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mmeineke |
60 |
#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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#include "pov_writer.h" |
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#include "atom_parser.h" |
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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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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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void make_bonds(struct coords *, int); |
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struct linked_bond_list *bl_head; |
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void clean_bonds(void); |
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mmeineke |
508 |
void initBondList(void){ |
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bl_head = NULL; |
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} |
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mmeineke |
60 |
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void pov_write(FILE *out_file, struct coords *the_coords, int n_atoms, |
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gezelter |
864 |
int d_hydrogens, int d_bonds, int d_atoms, int d_vectors){ |
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mmeineke |
60 |
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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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struct linked_bond_list *current_bond; /*keeps track of the linked list*/ |
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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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if(d_atoms){ |
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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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gezelter |
864 |
|
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mmeineke |
60 |
for(i = 0; i < n_atoms; i++){ |
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gezelter |
864 |
skip_atom = 0; |
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mmeineke |
60 |
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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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gezelter |
864 |
if(!skip_atom){ |
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mmeineke |
60 |
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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gezelter |
864 |
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mmeineke |
60 |
fprintf(out_file, |
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"\n" |
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"\n"); |
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gezelter |
864 |
} |
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if (d_vectors) { |
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fprintf(out_file, |
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"//************************************************************\n" |
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"// The list of vectors\n" |
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"//************************************************************\n" |
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"\n" |
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"\n"); |
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mmeineke |
60 |
|
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gezelter |
864 |
for(i = 0; i < n_atoms; i++){ |
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if (the_coords[i].hasVector) { |
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fprintf(out_file, |
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"make_%s_vector(%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].ux, |
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the_coords[i].uz, |
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the_coords[i].uy); |
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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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mmeineke |
60 |
} |
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gezelter |
864 |
|
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mmeineke |
60 |
if(d_bonds){ |
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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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mmeineke |
508 |
if( bl_head == NULL ) make_bonds(the_coords, n_atoms); |
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mmeineke |
60 |
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current_bond = bl_head->next; |
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while(current_bond != NULL){ |
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skip_bond = 0; |
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i = current_bond->the_bond.i; |
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j = current_bond->the_bond.j; |
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if(!d_hydrogens){ |
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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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skip_bond = (test1 || test2); |
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} |
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if(!skip_bond){ |
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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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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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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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fprintf(out_file, "\n"); |
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} |
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current_bond = current_bond->next; |
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} |
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mmeineke |
508 |
if( regenerateBonds )clean_bonds(); |
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mmeineke |
60 |
} |
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} |
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void make_bonds(struct coords *the_coords, int n_atoms){ |
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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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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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int test; /* booleans */ |
