Merge pull request #147 from pegerto/m1_modfile

compile M1/M2 chip molfile plugin

.github/workflows/c-cpp.yml

@@ -15,10 +15,10 @@ jobs:
       run: sudo apt-get install libnetcdf-dev
     - name: make
       run: make fpocket
-    - name: Set up Python 3.7
+    - name: Set up Python 3.12
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.12
     - name: create conda environment
       run: conda env update -f ./tests/environment.yml   
     - name : activate

Dockerfile

@@ -0,0 +1,22 @@
+FROM debian:bookworm-slim
+RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
+RUN apt update -y && apt install -y gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/*
+
+# all of this mess is essentially to have a minimalistic build at the end
+COPY makefile /opt/fpocket/
+COPY src /opt/fpocket/src
+COPY man /opt/fpocket/man
+COPY headers /opt/fpocket/headers
+COPY obj /opt/fpocket/obj
+COPY scripts /opt/fpocket/scripts
+COPY bin /opt/fpocket/bin
+COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
+COPY plugins/include /opt/fpocket/plugins/include
+COPY plugins/noarch /opt/fpocket/plugins/noarch
+
+WORKDIR /opt/fpocket
+
+RUN make && make install && make clean
+USER fpocket
+WORKDIR /tmp
+CMD ["fpocket"]

Dockerfile-debian-slim

@@ -1,4 +1,4 @@
-FROM debian:bullseye-slim
+FROM debian:bookworm-slim
 RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
 RUN apt update -y && apt install -y gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/*
 

README.md

@@ -81,10 +81,10 @@ docker build -t fpocket/fpocket .
 This will build fpocket into your local fpocket/fpocket image. You can then run fpocket/mdpocket etc using: 
 
 ```bash
-docker run -v `pwd`:/WORKDIR fpocket/fpocket fpocket -f data/sample/1UYD.pdb
+docker run -v `pwd`:/workdir fpocket/fpocket fpocket -f /workdir/yourfile.pdb
 ```
 
-Here you mount your current directory with your input files into the preconfigured `/WORKDIR` in the docker container and then run fpocket on a file in that mounted folder.
+Here you mount your current directory with your input files into the preconfigured `/workdir` in the docker container and then run fpocket on a file in that mounted folder. Make sure that the folder is writeable to others if you run it through docker.
 
 ### Installing
 
@@ -107,6 +107,11 @@ make ARCH=MACOSXX86_64
 sudo make install
 ```
 
+For M1 and M2, use the MACOSXARM64 architecture:
+```
+ARCH=MACOSXARM64 make
+```
+
 #### Using conda
 
 There's also a conda package of fpocket available thanks to Simon Bray. You can install fpocket using conda with:

headers/atom.h

@@ -37,12 +37,14 @@ typedef struct s_atm
     char name[5],		/**< Atom name */
          type[7],		/**< Atom type */
          chain[16],		/**< Chain name */
+         label_asym_id[16],
          symbol[3],		/**< Chemical symbol of the atom */
          res_name[8];		/**< Atom residue name */
 
     int id,			/**< Atom id */
         seen,                   /**< Say if we have seen this atom during a neighbor search */
         res_id,			/**< Atom residue ID */
+        label_seq_id,   /**<MMCIF label seq ID*/
         atype,
         charge,                 /**< Atom charge */
         abpa;                   /**< 1 if atom is an abpa, 0 otherwise*/	

headers/fparams.h

@@ -55,6 +55,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_DB_RUN 0 /**< default value for running fpocket for populating a database, 0 default*/
 
 #define M_MAX_CHAINS_DELETE 20
+#define M_MAX_CHAIN_NAME_LENGTH 20
+#define M_MAX_LIG_RESNAME_LENGTH 20
 
 #define M_MIN_AS_DENSITY 0.7
 
@@ -121,7 +123,7 @@ 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'
@@ -184,8 +186,8 @@ typedef struct s_fparams
 	char custom_ligand[M_MAX_PDB_NAME_LEN]; /**container for custom pocket detection using a particular ligand*/
 	char custom_pocket_arg[M_MAX_CUSTOM_POCKET_LEN];
 	char **pdb_lst;
-	char xlig_chain_code[3];
-	char xlig_resname[3];
+	char *xlig_chain_code;
+	char *xlig_resname;
 	int xlig_resnumber;
 	int xpocket_n; /**number of residues defining the pocket to consider*/
 	char *xpocket_chain_code;
@@ -204,7 +206,8 @@ typedef struct s_fparams
 												 to be an apolar a-sphere */
 		nb_mcv_iter,						  /**< Number of iteration for the Monte Carlo volume
 												 calculation */
-		basic_volume_div,					  /**< Box division factor for basic volume calculation */
+		basic_volume_div;					  /**< Box division factor for basic volume calculation */
+	unsigned short
 		min_pock_nb_asph;					  /**< Minimump number of alpha spheres per pocket */
 
 	float clust_max_dist,				/**< First clustering distance criteria */
@@ -214,8 +217,10 @@ typedef struct s_fparams
 		asph_min_size,						/**< Minimum size of alpha spheres to keep */
 		min_as_density,						/**<Minimum alpha sphere density for a pocket to be retained*/
 		asph_max_size;						/**< Maximum size of alpha spheres to keep */
-	char chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
-	char chain_as_ligand[M_MAX_CHAINS_DELETE];
+	char *chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
+	unsigned short n_chains_to_delete;
+	unsigned short n_chains_as_ligand;
+	char *chain_as_ligand[M_MAX_CHAINS_DELETE];
 	int chain_is_kept;	/* To choose if we keep the chains or not*/
 	char write_par[10]; /*write mode : d -> default | b -> both pdb and mmcif | p ->pdb | m  -> mmcif*/
 

headers/refine.h

@@ -31,7 +31,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 /* --------------------------PROTOTYPES---------------------------------------*/
 
 void refinePockets(c_lst_pockets *pockets, s_fparams *params);
-void apply_clustering(c_lst_pockets *pockets, s_fparams *params);
+void apply_clustering(c_lst_pockets *pockets);
 void reIndexPockets(c_lst_pockets *pockets);
 void dropSmallNpolarPockets(c_lst_pockets *pockets, s_fparams *params);
 void drop_tiny(c_lst_pockets *pockets, s_fparams *params) ;

headers/rpdb.h

@@ -146,6 +146,6 @@ void fill_coord_grid(s_pdb *pdb);
 
 
 short get_mm_type_from_element(char *symbol);
-int chains_to_delete(char *chains_selected, char current_line_chain, int is_chain_kept);
-int is_ligand(char *chains_selected, char current_line_chain);
+int chains_to_delete(char *chains_selected[20], char *current_line_chain, int is_chain_kept,unsigned short n_chains_to_delete);
+int is_ligand(char *chains_selected[20], char *current_line_chain, unsigned short n_chains_as_ligand);
 #endif

headers/utils.h

@@ -33,7 +33,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 /* ------------------------------- PUBLIC MACROS ---------------------------- */
 
-#define M_MAX_PDB_NAME_LEN 200  /**< maximum pdb filename length*/
+#define M_MAX_PDB_NAME_LEN 2000  /**< maximum pdb filename length*/
 #define M_MAX_CUSTOM_POCKET_LEN 8000 /** maximum length for a custom pocket string*/
 #define M_SIGN 1
 #define M_NO_SIGN 0

headers/writepdb.h

@@ -28,6 +28,6 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom
 
 void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[], 
 						 char alt_loc, const char res_name[], const char chain[], 
-						 int res_id, const char insert, float x, float y, float z, float occ, 
+						 int res_id,  const char label_asym_id[],int label_seq_id, const char insert, float x, float y, float z, float occ, 
 						 float bfactor, int abpa, const char *symbol, int charge,float abpa_prob) ;
 #endif

headers/writepocket.h

@@ -40,6 +40,7 @@ void write_pdb_atoms(FILE *f, s_atm *atoms, int natoms) ;
 void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets,s_pdb *pdb);
 void write_pocket_pqr_DB(const char out[], s_pocket *pocket);
 void write_pocket_pdb_DB(const char out[], s_pocket *pocket,s_pdb *pdb);
+void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb);
 
 void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms);
 void write_pockets_single_mmcif(const char out[], s_pdb *pdb, c_lst_pockets *pockets);

makefile

