Fix overflow in pocket file writing.

issue-151 fix of chain reading atoms in read_mmcif & descriptor outpu…

headers/descriptors.h

@@ -81,8 +81,8 @@ typedef struct s_desc
                 characterChain2,                         /**< 0 if protein, 1 if nucl acid pocket, 2 if HETATM pocket*/
                 numResChain1,                            /**<number of resdiues on chain 1*/
                 numResChain2;                           /**<number of res on chain 2*/
-        char nameChain1[2],        /**<name of the first chain in contact with the pocket*/
-                nameChain2[2];     /**<name of the second chain in contact with the pocket, if there is*/
+        char nameChain1[255],        /**<name of the first chain in contact with the pocket*/
+                nameChain2[255];     /**<name of the second chain in contact with the pocket, if there is*/
         char ligTag[8];           /**<het atom tag of ligands situated in the pocket*/
         
 } s_desc ;

src/descriptors.c

@@ -65,7 +65,6 @@ s_desc* allocate_s_desc(void)
 	s_desc *desc = (s_desc*)my_malloc(sizeof(s_desc)) ;
 	
 	reset_desc(desc) ;
-
 	return desc ;
 }
 
@@ -364,7 +363,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
 		nb_res_ids = 0 ;	/* Current number of residus */
 
 	int nb_polar_atm = 0 ;
-        char curChainName[2];
+        char *curChainName = (char*)my_malloc(255*sizeof(char));
         
         if(atoms && natoms>1){
             firstatom=atoms[0];
@@ -373,8 +372,8 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
             if(element_in_std_res(firstatom->res_name))             desc->characterChain1=0;
             else if(element_in_nucl_acid(firstatom->res_name))      desc->characterChain1=1;
             else if(element_in_kept_res(firstatom->res_name))       desc->characterChain1=2;
-            strncpy(desc->nameChain1,firstatom->chain,2);
-            strncpy(curChainName,firstatom->chain,2);
+            strcpy(desc->nameChain1,firstatom->chain);
+            strcpy(curChainName,firstatom->chain);
             desc->numResChain1 = countResidues(all_atoms,all_natoms,firstatom->chain);
 
             for(i = 0 ; i < natoms ; i++) {
@@ -384,7 +383,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
                             desc->interChain = 1;
                             if(!desc->numResChain2){
                                 desc->numResChain2 = countResidues(all_atoms,all_natoms,curatom->chain);
-                                strncpy(curChainName,curatom->chain,1);
+                                strcpy(curChainName,curatom->chain);
                             }
                         }
 

src/read_mmcif.c

@@ -124,9 +124,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             if (par->xlig_resnumber > -1)
             {
 
-                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
+                // if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
+                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && strcmp(at_in[i].chain_auth,par->xlig_chain_code)==0 && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
+
                 {
+
                     pdb->n_xlig_atoms++;
+
                 }
             }
         }
@@ -630,9 +634,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
 
                 unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
 
-                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
-                {
-                                        
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && strcmp(at_in[i].chain_auth, params->xlig_chain_code)==0 && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && strcmp(at_in[i].chain_auth, params->xlig_chain_code)==0 && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                {                      
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                     *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
                     *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];

src/writepocket.c

@@ -79,7 +79,7 @@ static const char atomSiteHeader[] =
 
 void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_pdb *pdb) {
     int out_len = strlen(out_path);
-    char out[out_len + 20];
+    char out[out_len + 40];
     out[0] = '\0';
 
     node_pocket *pcur;
@@ -500,7 +500,7 @@ void write_mdpockets_concat_pqr(FILE *f, c_lst_pockets *pockets) {
  */
 void write_each_pocket(const char out_path[], c_lst_pockets *pockets) {
     int out_len = strlen(out_path);
-    char out[out_len + 20];
+    char out[out_len + 40];
     out[0] = '\0';
 
     node_pocket *pcur;