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double dx, dy, dz, dr2, dcv, dcv2; // used to determine bond existence |
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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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for(i = 0; i < (n_atoms - 1); i++){ |
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for(j = (i+1); j < n_atoms; j++){ |
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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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dr2 = dx * dx + dy * dy + dz * dz; |
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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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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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dcv = bond_fudge * (type_i.covalentRadii + type_j.covalentRadii); |
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dcv2 = dcv * dcv; |
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if(dr2 <= dcv2){ |
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temp_bond = |
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(struct linked_bond_list *)malloc(sizeof(struct linked_bond_list)); |
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bl_head->the_bond.i = i; |
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bl_head->the_bond.j = j; |
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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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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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current_bond = bl_head->next; |
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while(current_bond != NULL){ |
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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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bl_head->next = NULL; |
| 244 |
mmeineke |
508 |
free( bl_head ); |
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bl_head = NULL; |
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mmeineke |
60 |
} |
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void make_header_macros(FILE *out_file){ |
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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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char *name; |
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double red, green, blue; |
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double radius; |
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type_list = get_type_list(); |
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current_type = type_list->next; |
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while(current_type != NULL){ |
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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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fprintf(out_file, |
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"//****************************************************\n" |
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"// DEFINE %s MACROS\n" |
| 274 |
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"//****************************************************\n" |
| 275 |
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"\n" |
| 276 |
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"#macro make_%s_bond " |
| 277 |
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"(end_1x, end_1y, end_1z, end_2x, end_2y, end_2z)\n" |
| 278 |
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"\n" |
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" #local x1 = end_1x;\n" |
| 280 |
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" #local y1 = end_1y;\n" |
| 281 |
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" #local z1 = end_1z;\n" |
| 282 |
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" #local x2 = end_2x;\n" |
| 283 |
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" #local y2 = end_2y;\n" |
| 284 |
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" #local z2 = end_2z;\n" |
| 285 |
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"\n" |
| 286 |
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" #if(ROTATE)\n" |
| 287 |
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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" |
| 289 |
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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" |
| 292 |
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" #local y2_new = A21 * x2 + A22 * y2 + A23 * z2;\n" |
| 293 |
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" #local z2_new = A31 * x2 + A32 * y2 + A33 * z2;\n" |
| 294 |
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"\n" |
| 295 |
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" #else\n" |
| 296 |
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" #local x1_new = x1;" |
| 297 |
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" #local y1_new = y1;" |
| 298 |
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" #local z1_new = z1;" |
| 299 |
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"\n" |
| 300 |
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" #local x2_new = x2;" |
| 301 |
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" #local y2_new = y2;" |
| 302 |
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" #local z2_new = z2;" |
| 303 |
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"\n" |
| 304 |
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" #end\n" |
| 305 |
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"\n" |
| 306 |
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" cylinder{\n" |
| 307 |
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" < x1_new, y1_new, z1_new >,\n" |
| 308 |
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" < x2_new, y2_new, z2_new >,\n" |
| 309 |
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" BOND_RADIUS\n" |
| 310 |
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" texture{\n" |
| 311 |
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" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 312 |
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" finish{\n" |
| 313 |
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" ambient .2\n" |
| 314 |
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" diffuse .6\n" |
| 315 |
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" specular 1\n" |
| 316 |
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" roughness .001\n" |
| 317 |
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" metallic\n" |
| 318 |
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" }\n" |
| 319 |
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" }\n" |