@@ -1,7 +1,7 @@
 #------------------------------------------------------------
 # Makefile.
 #------------------------------------------------------------
-#ARCH	    = MACOSXX86_64
+# ARCH	    = MACOSXX86_64
 ARCH	    = LINUXAMD64
 export ARCH
 
@@ -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 

plugins/MACOSXARM64/molfile/libmolfile_plugin.h

@@ -0,0 +1,415 @@
+#ifndef LIBMOLFILE_PLUGIN_H
+#define LIBMOLFILE_PLUGIN_H
+#include "vmdplugin.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int molfile_abinitplugin_init(void);
+extern int molfile_abinitplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_abinitplugin_fini(void);
+extern int molfile_amiraplugin_init(void);
+extern int molfile_amiraplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_amiraplugin_fini(void);
+extern int molfile_avsplugin_init(void);
+extern int molfile_avsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_avsplugin_fini(void);
+extern int molfile_babelplugin_init(void);
+extern int molfile_babelplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_babelplugin_fini(void);
+extern int molfile_basissetplugin_init(void);
+extern int molfile_basissetplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_basissetplugin_fini(void);
+extern int molfile_bgfplugin_init(void);
+extern int molfile_bgfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_bgfplugin_fini(void);
+extern int molfile_binposplugin_init(void);
+extern int molfile_binposplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_binposplugin_fini(void);
+extern int molfile_biomoccaplugin_init(void);
+extern int molfile_biomoccaplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_biomoccaplugin_fini(void);
+extern int molfile_brixplugin_init(void);
+extern int molfile_brixplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_brixplugin_fini(void);
+extern int molfile_carplugin_init(void);
+extern int molfile_carplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_carplugin_fini(void);
+extern int molfile_ccp4plugin_init(void);
+extern int molfile_ccp4plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_ccp4plugin_fini(void);
+extern int molfile_corplugin_init(void);
+extern int molfile_corplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_corplugin_fini(void);
+extern int molfile_cpmdplugin_init(void);
+extern int molfile_cpmdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_cpmdplugin_fini(void);
+extern int molfile_crdplugin_init(void);
+extern int molfile_crdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_crdplugin_fini(void);
+extern int molfile_cubeplugin_init(void);
+extern int molfile_cubeplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_cubeplugin_fini(void);
+extern int molfile_dcdplugin_init(void);
+extern int molfile_dcdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dcdplugin_fini(void);
+extern int molfile_dlpolyplugin_init(void);
+extern int molfile_dlpolyplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dlpolyplugin_fini(void);
+extern int molfile_dsn6plugin_init(void);
+extern int molfile_dsn6plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dsn6plugin_fini(void);
+extern int molfile_dxplugin_init(void);
+extern int molfile_dxplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dxplugin_fini(void);
+extern int molfile_edmplugin_init(void);
+extern int molfile_edmplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_edmplugin_fini(void);
+extern int molfile_fs4plugin_init(void);
+extern int molfile_fs4plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_fs4plugin_fini(void);
+extern int molfile_gamessplugin_init(void);
+extern int molfile_gamessplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gamessplugin_fini(void);
+extern int molfile_graspplugin_init(void);
+extern int molfile_graspplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_graspplugin_fini(void);
+extern int molfile_grdplugin_init(void);
+extern int molfile_grdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_grdplugin_fini(void);
+extern int molfile_gridplugin_init(void);
+extern int molfile_gridplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gridplugin_fini(void);
+extern int molfile_gromacsplugin_init(void);
+extern int molfile_gromacsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gromacsplugin_fini(void);
+extern int molfile_jsplugin_init(void);
+extern int molfile_jsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_jsplugin_fini(void);
+extern int molfile_lammpsplugin_init(void);
+extern int molfile_lammpsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_lammpsplugin_fini(void);
+extern int molfile_mapplugin_init(void);
+extern int molfile_mapplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mapplugin_fini(void);
+extern int molfile_mdfplugin_init(void);
+extern int molfile_mdfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mdfplugin_fini(void);
+extern int molfile_mol2plugin_init(void);
+extern int molfile_mol2plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mol2plugin_fini(void);
+extern int molfile_moldenplugin_init(void);
+extern int molfile_moldenplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_moldenplugin_fini(void);
+extern int molfile_molemeshplugin_init(void);
+extern int molfile_molemeshplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_molemeshplugin_fini(void);
+extern int molfile_msmsplugin_init(void);
+extern int molfile_msmsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_msmsplugin_fini(void);
+extern int molfile_namdbinplugin_init(void);
+extern int molfile_namdbinplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_namdbinplugin_fini(void);
+extern int molfile_offplugin_init(void);
+extern int molfile_offplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_offplugin_fini(void);
+extern int molfile_parm7plugin_init(void);
+extern int molfile_parm7plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_parm7plugin_fini(void);
+extern int molfile_parmplugin_init(void);
+extern int molfile_parmplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_parmplugin_fini(void);
+extern int molfile_pbeqplugin_init(void);
+extern int molfile_pbeqplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pbeqplugin_fini(void);
+extern int molfile_pdbplugin_init(void);
+extern int molfile_pdbplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pdbplugin_fini(void);
+extern int molfile_pdbxplugin_init(void);
+extern int molfile_pdbxplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pdbxplugin_fini(void);
+extern int molfile_phiplugin_init(void);
+extern int molfile_phiplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_phiplugin_fini(void);
+extern int molfile_pltplugin_init(void);
+extern int molfile_pltplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pltplugin_fini(void);
+extern int molfile_plyplugin_init(void);
+extern int molfile_plyplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_plyplugin_fini(void);
+extern int molfile_pqrplugin_init(void);
+extern int molfile_pqrplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pqrplugin_fini(void);
+extern int molfile_psfplugin_init(void);
+extern int molfile_psfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_psfplugin_fini(void);
+extern int molfile_raster3dplugin_init(void);
+extern int molfile_raster3dplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_raster3dplugin_fini(void);
+extern int molfile_rst7plugin_init(void);
+extern int molfile_rst7plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_rst7plugin_fini(void);
+extern int molfile_situsplugin_init(void);
+extern int molfile_situsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_situsplugin_fini(void);
+extern int molfile_spiderplugin_init(void);
+extern int molfile_spiderplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_spiderplugin_fini(void);
+extern int molfile_stlplugin_init(void);
+extern int molfile_stlplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_stlplugin_fini(void);
+extern int molfile_tinkerplugin_init(void);
+extern int molfile_tinkerplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_tinkerplugin_fini(void);
+extern int molfile_uhbdplugin_init(void);
+extern int molfile_uhbdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_uhbdplugin_fini(void);
+extern int molfile_vaspchgcarplugin_init(void);
+extern int molfile_vaspchgcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspchgcarplugin_fini(void);
+extern int molfile_vaspoutcarplugin_init(void);
+extern int molfile_vaspoutcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspoutcarplugin_fini(void);
+extern int molfile_vaspparchgplugin_init(void);
+extern int molfile_vaspparchgplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspparchgplugin_fini(void);
+extern int molfile_vaspposcarplugin_init(void);
+extern int molfile_vaspposcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspposcarplugin_fini(void);
+extern int molfile_vasp5xdatcarplugin_init(void);
