
//printf("the molecular weight is %f\n",tmm);
if(tmm==0){mywhine("molecular weight of molecule %s is zero.\n(Have types/masses been assigned?");}
// glucose $molwt=174.078;

m[0].COM.i=0;
m[0].COM.j=0;
m[0].COM.k=0; 
//printf("center of mass is at: %f %f %f \n",m[0].COM.i,m[0].COM.j,m[0].COM.k);
// calculate the center of mass
for(ta=0;ta<m[0].r[0].na;ta++){ // COM = sum(m_i * r_i) / sum(m_i)
        m[0].COM.i+=m[0].r[0].a[ta].x.i*ATYPE[m[0].r[0].a[ta].t].m;
        m[0].COM.j+=m[0].r[0].a[ta].x.j*ATYPE[m[0].r[0].a[ta].t].m;
        m[0].COM.k+=m[0].r[0].a[ta].x.k*ATYPE[m[0].r[0].a[ta].t].m;
        }
//printf("center of mass is at: %f %f %f \n",m[0].COM.i,m[0].COM.j,m[0].COM.k);
m[0].COM.i/=tmm;
m[0].COM.j/=tmm;
m[0].COM.k/=tmm; 
//printf("center of mass is at: %20.12e %20.12e %20.12e \n",m[0].COM.i,m[0].COM.j,m[0].COM.k);

// move center of mass to specified location
if(tw==-1){
        for(ta=0;ta<m[0].r[0].na;ta++){ // xyz(new) = xyz(old) - COM
                m[0].r[0].a[ta].x.i-=m[0].COM.i;
                m[0].r[0].a[ta].x.j-=m[0].COM.j;
                m[0].r[0].a[ta].x.k-=m[0].COM.k;
                }
        }
else{
        for(ta=0;ta<m[0].r[0].na;ta++){ // xyz(new) = xyz(old) - COM
                tuse=malloc_usable_size(m[0].r[0].a[ta].xa);
                tsz=sizeof(coord_3D);
                if(tsz==0){mywhine("memory issue: sizeof(coord_3D) given as zero in translate_to_COM.c");}
                tbins=tuse/tsz; 
                //print_coord_3D(&m[0].r[0].a[ta].x);
                if(tbins<(tw+1)){mywhine("insufficient memory allocated before translate_to_COM");}
                m[0].r[0].a[ta].xa[tw].i=m[0].r[0].a[ta].x.i-m[0].COM.i;
                m[0].r[0].a[ta].xa[tw].j=m[0].r[0].a[ta].x.j-m[0].COM.j;
                m[0].r[0].a[ta].xa[tw].k=m[0].r[0].a[ta].x.k-m[0].COM.k;
                }
        }
return;
}
*/

// Function written by B. Lachele Foley, 2007
//#include "../inc/mylib.h"
//#include "../inc/molecules.h"
/****************** translate_zero_to_coord_M() *********************/
/* Translates the specifiec coords (location xs) so that the coordinate
indicated by c is at the origin.  Places the translated coords in xt. */
/*
void translate_zero_to_coord_M(molecule *m,int xs,int xt,coord_3D c){
int ta=0,tb,tuse=0,tsz=0,tbins=0;

// move center of mass to specified location
if((xs==-1)&&(xt==-1)){
        for(ta=0;ta<m[0].nr;ta++){ 
                for(tb=0;tb<m[0].r[ta].na;tb++){ 
                        m[0].r[ta].a[tb].x=subtract_coord(m[0].r[ta].a[tb].x,c);
                        }
                }
        }
if((xs!=-1)&&(xt==-1)){
        for(ta=0;ta<m[0].nr;ta++){ 
                for(tb=0;tb<m[0].r[ta].na;tb++){ 
                        tuse=malloc_usable_size(m[0].r[ta].a[tb].xa);
                        tsz=sizeof(coord_3D);
                        tbins=tuse/tsz; 
                        if(tbins<(xs+1)){mywhine("memory issue: source coords not allocated in translate_zero_to_coord");}
                        m[0].r[ta].a[tb].x=subtract_coord(m[0].r[ta].a[tb].xa[xs],c);
                        }
                }
        }
if((xs==-1)&&(xt!=-1)){
        for(ta=0;ta<m[0].nr;ta++){ 
                for(tb=0;tb<m[0].r[ta].na;tb++){ 
                        tuse=malloc_usable_size(m[0].r[ta].a[tb].xa);
                        tsz=sizeof(coord_3D);
                        tbins=tuse/tsz; 
                        if(tbins<(xt+1)){mywhine("memory issue: translated coords not allocated in translate_zero_to_coord");}
                        m[0].r[ta].a[tb].xa[xt]=subtract_coord(m[0].r[ta].a[tb].x,c);
                        }
                }
        }
if((xs!=-1)&&(xt!=-1)){
        for(ta=0;ta<m[0].nr;ta++){ 
                for(tb=0;tb<m[0].r[ta].na;tb++){ 
                        tuse=malloc_usable_size(m[0].r[ta].a[tb].xa);
                        tsz=sizeof(coord_3D); 
                        tbins=tuse/tsz; 
                        if(tbins<(xs+1)){mywhine("memory issue: source coords not allocated in translate_zero_to_coord");}
                        if(tbins<(xt+1)){mywhine("memory issue: translated coords not allocated in translate_zero_to_coord");}
                        m[0].r[ta].a[tb].xa[xt]=subtract_coord(m[0].r[ta].a[tb].xa[xs],c);
                        }
                }
        }
return;
}
*/