| 320 |
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" }\n" |
| 321 |
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"#end\n" |
| 322 |
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"#macro make_%s_atom " |
| 323 |
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"(center_x, center_y, center_z)\n" |
| 324 |
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"\n" |
| 325 |
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" #local x1 = center_x;\n" |
| 326 |
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" #local y1 = center_y;\n" |
| 327 |
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" #local z1 = center_z;\n" |
| 328 |
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"\n" |
| 329 |
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" #if(ROTATE)\n" |
| 330 |
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"\n" |
| 331 |
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" #local x1_new = A11 * x1 + A12 * y1 + A13 * z1;\n" |
| 332 |
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" #local y1_new = A21 * x1 + A22 * y1 + A23 * z1;\n" |
| 333 |
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" #local z1_new = A31 * x1 + A32 * y1 + A33 * z1;\n" |
| 334 |
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"\n" |
| 335 |
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" #else\n" |
| 336 |
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"\n" |
| 337 |
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" #local x1_new = x1;" |
| 338 |
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" #local y1_new = y1;" |
| 339 |
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" #local z1_new = z1;" |
| 340 |
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"\n" |
| 341 |
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" #end\n" |
| 342 |
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"\n" |
| 343 |
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" sphere{\n" |
| 344 |
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" < x1_new, y1_new, z1_new >,\n" |
| 345 |
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" ATOM_SPHERE_FACTOR * %lf\n" |
| 346 |
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" texture{\n" |
| 347 |
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" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 348 |
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" finish{\n" |
| 349 |
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" ambient .2\n" |
| 350 |
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" diffuse .6\n" |
| 351 |
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" specular 1\n" |
| 352 |
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" roughness .001\n" |
| 353 |
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" metallic\n" |
| 354 |
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" }\n" |
| 355 |
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" }\n" |
| 356 |
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" }\n" |
| 357 |
|
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"#end\n" |
| 358 |
gezelter |
864 |
"#macro make_%s_vector " |
| 359 |
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"(center_x, center_y, center_z, ux, uy, uz)\n" |
| 360 |
mmeineke |
60 |
"\n" |
| 361 |
gezelter |
864 |
" #local vx = VECTOR_SCALE * ux;\n" |
| 362 |
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" #local vy = VECTOR_SCALE * uy;\n" |
| 363 |
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" #local vz = VECTOR_SCALE * uz;\n" |
| 364 |
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" #local x1 = center_x - 0.5 * vx;\n" |
| 365 |
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" #local y1 = center_y - 0.5 * vy;\n" |
| 366 |
|
|
" #local z1 = center_z - 0.5 * vz;\n" |
| 367 |
|
|
" #local x2 = center_x + 0.5 * vx;\n" |
| 368 |
|
|
" #local y2 = center_y + 0.5 * vy;\n" |
| 369 |
|
|
" #local z2 = center_z + 0.5 * vz;\n" |
| 370 |
|
|
" #local v2 = vx*vx + vy*vy + vz*vz;\n" |
| 371 |
|
|
" #local vl = sqrt(v2);\n" |
| 372 |
|
|
" #local x3 = x1 + vx * (1.0 - CONE_FRACTION);\n" |
| 373 |
|
|
" #local y3 = y1 + vy * (1.0 - CONE_FRACTION);\n" |
| 374 |
|
|
" #local z3 = z1 + vz * (1.0 - CONE_FRACTION);\n" |
| 375 |
|
|
"\n" |
| 376 |
|
|
" #if(ROTATE)\n" |
| 377 |
|
|
" #local x1_new = A11 * x1 + A12 * y1 + A13 * z1;\n" |
| 378 |
|
|
" #local y1_new = A21 * x1 + A22 * y1 + A23 * z1;\n" |
| 379 |
|
|
" #local z1_new = A31 * x1 + A32 * y1 + A33 * z1;\n" |
| 380 |
|
|
"\n" |
| 381 |
|
|
" #local x2_new = A11 * x2 + A12 * y2 + A13 * z2;\n" |
| 382 |
|
|
" #local y2_new = A21 * x2 + A22 * y2 + A23 * z2;\n" |
| 383 |
|
|
" #local z2_new = A31 * x2 + A32 * y2 + A33 * z2;\n" |
| 384 |
|
|
"\n" |
| 385 |
|
|
" #local x3_new = A11 * x3 + A12 * y3 + A13 * z3;\n" |
| 386 |
|
|
" #local y3_new = A21 * x3 + A22 * y3 + A23 * z3;\n" |
| 387 |
|
|
" #local z3_new = A31 * x3 + A32 * y3 + A33 * z3;\n" |
| 388 |
|
|
"\n" |
| 389 |
|
|
" #else\n" |
| 390 |
|
|
" #local x1_new = x1;" |
| 391 |
|
|
" #local y1_new = y1;" |
| 392 |
|
|
" #local z1_new = z1;" |
| 393 |
|
|
"\n" |
| 394 |
|
|
" #local x2_new = x2;" |
| 395 |
|
|
" #local y2_new = y2;" |
| 396 |
|
|
" #local z2_new = z2;" |
| 397 |
|
|
"\n" |
| 398 |
|
|
" #local x3_new = x3;" |
| 399 |
|
|
" #local y3_new = y3;" |
| 400 |
|
|
" #local z3_new = z3;" |
| 401 |
|
|
"\n" |
| 402 |
|
|
" #end\n" |
| 403 |
|
|
"\n" |
| 404 |
|
|
" cylinder{\n" |
| 405 |
|
|
" < x1_new, y1_new, z1_new >,\n" |
| 406 |
|
|
" < x3_new, y3_new, z3_new >,\n" |
| 407 |
|
|
" STICK_RADIUS\n" |
| 408 |
|
|
" texture{\n" |
| 409 |
|
|
" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 410 |
|
|
" finish{\n" |
| 411 |
|
|
" ambient .2\n" |
| 412 |
|
|
" diffuse .6\n" |
| 413 |
|
|
" specular 1\n" |
| 414 |
|
|
" roughness .001\n" |
| 415 |
|
|
" metallic\n" |
| 416 |
|
|
" }\n" |
| 417 |
|
|
" }\n" |
| 418 |
|
|
" }\n" |
| 419 |
|
|
" cone{\n" |
| 420 |
|
|
" < x2_new, y2_new, z2_new >, 0.0\n" |
| 421 |
|
|
" < x3_new, y3_new, z3_new >, CONE_RADIUS\n" |
| 422 |
|
|
" texture{\n" |
| 423 |
|
|
" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 424 |
|
|
" finish{\n" |
| 425 |
|
|
" ambient .2\n" |
| 426 |
|
|
" diffuse .6\n" |
| 427 |
|
|
" specular 1\n" |
| 428 |
|
|
" roughness .001\n" |
| 429 |
|
|
" metallic\n" |
| 430 |
|
|
" }\n" |
| 431 |
|
|
" }\n" |
| 432 |
|
|
" }\n" |
| 433 |
|
|
"#end\n" |
| 434 |
|
|
"\n" |
| 435 |
mmeineke |
60 |
"\n", |
| 436 |
|
|
name, |
| 437 |
|
|
name, |
| 438 |
|
|
red, green, blue, |
| 439 |
|
|
name, |
| 440 |
|
|
radius, |
| 441 |
gezelter |
864 |
red, green, blue, |
| 442 |
|
|
name, |
| 443 |
|
|
red, green, blue, |
| 444 |
mmeineke |
60 |
red, green, blue); |
| 445 |
|
|
|
| 446 |
|
|
current_type = current_type->next; |
| 447 |
|
|
} |
| 448 |
|
|
} |