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'

makefile

@@ -47,7 +47,7 @@ COS         = -DM_OS_LINUX
 CDEBUG      = -DMNO_MEM_DEBUG
 CWARN       = -W -Wextra -Wwrite-strings -Wstrict-prototypes
 
-CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
+CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=gnu99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
 QCFLAGS     = -O -g -pg -ansi
 
 LGSL        = -L$(PATH_GSL)lib -lgsl -lgslcblas 

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]))