Raj and Yoav session in making multiple protein species

Samo Penic

2021-05-10 6487a03362d35589c286d0660eba123a7ab00535

Raj and Yoav session in making multiple protein species

 src/energy.c

@@ -213,7 +213,7 @@
}

ts_double direct_force_energy(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *vtx_old){
    if(fabs(vtx->c)<1e-15) return 0.0;
    if(fabs(vtx->direct_interaction_force)<1e-15) return 0.0;
//    printf("was here");
    if(fabs(vesicle->tape->F)<1e-15) return 0.0;


 src/general.h

@@ -158,6 +158,7 @@
        ts_double solAngle;
        struct ts_poly *grafted_poly;
        struct ts_cluster *cluster;
    ts_double direct_interaction_force;
};
typedef struct ts_vertex ts_vertex;


 src/initial_distribution.c

@@ -137,6 +137,7 @@
                continue;
            }
            vesicle->vlist->vtx[rndvtx]->c=tape->c0;
            vesicle->vlist->vtx[rndvtx]->direct_interaction_force=tape->F;
        }
        mean_curvature_and_energy(vesicle);
        if(fabs(tape->w)>1e-16){ //if nonzero energy

 src/io.c

@@ -935,6 +935,30 @@
            }
        }
    fprintf(fh,"</DataArray>\n");
    fprintf(fh,"<DataArray type=\"Float64\" Name=\"direct_interaction_force\" format=\"ascii\">");
    for(i=0;i<vlist->n;i++){
        fprintf(fh,"%.17e ",vtx[i]->direct_interaction_force);
    }
        //polymeres
        if(poly){
            poly_idx=vlist->n;
            for(i=0;i<vesicle->poly_list->n;i++){
                for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
                    fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->direct_interaction_force);
                }
            }
        }
        //filaments
        if(fil){
            poly_idx=vlist->n+monono*polyno;
            for(i=0;i<vesicle->filament_list->n;i++){
                for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
        //    fprintf(stderr,"was here\n");
                    fprintf(fh,"%.17e ",  vesicle->filament_list->poly[i]->vlist->vtx[j]->direct_interaction_force);
                }
            }
        }
    fprintf(fh,"</DataArray>\n");

    //here comes additional data. Energy!
    fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");

 src/restore.c

@@ -362,6 +362,29 @@
                }
                xmlFree(values);        
            }
            if(!xmlStrcmp(property_name,(const xmlChar *)"direct_interaction_force")){
                values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
                vals=(char *)values;
                token=strtok(vals," ");
                idx=0;
                while(token!=NULL){
                    if(idx<vesicle->vlist->n){
                        vesicle->vlist->vtx[idx]->direct_interaction_force=atof(token);
                    } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
                        polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
                        monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
                        vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->direct_interaction_force=atof(token);
                    } else {
                        filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
                        fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
                        //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
                        vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->direct_interaction_force=atof(token);
                    }
                    idx++;
                    token=strtok(NULL," ");
                }
                xmlFree(values);		
            }
            xmlFree(property_name);
        }
        

 src/tape

@@ -30,9 +30,9 @@

####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=10
npoly=0
# nmono is a number of monomers in each polymer
nmono=20
nmono=0
# Spring constant between monomers of the polymer
k_spring=800
#set to 1 if half of the polymeres are inside the vesicle
@@ -92,9 +92,9 @@


#number of vertices with spontaneous curvature (integer)
number_of_vertices_with_c0=0
number_of_vertices_with_c0=200
#c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float)
c0=0.5
c0=1.0
#energy of attraction of vertices with spontaneous curvature (float, positive value for attraction)
w=10.0
#direct force on vesicles with spontaneous curvature (float)