+extern int molfile_vasp5xdatcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vasp5xdatcarplugin_fini(void);
+extern int molfile_vaspxdatcarplugin_init(void);
+extern int molfile_vaspxdatcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspxdatcarplugin_fini(void);
+extern int molfile_vaspxmlplugin_init(void);
+extern int molfile_vaspxmlplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspxmlplugin_fini(void);
+extern int molfile_vtkplugin_init(void);
+extern int molfile_vtkplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vtkplugin_fini(void);
+extern int molfile_xbgfplugin_init(void);
+extern int molfile_xbgfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xbgfplugin_fini(void);
+extern int molfile_xsfplugin_init(void);
+extern int molfile_xsfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xsfplugin_fini(void);
+extern int molfile_xyzplugin_init(void);
+extern int molfile_xyzplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xyzplugin_fini(void);
+extern int molfile_dtrplugin_init(void);
+extern int molfile_dtrplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dtrplugin_fini(void);
+extern int molfile_maeffplugin_init(void);
+extern int molfile_maeffplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_maeffplugin_fini(void);
+
+#define MOLFILE_INIT_ALL \
+    molfile_abinitplugin_init(); \
+    molfile_amiraplugin_init(); \
+    molfile_avsplugin_init(); \
+    molfile_babelplugin_init(); \
+    molfile_basissetplugin_init(); \
+    molfile_bgfplugin_init(); \
+    molfile_binposplugin_init(); \
+    molfile_biomoccaplugin_init(); \
+    molfile_brixplugin_init(); \
+    molfile_carplugin_init(); \
+    molfile_ccp4plugin_init(); \
+    molfile_corplugin_init(); \
+    molfile_cpmdplugin_init(); \
+    molfile_crdplugin_init(); \
+    molfile_cubeplugin_init(); \
+    molfile_dcdplugin_init(); \
+    molfile_dlpolyplugin_init(); \
+    molfile_dsn6plugin_init(); \
+    molfile_dxplugin_init(); \
+    molfile_edmplugin_init(); \
+    molfile_fs4plugin_init(); \
+    molfile_gamessplugin_init(); \
+    molfile_graspplugin_init(); \
+    molfile_grdplugin_init(); \
+    molfile_gridplugin_init(); \
+    molfile_gromacsplugin_init(); \
+    molfile_jsplugin_init(); \
+    molfile_lammpsplugin_init(); \
+    molfile_mapplugin_init(); \
+    molfile_mdfplugin_init(); \
+    molfile_mol2plugin_init(); \
+    molfile_moldenplugin_init(); \
+    molfile_molemeshplugin_init(); \
+    molfile_msmsplugin_init(); \
+    molfile_namdbinplugin_init(); \
+    molfile_offplugin_init(); \
+    molfile_parm7plugin_init(); \
+    molfile_parmplugin_init(); \
+    molfile_pbeqplugin_init(); \
+    molfile_pdbplugin_init(); \
+    molfile_pdbxplugin_init(); \
+    molfile_phiplugin_init(); \
+    molfile_pltplugin_init(); \
+    molfile_plyplugin_init(); \
+    molfile_pqrplugin_init(); \
+    molfile_psfplugin_init(); \
+    molfile_raster3dplugin_init(); \
+    molfile_rst7plugin_init(); \
+    molfile_situsplugin_init(); \
+    molfile_spiderplugin_init(); \
+    molfile_stlplugin_init(); \
+    molfile_tinkerplugin_init(); \
+    molfile_uhbdplugin_init(); \
+    molfile_vaspchgcarplugin_init(); \
+    molfile_vaspoutcarplugin_init(); \
+    molfile_vaspparchgplugin_init(); \
+    molfile_vaspposcarplugin_init(); \
+    molfile_vasp5xdatcarplugin_init(); \
+    molfile_vaspxdatcarplugin_init(); \
+    molfile_vaspxmlplugin_init(); \
+    molfile_vtkplugin_init(); \
+    molfile_xbgfplugin_init(); \
+    molfile_xsfplugin_init(); \
+    molfile_xyzplugin_init(); \
+    molfile_dtrplugin_init(); \
+    molfile_maeffplugin_init(); \
+
+#define MOLFILE_REGISTER_ALL(v, cb) \
+    molfile_abinitplugin_register(v, cb); \
+    molfile_amiraplugin_register(v, cb); \
+    molfile_avsplugin_register(v, cb); \
+    molfile_babelplugin_register(v, cb); \
+    molfile_basissetplugin_register(v, cb); \
+    molfile_bgfplugin_register(v, cb); \
+    molfile_binposplugin_register(v, cb); \
+    molfile_biomoccaplugin_register(v, cb); \
+    molfile_brixplugin_register(v, cb); \
+    molfile_carplugin_register(v, cb); \
+    molfile_ccp4plugin_register(v, cb); \
+    molfile_corplugin_register(v, cb); \
+    molfile_cpmdplugin_register(v, cb); \
+    molfile_crdplugin_register(v, cb); \
+    molfile_cubeplugin_register(v, cb); \
+    molfile_dcdplugin_register(v, cb); \
+    molfile_dlpolyplugin_register(v, cb); \
+    molfile_dsn6plugin_register(v, cb); \
+    molfile_dxplugin_register(v, cb); \
+    molfile_edmplugin_register(v, cb); \
+    molfile_fs4plugin_register(v, cb); \
+    molfile_gamessplugin_register(v, cb); \
+    molfile_graspplugin_register(v, cb); \
+    molfile_grdplugin_register(v, cb); \
+    molfile_gridplugin_register(v, cb); \
+    molfile_gromacsplugin_register(v, cb); \
+    molfile_jsplugin_register(v, cb); \
+    molfile_lammpsplugin_register(v, cb); \
+    molfile_mapplugin_register(v, cb); \
+    molfile_mdfplugin_register(v, cb); \
+    molfile_mol2plugin_register(v, cb); \
+    molfile_moldenplugin_register(v, cb); \
+    molfile_molemeshplugin_register(v, cb); \
+    molfile_msmsplugin_register(v, cb); \
+    molfile_namdbinplugin_register(v, cb); \
+    molfile_offplugin_register(v, cb); \
+    molfile_parm7plugin_register(v, cb); \
+    molfile_parmplugin_register(v, cb); \
+    molfile_pbeqplugin_register(v, cb); \
+    molfile_pdbplugin_register(v, cb); \
+    molfile_pdbxplugin_register(v, cb); \
+    molfile_phiplugin_register(v, cb); \
+    molfile_pltplugin_register(v, cb); \
+    molfile_plyplugin_register(v, cb); \
+    molfile_pqrplugin_register(v, cb); \
+    molfile_psfplugin_register(v, cb); \
+    molfile_raster3dplugin_register(v, cb); \
+    molfile_rst7plugin_register(v, cb); \
+    molfile_situsplugin_register(v, cb); \
+    molfile_spiderplugin_register(v, cb); \
+    molfile_stlplugin_register(v, cb); \
+    molfile_tinkerplugin_register(v, cb); \
+    molfile_uhbdplugin_register(v, cb); \
+    molfile_vaspchgcarplugin_register(v, cb); \
+    molfile_vaspoutcarplugin_register(v, cb); \
+    molfile_vaspparchgplugin_register(v, cb); \
+    molfile_vaspposcarplugin_register(v, cb); \
+    molfile_vasp5xdatcarplugin_register(v, cb); \
+    molfile_vaspxdatcarplugin_register(v, cb); \
+    molfile_vaspxmlplugin_register(v, cb); \
+    molfile_vtkplugin_register(v, cb); \
+    molfile_xbgfplugin_register(v, cb); \
+    molfile_xsfplugin_register(v, cb); \
+    molfile_xyzplugin_register(v, cb); \
+    molfile_dtrplugin_register(v, cb); \
+    molfile_maeffplugin_register(v, cb); \
+
+#define MOLFILE_FINI_ALL \
+    molfile_abinitplugin_fini(); \
+    molfile_amiraplugin_fini(); \
+    molfile_avsplugin_fini(); \
+    molfile_babelplugin_fini(); \
+    molfile_basissetplugin_fini(); \
+    molfile_bgfplugin_fini(); \
+    molfile_binposplugin_fini(); \
+    molfile_biomoccaplugin_fini(); \
+    molfile_brixplugin_fini(); \
+    molfile_carplugin_fini(); \
+    molfile_ccp4plugin_fini(); \
+    molfile_corplugin_fini(); \
+    molfile_cpmdplugin_fini(); \
+    molfile_crdplugin_fini(); \
+    molfile_cubeplugin_fini(); \
+    molfile_dcdplugin_fini(); \
+    molfile_dlpolyplugin_fini(); \
+    molfile_dsn6plugin_fini(); \
+    molfile_dxplugin_fini(); \
+    molfile_edmplugin_fini(); \
+    molfile_fs4plugin_fini(); \
+    molfile_gamessplugin_fini(); \
+    molfile_graspplugin_fini(); \
+    molfile_grdplugin_fini(); \
+    molfile_gridplugin_fini(); \
+    molfile_gromacsplugin_fini(); \
+    molfile_jsplugin_fini(); \
+    molfile_lammpsplugin_fini(); \
+    molfile_mapplugin_fini(); \
+    molfile_mdfplugin_fini(); \
+    molfile_mol2plugin_fini(); \
+    molfile_moldenplugin_fini(); \
+    molfile_molemeshplugin_fini(); \
+    molfile_msmsplugin_fini(); \
+    molfile_namdbinplugin_fini(); \
+    molfile_offplugin_fini(); \
+    molfile_parm7plugin_fini(); \
+    molfile_parmplugin_fini(); \
+    molfile_pbeqplugin_fini(); \
+    molfile_pdbplugin_fini(); \
+    molfile_pdbxplugin_fini(); \
+    molfile_phiplugin_fini(); \
+    molfile_pltplugin_fini(); \
+    molfile_plyplugin_fini(); \
+    molfile_pqrplugin_fini(); \
+    molfile_psfplugin_fini(); \
+    molfile_raster3dplugin_fini(); \
+    molfile_rst7plugin_fini(); \
+    molfile_situsplugin_fini(); \
+    molfile_spiderplugin_fini(); \
+    molfile_stlplugin_fini(); \
+    molfile_tinkerplugin_fini(); \
+    molfile_uhbdplugin_fini(); \
+    molfile_vaspchgcarplugin_fini(); \
+    molfile_vaspoutcarplugin_fini(); \
+    molfile_vaspparchgplugin_fini(); \
+    molfile_vaspposcarplugin_fini(); \
+    molfile_vasp5xdatcarplugin_fini(); \
+    molfile_vaspxdatcarplugin_fini(); \
+    molfile_vaspxmlplugin_fini(); \
+    molfile_vtkplugin_fini(); \
+    molfile_xbgfplugin_fini(); \
+    molfile_xsfplugin_fini(); \
+    molfile_xyzplugin_fini(); \
+    molfile_dtrplugin_fini(); \
+    molfile_maeffplugin_fini(); \
+
+#ifdef __cplusplus
+}
+#endif
+#endif

src/fparams.c

@@ -89,6 +89,8 @@ s_fparams *init_def_fparams(void)
     par->write_par[0] = 'd';
     par->xpocket_n = 0;
