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Merge pull request #118 from Discngine/issue-80

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Issue 80
This commit is contained in:
Peter Schmidtke
2023-11-23 09:08:50 +01:00
committed by GitHub
parent 0a150455e0 225fd07b15
commit 5614b44600
3 changed files with 15 additions and 20 deletions
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2
headers/rpdb.h
View File

@@ -142,7 +142,7 @@ s_min_max_coords *float_get_min_max_from_pdb(s_pdb *pdb);
void init_coord_grid(s_pdb *pdb);
void create_coord_grid(s_pdb *pdb);
void fill_coord_grid(s_pdb *pdb);
s_atom_ptr_list *init_atom_ptr_list(void);
// s_atom_ptr_list *init_atom_ptr_list(void);
short get_mm_type_from_element(char *symbol);

23
src/fpout.c
View File

@@ -58,6 +58,7 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
char pdb_code[350] = "";
char pdb_path[350] = "";
char out_path[350] = "";
char out_path_tmp[350] = "";
char pdb_out_path[350] = "";
char info_out_path[350] = "";
char mmcif_out_path[350] = "";
@@ -85,34 +86,34 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
return;
}
sprintf(out_path, "%s/%s", out_path, pdb_code);
sprintf(pdb_out_path, "%s_out.pdb", out_path);
sprintf(out_path_tmp, "%s/%s", out_path, pdb_code);
sprintf(pdb_out_path, "%s_out.pdb", out_path_tmp);
sprintf(mmcif_out_path, "%s_out.cif", out_path);
sprintf(mmcif_out_path, "%s_out.cif", out_path_tmp);
/* Write vmd and pymol scripts */
sprintf(fout, "%s_out.pdb", pdb_code);
write_visualization(out_path, fout);
write_visualization(out_path_tmp, fout);
/* Writing full pdb */
//printf("%s\n",write_mode);
if(write_mode[0] == 'p' || write_mode[0] == 'b'){
sprintf(pdb_out_path, "%s_out.pdb", out_path);
sprintf(pdb_out_path, "%s_out.pdb", out_path_tmp);
write_pockets_single_pdb(pdb_out_path, pdb, pockets);
}
/*Writing full mmcif*/
if(write_mode[0] == 'm' || write_mode[0] == 'b'){
sprintf(mmcif_out_path, "%s_out.cif", out_path);
sprintf(mmcif_out_path, "%s_out.cif", out_path_tmp);
write_pockets_single_mmcif(mmcif_out_path, pdb, pockets);
}
sprintf(info_out_path, "%s_info.txt", out_path);
sprintf(info_out_path, "%s_info.txt", out_path_tmp);
write_out_fpocket_info_file(pockets, info_out_path);
/* Writing pockets as a single pqr */
sprintf(fout, "%s_pockets.pqr", out_path);
sprintf(fout, "%s_pockets.pqr", out_path_tmp);
write_pockets_single_pqr(fout, pockets);
/* Writing individual pockets pqr */
@@ -121,14 +122,14 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
else
sprintf(out_path, "%s_out", pdb_code);
sprintf(out_path, "%s/pockets", out_path);
sprintf(command, "mkdir %s", out_path);
sprintf(out_path_tmp, "%s/pockets", out_path);
sprintf(command, "mkdir %s", out_path_tmp);
status = system(command);
/*if(status != 0) {
return ;
}*/
write_each_pocket(out_path, pockets);
write_each_pocket(out_path_tmp, pockets);
}
}
/**

10
src/rpdb.c
View File

@@ -186,13 +186,6 @@ s_min_max_coords *float_get_min_max_from_pdb(s_pdb *pdb)
return (NULL);
}
s_atom_ptr_list *init_atom_ptr_list()
{
s_atom_ptr_list *ret = my_malloc(sizeof(s_atom_ptr_list));
ret->natoms = 0;
ret->latoms = (s_atm **)my_malloc(sizeof(s_atm *));
return (ret);
}
void create_coord_grid(s_pdb *pdb)
{
@@ -284,7 +277,8 @@ void init_coord_grid(s_pdb *pdb)
g->atom_ptr[cx][cy] = (s_atom_ptr_list *)my_malloc(sizeof(s_atom_ptr_list) * g->nz);
for (cz = 0; cz < g->nz; cz++)
{
g->atom_ptr[cx][cy][cz] = *init_atom_ptr_list();
g->atom_ptr[cx][cy][cz].natoms = 0;
g->atom_ptr[cx][cy][cz].latoms = (s_atm **)my_malloc(sizeof(s_atm *));
}
}
}