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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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|
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#include "pov_writer.h" |
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#include "atom_parser.h" |
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|
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struct bond{ |
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int i; |
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int j; |
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}; |
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|
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struct linked_bond_list{ |
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struct bond the_bond; |
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struct linked_bond_list *next; |
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}; |
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|
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void make_bonds(struct coords *, int); |
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|
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struct linked_bond_list *bl_head; |
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|
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void clean_bonds(void); |
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|
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void initBondList(void){ |
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bl_head = NULL; |
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} |
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|
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void pov_write(FILE *out_file, struct coords *the_coords, int n_atoms, |
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int d_hydrogens, int d_bonds, int d_atoms){ |
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|
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int i,j; /*loop counters */ |
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int skip_atom, skip_bond, test1, test2; /*booleans */ |
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double dx, dy, dz; /* used in making the bonds */ |
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|
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struct linked_bond_list *current_bond; /*keeps track of the linked list*/ |
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|
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for(i = 0; i < n_atoms; i++){ |
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update_types(the_coords[i].name); |
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} |
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|
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if(d_atoms){ |
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|
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fprintf(out_file, |
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"//************************************************************\n" |
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"// The list of atoms\n" |
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"//************************************************************\n" |
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"\n" |
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"\n"); |
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|
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for(i = 0; i < n_atoms; i++){ |
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|
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skip_atom = 0; |
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|
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if(!d_hydrogens){ |
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skip_atom = !strcmp("H", the_coords[i].name); |
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} |
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|
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if(!skip_atom){ |
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|
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fprintf(out_file, |
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"make_%s_atom( %lf, %lf, %lf )\n", |
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the_coords[i].name, |
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the_coords[i].x, |
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the_coords[i].z, |
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the_coords[i].y); |
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} |
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} |
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|
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fprintf(out_file, |
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"\n" |
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"\n"); |
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|
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} |
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|
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if(d_bonds){ |
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|
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fprintf(out_file, |
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"//************************************************************\n" |
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"// The list of bonds\n" |
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"//************************************************************\n" |
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"\n" |
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"\n"); |
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|
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if( bl_head == NULL ) make_bonds(the_coords, n_atoms); |
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|
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current_bond = bl_head->next; |
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|
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while(current_bond != NULL){ |
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|
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skip_bond = 0; |
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|
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i = current_bond->the_bond.i; |
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j = current_bond->the_bond.j; |
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|
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if(!d_hydrogens){ |
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|
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test1 = !strcmp("H", the_coords[i].name); |
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test2 = !strcmp("H", the_coords[j].name); |
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|
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skip_bond = (test1 || test2); |
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} |
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|
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if(!skip_bond){ |
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|
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dx = (the_coords[j].x - the_coords[i].x) / 2.0; |
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dy = (the_coords[j].y - the_coords[i].y) / 2.0; |
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dz = (the_coords[j].z - the_coords[i].z) / 2.0; |
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|
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fprintf(out_file, |
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"make_%s_bond( %lf, %lf, %lf, %lf, %lf, %lf )\n", |
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the_coords[i].name, |
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the_coords[i].x, |
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the_coords[i].z, |
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the_coords[i].y, |
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(the_coords[i].x + dx), |
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(the_coords[i].z + dz), |
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(the_coords[i].y + dy)); |
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|
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fprintf(out_file, |
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"make_%s_bond( %lf, %lf, %lf, %lf, %lf, %lf )\n", |
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the_coords[j].name, |
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the_coords[j].x, |
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the_coords[j].z, |
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the_coords[j].y, |
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(the_coords[j].x - dx), |
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(the_coords[j].z - dz), |
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(the_coords[j].y - dy)); |
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|
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fprintf(out_file, "\n"); |
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} |
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|
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current_bond = current_bond->next; |
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} |
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|
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if( regenerateBonds )clean_bonds(); |
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} |
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} |
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|
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|
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void make_bonds(struct coords *the_coords, int n_atoms){ |
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|
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int i, j; /*counters */ |
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struct linked_bond_list *temp_bond; /*bond place holder */ |
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|
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const double bond_fudge = 1.12; // a fudge factor |
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struct atom type_i, type_j; /* holds the atom types */ |
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|
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int test; /* booleans */ |
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double dx, dy, dz, dr2, dcv, dcv2; // used to determine bond existence |
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|
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|
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bl_head = (struct linked_bond_list *)malloc(sizeof(struct linked_bond_list)); |
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bl_head->next = NULL; |
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|
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for(i = 0; i < (n_atoms - 1); i++){ |
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|
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for(j = (i+1); j < n_atoms; j++){ |
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|
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dx = the_coords[j].x - the_coords[i].x; |
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dy = the_coords[j].y - the_coords[i].y; |
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dz = the_coords[j].z - the_coords[i].z; |
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|
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dr2 = dx * dx + dy * dy + dz * dz; |
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|
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test = !findAtomType(the_coords[i].name, &type_i); |
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if(test){ |
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fprintf(stderr, "Atom Type %s, not found!\n", |
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the_coords[i].name); |
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exit(8); |
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} |
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|