     par->min_n_explicit_pocket_atoms = M_MIN_N_EXPLICIT_POCKET;
+    par->n_chains_to_delete=0;
+    par->n_chains_as_ligand=0;
     return par;
 }
 
@@ -122,7 +124,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
     char *apt;
     char *residue_string[M_MAX_CUSTOM_POCKET_LEN];
     short custom_ligand_i = 0;
-
+    const char *separators = ",:";
     static struct option fplong_options[] = {/*long options args located in fparams.h*/
                                              {"file", required_argument, 0, M_PAR_PDB_FILE},
                                              {"min_alpha_size", required_argument, 0, M_PAR_MIN_ASHAPE_SIZE},
@@ -185,54 +187,53 @@ s_fparams *get_fpocket_args(int nargs, char **args)
         case M_PAR_CHAIN_AS_LIGAND: /*option with -a "name of the chain" to be specified as a ligand*/
             /*select the chains as ligand*/
             status++;
-            strcpy(par->chain_as_ligand, optarg); /*par->chain_as_ligand contains the arg given in cmd line*/
-            const char *separatorss = ",";        /* defining separators*/
-            pt = strtok(par->chain_as_ligand, separatorss);
+            pt = strtok(optarg, separators);
             int nn = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_as_ligand[nn]), pt, 1);
+                par->chain_as_ligand[nn] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_as_ligand[nn], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_as_ligand[nn][M_MAX_CHAIN_NAME_LENGTH]='\0';
                 nn++;
-                pt = strtok(NULL, separatorss);
+                pt = strtok(NULL, separators);
             }
+            par->n_chains_as_ligand=nn;
             par->xlig_resnumber = 0;
-            // printf("lig %s\n",par->chain_as_ligand);
             break;
 
         case M_PAR_DROP_CHAINS:                /*option with -c "name of the chains"*/
                                                /*drop the selected chains from the pdb file*/
-            strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
-            // printf("%s and %s",par->custom_ligand,optarg);
-            const char *separators = ",:"; /* defining separators for drop chains args*/
-            pt = strtok(par->chain_delete, separators);
+            pt = strtok(optarg, separators);
             int n = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_delete[n]), pt, 1);
+                par->chain_delete[n] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_delete[n], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_delete[n][M_MAX_CHAIN_NAME_LENGTH]='\0';
 
                 n++;
                 pt = strtok(NULL, separators);
             }
             par->chain_is_kept = 0;
-
-            // printf("%s\n",par->chain_delete);
+            par->n_chains_to_delete=n;
             status++;
             break;
 
         case M_PAR_KEEP_CHAINS: /*option with -k "name of the chains"*/
                                 /*drop the selected chains from the pdb file*/
 
-            strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
-            // printf("%s and %s",par->custom_ligand,optarg);
-            const char *separator = ",:"; /* defining separators for drop chains args*/
-            pt = strtok(par->chain_delete, separator);
+            pt = strtok(optarg, separators);
             int nk = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_delete[nk]), pt, 1);
+                
+                par->chain_delete[nk] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_delete[nk], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_delete[nk][M_MAX_CHAIN_NAME_LENGTH]='\0';
                 nk++;
-                pt = strtok(NULL, separator);
+                pt = strtok(NULL, separators);
             }
+            par->n_chains_to_delete=nk;
             // printf("%s\n",par->chain_delete);
             par->chain_is_kept = 1;
             status++;
@@ -246,26 +247,29 @@ s_fparams *get_fpocket_args(int nargs, char **args)
 
             status++;
 
-            strcpy(par->custom_ligand, optarg);
+            // strcpy(par->custom_ligand, optarg);
             // printf("%s and %s",par->custom_ligand,optarg);
-            pt = strtok(par->custom_ligand, ":");
+            pt = strtok(optarg, ":");
 
             while (pt != NULL)
             {
                 custom_ligand_i++;
                 if (custom_ligand_i == 1)
                     par->xlig_resnumber = atoi(pt);
-                else if (custom_ligand_i == 2)
-                    strncpy(&(par->xlig_resname), pt, 3);
-                else if (custom_ligand_i == 3)
-                    strncpy(&(par->xlig_chain_code), pt, 1);
-                /*int a = atoi(pt);
-                    printf("%d\n", a);*/
+                else if (custom_ligand_i == 2){
+                    par->xlig_resname= (char *)malloc((M_MAX_LIG_RESNAME_LENGTH + 1) * sizeof(char));
+                    strncpy(par->xlig_resname, pt, M_MAX_LIG_RESNAME_LENGTH);
+                    par->xlig_resname[M_MAX_LIG_RESNAME_LENGTH]='\0';
+                }
+                else if (custom_ligand_i == 3){
+                    par->xlig_chain_code= (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                    strncpy(par->xlig_chain_code, pt, M_MAX_CHAIN_NAME_LENGTH);
+                    par->xlig_chain_code[M_MAX_CHAIN_NAME_LENGTH]='\0';
+                }
                 pt = strtok(NULL, ":");
             }
 
             break;
-
         case M_PAR_CUSTOM_POCKET:
 
             // parse pocket specification that has to be given as
@@ -292,7 +296,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
                 strcpy(&residue_string, pt);
                 rest2 = residue_string;
                 apti = 0;
-                while (apt = strtok_r(rest2, ":", &rest2))
+                while ((apt = strtok_r(rest2, ":", &rest2)))
                 {
                     switch (apti)
                     {
@@ -971,10 +975,10 @@ void print_pocket_usage(FILE *f)
     fprintf(f, "\t-%c --%s (string)\t\t: String specifying a ligand like: \n\
 \t\t\t\t\t\t  residuenumber:residuename:chain_code (ie. 1224:PU8:A).\t\n",
             M_PAR_CUSTOM_LIGAND, M_PAR_CUSTOM_LIGAND_LONG);
-    fprintf(f, "\t-%c --%s (string)\t\t: String specifying a pocket like: \n\ 
+    fprintf(f, "\t-%c --%s (string)\t\t: String specifying a pocket like: \n\
 \t\t\t\t\t\t  residuenumber1:insertion_code1('-' if empty):chain_code1.residuenumber2:insertion_code2:chain_code2 (ie. 138:-:A.139:-:A).\t\n",
             M_PAR_CUSTOM_POCKET, M_PAR_CUSTOM_POCKET_LONG);
-    fprintf(f, "\t-%c --%s (int)\t: If explicit pocket provided, minimum number \n\ 
+    fprintf(f, "\t-%c --%s (int)\t: If explicit pocket provided, minimum number \n\
 \t\t\t\t\t\t  of atoms of an alpha sphere that have to be in the selected pocket.\t\n",
             M_PAR_MIN_N_EXPLICIT_POCKET, M_PAR_MIN_N_EXPLICIT_POCKET_LONG);
     fprintf(f, "\t-%c --%s (char)\t\t: Character specifying a chain as a ligand\t\n", M_PAR_CHAIN_AS_LIGAND, M_PAR_CHAIN_AS_LIGAND_LONG);

src/fpmain.c

@@ -76,7 +76,7 @@ int main(int argc, char *argv[])
                 }
                 else
                 {
-                        if (params->pdb_path == NULL || strlen(params->pdb_path) <= 0)
+                        if (!params->pdb_path[0] || strlen(params->pdb_path) <= 0)
                         {
                                 fprintf(stdout, "! Invalid pdb name given.\n");
                                 print_pocket_usage(stdout);
@@ -222,8 +222,10 @@ void process_pdb(char *pdbname, s_fparams *params)
                         print_number_of_objects_in_memory();
                 }
         }
-        else
-                fprintf(stderr, "! PDB reading failed!\n");
+        else {
+                fprintf(stderr, "! Structure reading failed!\n");
+                exit( EXIT_FAILURE );
+        }
 }
 
 s_pdb *open_file_format(char *fpath, const char *ligan, const int keep_lig, int model_number, s_fparams *par)

src/fpocket.c

@@ -165,7 +165,7 @@ c_lst_pockets *search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)
         fflush(DEBUG_STREAM);
     }
 
-    apply_clustering(pockets, params);
+    apply_clustering(pockets);
     if (DEBUG)
     {
         fprintf(DEBUG_STREAM, "applied clustering to pockets");
@@ -216,7 +216,7 @@ c_lst_pockets *search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)
             print_number_of_objects_in_memory();
         //        int i;
 
-        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path)
+        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path[0])
             calculate_pocket_energy_grids(pockets, params, pdb);
         // params->fpocket_running &&
     }

src/mdparams.c

@@ -256,7 +256,7 @@ s_mdparams* get_mdpocket_args(int nargs, char **args) {
                 par = NULL;
                 print_mdpocket_usage(stdout);
             }
