Merge pull request #121 from Discngine/issue-119

Issue 119

headers/fparams.h

@@ -121,7 +121,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_PAR_CHAIN_AS_LIGAND 'a' /**flag, to define which chains are defined as a ligand*/
 #define M_PAR_CHAIN_AS_LIGAND_LONG "chain_as_ligand"
 
-#define M_PAR_WRITE_MODE 'w' /**flag, to define which chains are defined as a ligand*/
+#define M_PAR_WRITE_MODE 'w' /**flag, to define write mode for pocket output: d->same as input, b or both -> both (pdb & cif), p or pdb ->pdb, m or cif -> mmcif*/
 #define M_PAR_WRITE_MODE_LONG "write_mode"
 
 #define M_PAR_MIN_N_EXPLICIT_POCKET 'u'

headers/rpdb.h

@@ -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);

src/fpout.c

@@ -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);
    }
 }
 /**

src/read_mmcif.c

@@ -79,13 +79,11 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     model_flag = 1;
     for (i = 0; i < inatoms; i++) /*loop to go through all atoms*/
     {
-
         if (at_in[i].altloc[0] == '.' || at_in[i].altloc[0] == '\0')
             at_in[i].altloc[0] = ' ';
         if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
         {
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
-
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '?')
             {
                 if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
                 {
@@ -138,7 +136,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
         else if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(par->chain_as_ligand, at_in[i].chain[0])))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == '?' || at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
             {
 
                 if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
@@ -291,7 +289,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
         if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1' || at_in[i].altloc[0] == '?')
             { /*if within first occurence*/
                 /* Enter this if when arg in command line is -r */
 
@@ -448,7 +446,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
         else if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(params->chain_as_ligand, at_in[i].chain[0])))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1' || at_in[i].altloc[0] =='?')
             { /*first occurence*/
 
                 if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))

src/rpdb.c

@@ -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 *));
             }
         }
     }