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test = !findAtomType(the_coords[j].name, &type_j); |
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if(test){ |
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fprintf(stderr, "Atom Type %s, not found!\n", |
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the_coords[j].name); |
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exit(8); |
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} |
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|
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|
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dcv = bond_fudge * (type_i.covalentRadii + type_j.covalentRadii); |
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dcv2 = dcv * dcv; |
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|
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if(dr2 <= dcv2){ |
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|
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temp_bond = |
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(struct linked_bond_list *)malloc(sizeof(struct linked_bond_list)); |
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|
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bl_head->the_bond.i = i; |
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bl_head->the_bond.j = j; |
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|
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temp_bond->next = bl_head; |
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bl_head = temp_bond; |
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} |
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} |
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} |
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} |
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|
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|
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void clean_bonds(){ |
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struct linked_bond_list *current_bond; |
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struct linked_bond_list *next_bond; /* place holders */ |
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|
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|
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current_bond = bl_head->next; |
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|
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while(current_bond != NULL){ |
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|
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next_bond = current_bond->next; |
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free(current_bond); |
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current_bond = next_bond; |
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} |
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|
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bl_head->next = NULL; |
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free( bl_head ); |
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bl_head = NULL; |
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} |
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|
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|
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void make_header_macros(FILE *out_file){ |
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|
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struct linked_atom *type_list; // list of all atom types |
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struct linked_atom *current_type; // current atom type |
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|
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char *name; |
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double red, green, blue; |
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double radius; |
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|
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type_list = get_type_list(); |
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current_type = type_list->next; |
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|
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while(current_type != NULL){ |
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|
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name = current_type->myAtom.name; |
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radius = current_type->myAtom.vanDerWallRadii; |
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red = ((double)current_type->myAtom.red) / 255.0; |
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green = ((double)current_type->myAtom.green) / 255.0; |
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blue = ((double)current_type->myAtom.blue) / 255.0; |
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|
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|
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|
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fprintf(out_file, |
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"//****************************************************\n" |
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"// DEFINE %s MACROS\n" |
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"//****************************************************\n" |
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"\n" |
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"#macro make_%s_bond " |
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"(end_1x, end_1y, end_1z, end_2x, end_2y, end_2z)\n" |
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"\n" |
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" #local x1 = end_1x;\n" |
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" #local y1 = end_1y;\n" |
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" #local z1 = end_1z;\n" |
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" #local x2 = end_2x;\n" |
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" #local y2 = end_2y;\n" |
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" #local z2 = end_2z;\n" |
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"\n" |
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" #if(ROTATE)\n" |
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" #local x1_new = A11 * x1 + A12 * y1 + A13 * z1;\n" |
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" #local y1_new = A21 * x1 + A22 * y1 + A23 * z1;\n" |
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" #local z1_new = A31 * x1 + A32 * y1 + A33 * z1;\n" |
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"\n" |
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" #local x2_new = A11 * x2 + A12 * y2 + A13 * z2;\n" |
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" #local y2_new = A21 * x2 + A22 * y2 + A23 * z2;\n" |
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" #local z2_new = A31 * x2 + A32 * y2 + A33 * z2;\n" |
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"\n" |
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" #else\n" |
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" #local x1_new = x1;" |
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" #local y1_new = y1;" |
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" #local z1_new = z1;" |
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"\n" |
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" #local x2_new = x2;" |
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" #local y2_new = y2;" |
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" #local z2_new = z2;" |
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"\n" |
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" #end\n" |
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"\n" |
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" cylinder{\n" |
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" < x1_new, y1_new, z1_new >,\n" |
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" < x2_new, y2_new, z2_new >,\n" |
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" BOND_RADIUS\n" |
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" texture{\n" |
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" pigment{ rgb < %lf, %lf, %lf > }\n" |
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" finish{\n" |
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" ambient .2\n" |
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" diffuse .6\n" |
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" specular 1\n" |
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" roughness .001\n" |
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" metallic\n" |
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" }\n" |
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" }\n" |
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" }\n" |
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"#end\n" |
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"#macro make_%s_atom " |
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"(center_x, center_y, center_z)\n" |
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"\n" |
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" #local x1 = center_x;\n" |
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" #local y1 = center_y;\n" |
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" #local z1 = center_z;\n" |
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"\n" |
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" #if(ROTATE)\n" |
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"\n" |
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" #local x1_new = A11 * x1 + A12 * y1 + A13 * z1;\n" |
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" #local y1_new = A21 * x1 + A22 * y1 + A23 * z1;\n" |
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" #local z1_new = A31 * x1 + A32 * y1 + A33 * z1;\n" |
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"\n" |
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" #else\n" |
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"\n" |
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" #local x1_new = x1;" |
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" #local y1_new = y1;" |
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" #local z1_new = z1;" |
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"\n" |
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" #end\n" |
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"\n" |
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" sphere{\n" |
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" < x1_new, y1_new, z1_new >,\n" |
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" ATOM_SPHERE_FACTOR * %lf\n" |
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" texture{\n" |
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" pigment{ rgb < %lf, %lf, %lf > }\n" |
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" finish{\n" |
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" ambient .2\n" |
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" diffuse .6\n" |
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" specular 1\n" |
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" roughness .001\n" |
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" metallic\n" |
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" }\n" |
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" }\n" |
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" }\n" |
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"#end\n" |
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"\n" |
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"\n", |
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name, |
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name, |
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red, green, blue, |
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name, |
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radius, |
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red, green, blue); |
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|
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current_type = current_type->next; |
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} |
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} |