-        } else if ((!traj_file_defined || !traj_format_defined || !par->fpar->pdb_path)) {
+        } else if ((!traj_file_defined || !traj_format_defined || !par->fpar->pdb_path[0])) {
             fprintf(stdout, "! No input file given... Try again :).%d %d %s\n",traj_file_defined,traj_format_defined,par->fpar->pdb_path);
             free_mdparams(par);
             par = NULL;

src/pertable.c

@@ -260,15 +260,20 @@ float pte_get_enegativity(const char *symbol)
 */
 char *pte_get_element_from_number(int atomicnumber)
 {
+	
 	char *tmp=malloc(sizeof(char)*3) ;
 	if(atomicnumber>0 && atomicnumber<112){
 	
 		tmp[0] = ST_pte_symbol[atomicnumber][0] ;
 		tmp[1] = ST_pte_symbol[atomicnumber][1] ;
-		tmp[2] = '\0';
+		tmp[2]='\0';
 		return tmp;
-	} 
-	return -1 ;
+	} else {
+		tmp[0]='-';
+		tmp[1]='1';
+	}
+	tmp[2]='\0';
+	return tmp;
 }
 
 /**

src/qhull/src/qconvex/qconvex.c

@@ -42,7 +42,7 @@ int run_qconvex(FILE *fin,FILE *fout) {
   boolT ismalloc;
 
   int argc=2;
-  char *argv[2];
+  const char *argv[2];
   argv[0]=malloc(sizeof(char)*200);
   argv[0]="src/qhull/qconvex\0";
   argv[1]=malloc(sizeof(char)*2);

src/qhull/src/qvoronoi/qvoronoi.c

@@ -239,7 +239,7 @@ int run_qvoronoi(FILE *fin,FILE *fout) {
   coordT *points;
   boolT ismalloc;
   int argc=6;
-  char *argv[6];
+  const char *argv[6];
   argv[0]=malloc(sizeof(char)*200);
   argv[0]="src/qhull/qvoronoi\0";
   argv[1]=malloc(sizeof(char)*2);

src/read_mmcif.c

@@ -56,38 +56,39 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
 
     molfile_pdbxplugin_init();
     molfile_pdbxplugin_register(NULL, register_cb);
-    char *filetype = "cif";
+    const char *filetype = "cif";
     int inatoms; /*number of atoms in the  file determined by molfile api*/
     // printf("%s | %s |%d", fpath, filetype, inatoms);
     // printf("\n");
     void *h_in;
     molfile_timestep_t ts_in;
     molfile_atom_t *at_in;
-    int optflags = 0x0040;
+    int optflags[] = {0x0001,0x0040};
     int rc;
     int rc2;
     int j;
     int k;
-
     h_in = api->open_file_read(fpath, filetype, &inatoms);
+    if(inatoms==0){
+        fprintf(stderr, "! Structure reading failed or file is empty!\n");
+        exit( EXIT_FAILURE );
+    }
     at_in = (molfile_atom_t *)malloc(inatoms * sizeof(molfile_atom_t));
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
-    rc2 = api->read_structure(h_in, &optflags, at_in);
+    rc2 = api->read_structure(h_in, optflags, at_in);
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
     if (!model_number)
         model_number = 1;
     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].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
         {
-            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))
+                if (chains_to_delete(par->chain_delete, at_in[i].chain_auth, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     /* Atom entry: check if there is a ligand in there (just in case)... */
                     if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -99,7 +100,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                         }
                         /*check this function*/
                     }
-                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain_auth[0] == ligan[0])
                     { /*here we have a protein chain defined as ligand...a bit more complex then*/
                         if (keep_lig)
                         {
@@ -114,13 +115,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                 }
                 if (par->xlig_resnumber > -1)
                 {
-
-                    // if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == 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]) || (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++;
-                    // }
-
-                    if (is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                    if (is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                     {
                         pdb->n_xlig_atoms++;
                     }
@@ -129,26 +124,25 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             if (par->xlig_resnumber > -1)
             {
 
-                if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == 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]) || (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])))
                 {
                     pdb->n_xlig_atoms++;
                 }
             }
         }
-        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])))
+        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_auth,par->n_chains_as_ligand)))
         {
 
-            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))
+                if (chains_to_delete(par->chain_delete, at_in[i].chain_auth, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
                     {
                         natm_lig++;
                         natoms++;
                     }
-                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain_auth[0])
                     {
                         if (keep_lig)
                             natm_lig++;
@@ -157,13 +151,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                     else
                     {
                         /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, at_in[i].chain[0])))
+                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)))
                         {
 
                             natoms++;
                             nhetatm++;
                         }
-                        else if (!is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                        else if (!is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                         {
                             for (j = 0; j < ST_nb_keep_hetatm; j++)
                             {
@@ -178,14 +172,14 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                     }
                 }
 
-                if (is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                 {
                     pdb->n_xlig_atoms++;
                 }
             }
             if (par->xlig_resnumber > -1)
-            {
-                if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == 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]) || (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) && (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 && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && 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++;
                 }
@@ -260,7 +254,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     /*******************************************************************************/
     molfile_pdbxplugin_init();
     molfile_pdbxplugin_register(NULL, register_cb);
-    char *filetype = "cif";
+    const char *filetype = "cif";
     int inatoms; /*number of atoms in the  file determined by molfile api*/
 
     void *h_in;
@@ -277,6 +271,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
     rc2 = api->read_structure(h_in, &optflags, at_in);
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
+
     // printf("READ : %s | %s |%d\n", pdb->fname, filetype, inatoms);
     /* Loop over the pdb file */
     model_flag = 1;
@@ -285,25 +280,26 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     ; /*here we indicate that a particular model should be read only*/
     for (i = 0; i < inatoms; i++)
     {
+
         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(params->chain_as_ligand, at_in[i].chain[0]))
+        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_auth,params->n_chains_as_ligand))
         {
 
-            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 */
 
                 /* Enter this if when arg in command line is -a */
-                if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                 {
                     *(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];
                     i_explicit_ligand_atom++;
                 }
-                if (chains_to_delete(params->chain_delete, at_in[i].chain[0], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, at_in[i].chain_auth, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     /* Check if the desired ligand is in such an entry */
                     if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -317,8 +313,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -342,7 +340,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             ligfound = 1;
                         }
                     }
-                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain_auth[0] == ligan[0])
                     { /*here we have a protein chain defined as ligand...a bit more complex then*/
                         if (keep_lig)
                         {
@@ -354,9 +352,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
