Merge pull request #154 from Discngine/issue-151

Bugfix of wrong atom_site parsing

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"]

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/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
 

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/pertable.c

@@ -260,11 +260,13 @@ 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';
 		return tmp;
 	} else {
 		tmp[0]='-';

src/read_mmcif.c

@@ -63,7 +63,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     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;
@@ -75,7 +75,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     }
     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;
@@ -123,8 +123,8 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             }
             if (par->xlig_resnumber > -1)
             {
-
-                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
+                
+                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
                 {
                     pdb->n_xlig_atoms++;
                 }
@@ -179,7 +179,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             }
             if (par->xlig_resnumber > -1)
             {   
-                if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (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])) || (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]))
+                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++;
                 }
@@ -313,8 +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];
@@ -350,8 +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;
+                            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];
@@ -395,8 +399,11 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         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)];
@@ -429,7 +436,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
             {
                 unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
 
-                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && 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];
@@ -465,9 +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];
@@ -502,8 +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];
@@ -540,9 +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];
@@ -578,8 +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];
@@ -607,13 +624,13 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     }
                 }
             }
-
+                                                         
             if (pdb->n_xlig_atoms)
             {
 
                 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 == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && 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];

src/rpdb.c

@@ -1161,6 +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++;
@@ -1189,7 +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++;
 
@@ -1215,6 +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);
@@ -1284,7 +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;
 
@@ -1310,7 +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;
 
@@ -1338,7 +1350,9 @@ 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++;
@@ -1366,7 +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++;

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);
     }
 }

src/writepdb.c

@@ -206,7 +206,7 @@ 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, char insert, float x, float y, float z, float occ,
 						   float bfactor, int abpa, const char *symbol, int charge, float abpa_prob)
 {
 	int status = 0;
@@ -214,19 +214,13 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 		 res_id_buf[5] = "****",
 		 charge_buf[3] = "  \0";
 
-	if (id < 100000)
-		sprintf(id_buf, "%5d", id);
-	else
-		sprintf(id_buf, "%05x", id);
+	
+	sprintf(id_buf, "%d", id);
+	
+	sprintf(res_id_buf, "%d", res_id);
 
-	if (res_id < 10000)
-		sprintf(res_id_buf, "%4d", res_id);
-	else if (res_id < 65536)
-		sprintf(res_id_buf, "%04x", res_id);
-	else
-		sprintf(res_id_buf, "****");
-
-	alt_loc = (alt_loc == '\0') ? ' ' : alt_loc;
+	alt_loc = (alt_loc == '\0' || (alt_loc == ' '))  ? '?' : alt_loc;
+	insert = (insert == '\0' || insert==' ') ? '?' : insert;
 
 	if (charge == -1)
 		sprintf(charge_buf, " 0");
@@ -237,14 +231,8 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 	if (abpa)
 		finalabpa = abpa_prob;
 
-	//status = fprintf(f, "%-7s %6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s %4s %4s %2s %4s\n",
-	//				 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, res_id_buf, res_name, chain, atom_name);
+	status = fprintf(f, "%-7s %-6s %3s %4s %c %4s %6s %d %c %8.3f %8.3f %8.3f %6.2f %2s %d %s\n",
+					 rec_name, id_buf, symbol, atom_name,alt_loc, res_name, label_asym_id, label_seq_id,insert, x, y, z, occ, charge_buf, res_id,chain);
 
-	status = fprintf(f, "%-7s %-6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s  %2s\n",
-					 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, chain);
+}
 
-	/*"ATOM %d %s %s . %s %s . %d ? %f %f %f %f %f %s\n",
-            i + 1, atoms[i].name, atoms[i].type, atoms[i].resname, atoms[i].chain,
-            atoms[i].resid, *x, *y, *z, atoms[i].occupancy,
-            atoms[i].charge, atoms[i].chain);*/
-}

src/writepocket.c

@@ -44,7 +44,6 @@ static const char atomSiteHeader[] =
     "_atom_site.label_alt_id\n"
     "_atom_site.label_comp_id\n"
     "_atom_site.label_asym_id\n"
-    "_atom_site.label_entity_id\n"
     "_atom_site.label_seq_id\n"
     "_atom_site.pdbx_PDB_ins_code\n"
     "_atom_site.Cartn_x\n"
@@ -52,6 +51,7 @@ static const char atomSiteHeader[] =
     "_atom_site.Cartn_z\n"
     "_atom_site.occupancy\n"
     "_atom_site.pdbx_formal_charge\n"
+    "_atom_site.auth_seq_id\n"
     "_atom_site.auth_asym_id\n";
 
     /*static const char atomSiteHeader[] =
@@ -83,7 +83,6 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_p
     out[0] = '\0';
 
     node_pocket *pcur;
-
     int i = 0;
     if (pockets) {
         pcur = pockets->first;
@@ -92,13 +91,26 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_p
             sprintf(out, "%s/pocket%d_vert.pqr", out_path, i + 1);
             write_pocket_pqr_DB(out, pcur->pocket);
 
-            sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
-            write_pocket_pdb_DB(out, pcur->pocket, pdb);
-
-            
+            if(write_mode[0] == 'p' || write_mode[0] == 'b'){
+        
             sprintf(out, "%s/pocket%d_atm.pdb", out_path, i + 1);
             write_pocket_pdb(out, pcur->pocket);
 
