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'
@@ -182,10 +184,10 @@ typedef struct s_fparams
 	char pdb_path[M_MAX_PDB_NAME_LEN];		/**< The pdb file */
 	char topology_path[M_MAX_PDB_NAME_LEN]; /**< a putative topology file*/
 	char custom_ligand[M_MAX_PDB_NAME_LEN]; /**container for custom pocket detection using a particular ligand*/
-	char custom_pocket_arg[M_MAX_CUSTOM_PÖCKET_LEN];
+	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

@@ -90,6 +90,8 @@ typedef struct s_pdb
     char header[M_PDB_BUF_LEN] ; /**< Header container*/
     char fname[M_PDB_FILE_NAME_LEN];    /**< File name container*/
     float avg_bfactor;  /**<overall average B factor*/
+    float min_bfactor;  /**<overall minimum B factor*/
+    float max_bfactor;  /**<overall maximum B factor*/
     int model_flag; /**<flag set to 1 if a particular model / conformation was read*/
     int model_number; /**<number of the model read in*/
 
@@ -140,10 +142,10 @@ s_min_max_coords *float_get_min_max_from_pdb(s_pdb *pdb);
 void init_coord_grid(s_pdb *pdb);
 void create_coord_grid(s_pdb *pdb);
 void fill_coord_grid(s_pdb *pdb);
-s_atom_ptr_list *init_atom_ptr_list(void);
+// s_atom_ptr_list *init_atom_ptr_list(void);
 
 
 short get_mm_type_from_element(char *symbol);
-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

@@ -33,8 +33,8 @@ 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_CUSTOM_PÖCKET_LEN 8000 /** maximum length for a custom pocket string*/
+#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/descriptors.c

@@ -423,7 +423,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
             /*fprintf(stdout,":%s:",desc->ligTag);*/
             desc->hydrophobicity_score = desc->hydrophobicity_score/ (float) nb_res_ids ;
             desc->volume_score = desc->volume_score / (float) nb_res_ids ;
-
+			
             desc->flex /= natoms ;
             desc->prop_polar_atm = ((float) nb_polar_atm) / ((float) natoms) * 100.0 ;
         }

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;
 }
 
@@ -120,9 +122,9 @@ s_fparams *get_fpocket_args(int nargs, char **args)
     opterr = 0;
     char *pt;
     char *apt;
-    char *residue_string[M_MAX_CUSTOM_PÖCKET_LEN];
+    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)
                     {
@@ -971,18 +975,18 @@ 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);
 
     fprintf(f, "\n\n\033[1mOptional pocket detection parameters\033[0m (default parameters)           \n\
 \t-%c --%s (float)\t\t: Minimum radius of an alpha-sphere.\t(%.1f)\n",
-            M_PAR_MIN_ASHAPE_SIZE, M_PAR_LONG_MIN_ASHAPE_SIZE, M_MAX_ASHAPE_SIZE_DEFAULT);
-    fprintf(f, "\t-%c --%s (float)\t\t: Maximum radius of an alpha-sphere.\t(%.1f)\n", M_PAR_MAX_ASHAPE_SIZE, M_PAR_LONG_MAX_ASHAPE_SIZE, M_MIN_ASHAPE_SIZE_DEFAULT);
+            M_PAR_MIN_ASHAPE_SIZE, M_PAR_LONG_MIN_ASHAPE_SIZE, M_MIN_ASHAPE_SIZE_DEFAULT);
+    fprintf(f, "\t-%c --%s (float)\t\t: Maximum radius of an alpha-sphere.\t(%.1f)\n", M_PAR_MAX_ASHAPE_SIZE, M_PAR_LONG_MAX_ASHAPE_SIZE, M_MAX_ASHAPE_SIZE_DEFAULT);
     fprintf(f, "\t-%c --%s (float)\t: Distance threshold for clustering algorithm\t(%.1f)\n", M_PAR_CLUST_MAX_DIST, M_PAR_LONG_CLUST_MAX_DIST, M_CLUST_MAX_DIST);
     fprintf(f, "\t-%c --%s (char)\t\t: Specify the clustering method wanted for     \n\
 \t\t\t\t\t\t  grouping voronoi vertices together (%c)\n\

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/fpout.c

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

src/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);