-                            // fprintf(stdout, " here : %c\n", at_in[i].insertion[0]);
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -399,13 +398,13 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        // fprintf(stdout,"%s |%s|%d\n", atom->chain, at_in[i].chain,i);
-                        // fflush(stdout);
-                        strncpy(atom->chain, at_in[i].chain, 2);
-                        // fprintf(stdout,"%s |%s|%d\n", atom->chain, at_in[i].chain,i);
-                        atom->res_id = at_in[i].resid;
+
+                        strcpy(atom->chain, at_in[i].chain_auth);
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
-                        // printf("ins:%s",at_in[i].insertion);
 
                         atom->x = ts_in.coords[(3 * i)];
                         atom->y = ts_in.coords[(3 * i) + 1];
@@ -435,9 +434,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
             }
             if (pdb->n_xlig_atoms)
             {
-                if (at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == 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])
-                {
+                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]))
+                {
                     *(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];
@@ -445,23 +445,22 @@ 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])))
+        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_auth,params->n_chains_as_ligand)))
         {
 
-            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]))
+                if (is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                 {
                     *(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];
 
-                    // printf("%d\n", i_explicit_ligand_atom);
                     i_explicit_ligand_atom++;
                 }
                 // fflush(stdout);
-                if (chains_to_delete(params->chain_delete, at_in[i].chain[0], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, at_in[i].chain_auth, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     /* Check if the desired ligand is in HETATM entry */
                     if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -473,9 +472,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        strncpy(atom->chain, at_in[i].chain, 2);
-                        atom->res_id = at_in[i].resid;
+                        strcpy(atom->chain, at_in[i].chain_auth);
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
+
                         atom->x = ts_in.coords[(3 * i)];
                         atom->y = ts_in.coords[(3 * i) + 1];
                         atom->z = ts_in.coords[(3 * i) + 2];
@@ -497,7 +499,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         iatoms++;
                         ligfound = 1;
                     }
-                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain_auth[0])
                     {
 
                         if (keep_lig)
@@ -510,8 +512,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -539,7 +543,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     {
 
                         /* Keep specific HETATM given in the static list ST_keep_hetatm. */
-                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, at_in[i].chain[0])))
+                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand)))
                         {
 
                             atom = atoms + iatoms;
@@ -548,9 +552,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->chain, at_in[i].chain_auth);
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
+
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
                             atom->z = ts_in.coords[(3 * i) + 2];
@@ -570,7 +577,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             ihetatm++;
                             iatoms++;
                         }
-                        else if (!is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                        else if (!is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                         {
 
                             for (j = 0; j < ST_nb_keep_hetatm; j++)
@@ -586,8 +593,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                     strcpy(atom->name, at_in[i].type);
                                     atom->pdb_aloc = at_in[i].altloc[0];
                                     strcpy(atom->res_name, at_in[i].resname);
-                                    strncpy(atom->chain, at_in[i].chain, 2);
-                                    atom->res_id = at_in[i].resid;
+                                    strcpy(atom->chain, at_in[i].chain_auth);
+                                    strcpy(atom->label_asym_id, at_in[i].chain);
+                                    atom->res_id = at_in[i].resid_auth;
+                                    atom->label_seq_id=at_in[i].resid;
                                     atom->pdb_insert = at_in[i].insertion[0];
                                     atom->x = ts_in.coords[(3 * i)];
                                     atom->y = ts_in.coords[(3 * i) + 1];
@@ -615,16 +624,18 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     }
                 }
             }
+                                                         
             if (pdb->n_xlig_atoms)
             {
-                if ((at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == 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]) || (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 (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
 
+                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]))
+                {
+                                        
                     *(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];
-
                     i_explicit_ligand_atom++;
                 }
             }

src/refine.c

@@ -55,7 +55,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 	void
 
 */
-void apply_clustering(c_lst_pockets *pockets, s_fparams *params)
+void apply_clustering(c_lst_pockets *pockets)
 {
 	node_pocket *nextPocket;
 	node_pocket *curMobilePocket;

src/rpdb.c

@@ -803,6 +803,8 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
     int i;
     float x, y, z;
     int resnbuf = 0;
+    char *chainbuf=(char *)my_malloc(sizeof(char)*2);
+    chainbuf[1]='\0';
     int model_flag = 0;      /*by default we consider that no particular model is read*/
     int model_read = 0;      /*flag tracking the status if a current line is read or not*/
     int cur_model_count = 0; /*when reading NMR models, then count on which model you currently are*/
@@ -848,12 +850,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
         }
         if (pdb->model_flag == 0 || model_read == 1)
         {
-
-            if (!strncmp(buf, "ATOM ", 5) && !is_ligand(par->chain_as_ligand, buf[21]))
+            chainbuf[0]=buf[21];
+            if (!strncmp(buf, "ATOM ", 5) && !is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
             {
 
                 // printf("%s",par->chain_delete ); // deleting the chains we want to delete from pdb file
-                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+                if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     /* Check if this is the first occurence of this atom*/
                     rpdb_extract_atm_resname(buf, resb);
@@ -862,7 +864,7 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 }
                 if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
                 {
-                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+                    if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                     {
                         /* Atom entry: check if there is a ligand in there (just in case)... */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -891,20 +893,9 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                     /*handle explicit ligand input here*/
                     if (par->xlig_resnumber > -1)
                     {
-
-                        //                        if (resb[0] == par->xlig_resname[0] && resb[1] == par->xlig_resname[1] && resb[2] == par->xlig_resname[2]) {
-                        // fprintf(stdout,"%s\t%s\n",buf[16],par->xlig_chain_code);
-
-                        // if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                        // {
-                        //     pdb->n_xlig_atoms++;
-                        //     fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
-                        // }
-
-                        if (is_ligand(par->chain_as_ligand, buf[21]))
+                        if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                         {
                             pdb->n_xlig_atoms++;
-                            // fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
                         }
                     }
                 }
@@ -912,7 +903,11 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 {
                     if (par->xlig_resnumber > -1)
                     {
-                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                        if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
+                        {
+                            pdb->n_xlig_atoms++;
+                        }
+                        else if (par->xlig_chain_code!=NULL && buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
                         {
                             pdb->n_xlig_atoms++;
                         }
@@ -920,11 +915,11 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 }
             }
 
-            else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && is_ligand(par->chain_as_ligand, buf[21])))
+            else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand)))
             {
-                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
-                {
 
+                if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
+                {
                     /*Check again for the first occurence*/
                     rpdb_extract_atom_coordinates(buf, &x, &y, &z); /*extract and double check coordinates to avoid issues with wrong coordinates*/
                     resnbuf = rpdb_extract_atm_resumber(buf);
@@ -932,11 +927,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
                 {
                     /* Hetatom entry: check if there is a ligand in there too... */
-                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+
+                    if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                     {
                         rpdb_extract_atm_resname(buf, resb);
 
-                        // printf("%s ",ligan);
+                        
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
                         {
                             natm_lig++;
@@ -951,13 +947,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         else
                         {
                             /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, buf[21])))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand)))
                             {
-                                // printf("%s|%c ",resb,buf[21]);
                                 natoms++;
                                 nhetatm++;
                             }
-                            else if (!is_ligand(par->chain_as_ligand, buf[21]))
+                            else if (!is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                             {
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
                                 {
@@ -972,19 +967,9 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         }
                     }
 
-                    /*handle explicit ligand input here*/
-
-                    // if (par->xlig_resnumber > -1)
-                    // {
-                    //     if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                    //     {
-                    //         pdb->n_xlig_atoms++;
-                    //     }
-                    // }
-                    if (is_ligand(par->chain_as_ligand, buf[21]))
+                    if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                     {
                         pdb->n_xlig_atoms++;
-                        // fprintf(stdout, "H%d\t", pdb->n_xlig_atoms);
                     }
                 }
                 if (x < 9990 && y < 9990 && z < 9990)
@@ -994,9 +979,9 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
 
                     if (par->xlig_resnumber > -1)
                     {
-                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                        unsigned short is_chain_ligand=(is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
+                        if (is_chain_ligand || (par->xlig_chain_code!=NULL && buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2]))
                         {
-
                             pdb->n_xlig_atoms++;
                         }
                     }
@@ -1099,6 +1084,8 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
     int model_flag = 0;      /*by default we consider that no particular model is read*/
     int model_read = 0;      /*flag tracking the status if a current line is read or not*/
     int cur_model_count = 0; /*when reading NMR models, then count on which model you currently are*/
+    char *chainbuf=(char *)my_malloc(sizeof(char)*2);
+    chainbuf[1]='\0';
     s_atm *atom = NULL;
     s_atm *atoms = pdb->latoms;
     s_atm **atoms_p = pdb->latoms_p;
@@ -1125,10 +1112,10 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
         if (pdb->model_flag == 0 || model_read == 1)
         {
 
-            if (strncmp(pdb_line, "ATOM ", 5) == 0 && !is_ligand(params->chain_as_ligand, pdb_line[21]))
+            if (strncmp(pdb_line, "ATOM ", 5) == 0 && !is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
             {
-
-                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                chainbuf[0]=pdb_line[21];
+                if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     // printf("%s\n",params->chain_delete);
 
@@ -1139,30 +1126,20 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                 if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
                 { /*if within first occurence*/
                     /* Store ATOM entry */
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
 
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
                     }
-                    /* Enter this if when arg in command line is -r */
-                    // if (pdb->n_xlig_atoms)
-                    // {
-                    //     if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                    //     {
-
-                    //         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
-                    //         i_explicit_ligand_atom++;
-                    //     }
-                    // }
 
                     /* Enter this if when arg in command line is -a */
-                    if (is_ligand(params->chain_as_ligand, pdb_line[21]))
+                    if (is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                     {
                         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
                         i_explicit_ligand_atom++;
                     }
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         /* Check if the desired ligand is in such an entry */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -1184,6 +1161,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+
 
                                 atoms_p[iatoms] = atom;
                                 iatoms++;
@@ -1212,7 +1192,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 iatoms++;
 
@@ -1238,6 +1220,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                             atom->radius = pte_get_vdw_ray(atom->symbol);
                             atom->electroneg = pte_get_enegativity(atom->symbol);
                             atom->sort_x = -1;
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                             // printf("type : %s, id : %d, name : %s, aloc : %c, res_name : %s, chain  : %s, res_id : %d, pdb_insert : %c, occupancy : %f, b_factor : %f, symbol : %s, charge : %d\n",
                             // atom->type, atom->id,atom->name ,atom->pdb_aloc,atom->res_name,atom->chain,atom->res_id,atom->pdb_insert,atom->occupancy,atom->bfactor, atom->symbol,atom->charge);
                             // printf("electroneg : %s\n",atom->symbol);
@@ -1252,8 +1237,10 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
+                        
+                        unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
 
-                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                        if (is_chain_ligand || (params->xlig_chain_code!=NULL && (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])))
                         {
 
                             rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
@@ -1262,33 +1249,25 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     }
                 }
             }
-            else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && is_ligand(params->chain_as_ligand, pdb_line[21])))
+
+            else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand)))
             {
-                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                chainbuf[0]=pdb_line[21];
+                if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     rpdb_extract_atom_coordinates(pdb_line, &tmpx, &tmpy, &tmpz); /*extract and double check coordinates to avoid issues with wrong coordinates*/
+                    resnbuf = rpdb_extract_atm_resumber(pdb_line);
                 }
                 if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
                 { /*first occurence*/
                     /* Check HETATM entry */
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
-                        resnbuf = rpdb_extract_atm_resumber(pdb_line);
                     }
 
-                    // if (pdb->n_xlig_atoms)
-                    // {
-                    //     if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                    //     {
-                    //         // if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
-
-                    //         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
-
-                    //         i_explicit_ligand_atom++;
-                    //     }
-                    // }
-                    if (is_ligand(params->chain_as_ligand, pdb_line[21]))
+                    if (is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                     {
 
                         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
@@ -1296,7 +1275,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         i_explicit_ligand_atom++;
                     }
                     // fflush(stdout);
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         /* Check if the desired ligand is in HETATM entry */
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -1313,7 +1292,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                             atom->radius = pte_get_vdw_ray(atom->symbol);
                             atom->electroneg = pte_get_enegativity(atom->symbol);
                             atom->sort_x = -1;
-
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                             atoms_p[iatoms] = atom;
                             atm_lig[iatm_lig] = atom;
 
@@ -1339,7 +1320,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 atm_lig[iatm_lig] = atom;
 
@@ -1350,9 +1333,8 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         }
                         else if (pdb->lhetatm)
                         {
-
                             /* Keep specific HETATM given in the static list ST_keep_hetatm. */
-                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, pdb_line[21])))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand)))
                             {
 
                                 atom = atoms + iatoms;
@@ -1368,13 +1350,15 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 atom->radius = pte_get_vdw_ray(atom->symbol);
                                 atom->electroneg = pte_get_enegativity(atom->symbol);
                                 atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                 atoms_p[iatoms] = atom;
                                 pdb->lhetatm[ihetatm] = atom;
                                 ihetatm++;
                                 iatoms++;
                             }
-                            else if (!is_ligand(params->chain_as_ligand, pdb_line[21]))
+                            else if (!is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                             {
 
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
@@ -1396,7 +1380,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                         atom->radius = pte_get_vdw_ray(atom->symbol);
                                         atom->electroneg = pte_get_enegativity(atom->symbol);
                                         atom->sort_x = -1;
-
+                                        atom->label_seq_id=atom->res_id;
+                                        strcpy(atom->label_asym_id, atom->chain);
+                                
                                         atoms_p[iatoms] = atom;
                                         pdb->lhetatm[ihetatm] = atom;
                                         ihetatm++;
@@ -1416,7 +1402,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     {
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
                         rpdb_extract_atm_resname(pdb_line, resb);
-                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                        unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
+
+                        if (is_chain_ligand || (params->xlig_chain_code!=NULL && (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])))
                         {
 
                             rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
@@ -1426,6 +1414,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     }
                 }
             }
+            
             else if (strncmp(pdb_line, "CRYST1", 6) == 0)
             {
                 rpdb_extract_cryst1(pdb_line, &(pdb->alpha), &(pdb->beta), &(pdb->gamma),
@@ -1463,11 +1452,6 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
     int num_h_atoms = get_number_of_h_atoms(pdb);
     pdb->natoms_h = num_h_atoms;
     pdb->avg_bfactor /= (iatoms - num_h_atoms);
-    //        pdb->avg_bfactor=0.0;
-
-    /*if(guess_flag>0) {
-        fprintf(stderr, ">! Warning: You did not provide a standard PDB file.\nElements were guessed by fpocket, because not provided in the PDB file. \nThere is no guarantee on the results!\n");
-    }*/
 
     if (ligan && keep_lig && (ligfound == 0 || pdb->natm_lig <= 0))
     {
@@ -1574,50 +1558,49 @@ void free_pdb_atoms(s_pdb *pdb)
         int
 
  */
-int chains_to_delete(char *chains_selected, char current_line_chain, int is_chain_kept)
+int chains_to_delete(char *chains_selected[20], char *current_line_chain, int is_chain_kept,unsigned short n_chains_to_delete)
 { /*deletes the chains selected by command -c, returns true if the chain correspond false if not*/
 
     if (is_chain_kept == 0)
     {
         int is_deleted = 1;
         int i = 0;
-        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+        for (i = 0; i < n_chains_to_delete; i++)
         {
-            if (chains_selected[i] == current_line_chain)
+            if (!strcmp(chains_selected[i], current_line_chain))
             {
-                // printf("%c_%c ", chains_selected[i],current_line_chain);
                 is_deleted = 0;
             }
         }
-        // printf("\n");
         return is_deleted;
     }
     else
     {
-        int is_deleted = 0;
+        int is_kept = 0;
+
         int i = 0;
-        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+        for (i = 0; i < n_chains_to_delete; i++)
         {
-            if (chains_selected[i] == current_line_chain)
+            if (!strcmp(chains_selected[i], current_line_chain))
             {
-                // printf("%c_%c ", chains_selected[i],current_line_chain);
-                is_deleted = 1;
+                is_kept = 1;
             }
         }
-        // printf("\n");
-        return is_deleted;
+        return is_kept;
     }
 }
 
-int is_ligand(char *chains_selected, char current_line_chain)
+
+
+int is_ligand(char *chains_selected[20], char *current_line_chain, unsigned short n_chains_as_ligand)
 {
+    
     int is_a_ligand = 0;
     int i;
-    for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+    for (i = 0; i < n_chains_as_ligand; i++)
     {
-        if (chains_selected[i] == current_line_chain)
+        if (!strcmp(chains_selected[i],current_line_chain))
         {
-            // printf("%c_%c ", chains_selected[i],current_line_chain);
             is_a_ligand = 1;
         }
     }

src/voronoi.c

@@ -1488,23 +1488,23 @@ void write_mmcif_vert(FILE *f, s_vvertice *v, int i)
     if (v->electrostatic_energy <= -0.05)
     {
 
-        write_mmcif_atom_line(f, "HETATM", i, " POL",
-                              ' ', "ACC", "O", v->resid, ' ',
+        write_mmcif_atom_line(f, "HETATM", i, "POL",
+                              '.', "ACC", "O", v->resid, "O",v->resid,'.',
                               v->x, v->y, v->z, 0.0, 0.0, 0,
                               "V", -1, 0.0);
     }
     else if (v->electrostatic_energy >= 0.05)
     {
 
-        write_mmcif_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
-                              v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+        write_mmcif_atom_line(f, "HETATM", i, "POL", '.', "DON", "N",
+                              v->resid, "N",v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
                               "V", -1, 0.0);
     }
     else
     {
 
-        write_mmcif_atom_line(f, "HETATM", i, "APOL", ' ', "STP", "C",
-                              v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+        write_mmcif_atom_line(f, "HETATM", i, "APOL", '.', "STP", "C",
+                              v->resid, "C", v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
                               "V", -1, 0.0);
     }
 }