+            sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
+            write_pocket_pdb_DB(out, pcur->pocket, pdb);
+            // sprintf(out, "%s/pocket%d_atm.pdb", out_path, i+1);
+            // write_pocket_pdb_DB(out, pcur->pocket);
+            }
+
+            if(write_mode[0] == 'm' || write_mode[0] == 'b'){
+            sprintf(out, "%s/pocket%d_atm.cif", out_path, i + 1);
+            write_pocket_mmcif(out, pcur->pocket);
+
+            sprintf(out, "%s/pocket%d_env_atm.cif", out_path, i+1);
+            write_pocket_mmcif_DB(out, pcur->pocket,pdb);
+            }
+
+
             pcur = pcur->next;
             i++;
         }
@@ -144,14 +156,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
 
         node_vertice *nvcur = pocket->v_lst->first;
 
-       /* 
-                                fprintf(stdout, "A Pocket:\n") ;
-        */
         while (nvcur) {
-            /*
-                                            fprintf(stdout, "Vertice %d: %p %d %f\n", i, nvcur->vertice, nvcur->vertice->id, nvcur->vertice->ray) ;
-                                            fprintf(stdout, "Atom %s\n", nvcur->vertice->neigh[0]->name) ;
-             */
 
             tab_vert[nvert] = nvcur->vertice;
             nvcur = nvcur->next;
@@ -159,7 +164,6 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
         }
         sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
         for (i = 0; i < n_sa; i++) {
-            //atom = pocket->sou_atoms[i] ;
             atom = pdb->latoms_p[sa[i]];
             write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
                     atom->res_name, atom->chain, atom->res_id,
@@ -167,36 +171,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
                     atom->dA, atom->a0, atom->abpa, atom->symbol,
                     atom->charge, atom->abpa_sourrounding_prob);
         }
-        /*
-                    vcur = pocket->v_lst->first ;
-
-                        while(vcur){
-                                for(i = 0 ; i < 4 ; i++) {
-                                        if(!is_in_lst_atm(atms, cur_size, vcur->vertice->neigh[i]->id)) {
-                                                if(cur_size >= cur_allocated-1) {
-                                                        cur_allocated *= 2 ;
-                                                        atms = (s_atm**) my_realloc(atms, sizeof(s_atm)*cur_allocated) ;
-                                                }
-                                                atms[cur_size] = vcur->vertice->neigh[i] ;
-                                                cur_size ++ ;
-                                        }
-
-                                }
-                                vcur = vcur->next ;
-                        }
-         */
-        // Then write atoms...
-        /*
-                        for(i = 0 ; i < cur_size ; i++) {
-                                atom = atms[i] ;
-
-                                write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                                                                                atom->res_name, atom->chain, atom->res_id,
-                                                                                atom->pdb_insert, atom->x, atom->y, atom->z,
-                                                                                atom->occupancy, atom->bfactor, atom->symbol,
-                                                                                atom->charge);
-                        }
-         */
+        
         fprintf(f, "TER\nEND\n");
         fclose(f);
     } else {
@@ -207,6 +182,56 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
     my_free(atms);
 }
 
+
+
+void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
+    int i = 0, nvert = 0;
+    s_atm **atms = (s_atm **) my_malloc(sizeof (s_atm*)*10);
+    s_atm *atom = NULL;
+    int n_sa = 0;
+    int *sa = NULL; /*surrounding atoms container*/
+    s_vvertice **tab_vert = NULL;
+    char tmp[250];
+    strcpy(tmp,out);
+    remove_ext(tmp);
+    remove_path(tmp);
+    FILE *f = fopen(out, "w");
+    fprintf(f,"data_%s\n# \n",tmp);
+    fprintf(f,"%s",atomSiteHeader);/*print the header*/
+    if (f && pocket) {
+        // First get the list of atoms
+        tab_vert = (s_vvertice **) my_malloc(pocket->v_lst->n_vertices * sizeof (s_vvertice*));
+
+        node_vertice *nvcur = pocket->v_lst->first;
+
+        while (nvcur) {
+
+            tab_vert[nvert] = nvcur->vertice;
+            nvcur = nvcur->next;
+            nvert++;
+        }
+        sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
+        for (i = 0; i < n_sa; i++) {
+            atom = pdb->latoms_p[sa[i]];
+            write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
+                    atom->pdb_insert, atom->x, atom->y, atom->z,
+                    atom->dA, atom->a0, atom->abpa, atom->symbol,
+                    atom->charge, atom->abpa_sourrounding_prob);
+        }
+        
+        fprintf(f, "#\n");
+        fclose(f);
+    } else {
+        if (!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
+        else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
+    }
+
+    my_free(atms);
+}
+
+
+
 /**
    ## FUNCTION: 
         write_single_pdb
@@ -350,9 +375,9 @@ void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms) {
     for (i = 0; i < natoms; i++) {
         atom = atoms + i;
         //atom->chain[1]='\0';
-        //printf("%d:%s|symb:%s\t",i,atom->chain,atom->symbol);
+        // printf("%d:%s vs %s\n",i,atom->chain,atom->label_asym_id);
         write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                atom->res_name, atom->chain, atom->res_id,
+                atom->res_name, atom->chain,atom->res_id,atom->label_asym_id,atom->label_seq_id,
                 atom->pdb_insert, atom->x, atom->y, atom->z,
                 atom->dA, atom->a0, atom->abpa, atom->symbol,
                 atom->charge, atom->abpa_sourrounding_prob);
@@ -483,7 +508,7 @@ void write_each_pocket(const char out_path[], c_lst_pockets *pockets) {
     int i = 1;
     if (pockets) {
         pcur = pockets->first;
-        
+
         while (pcur) {
             sprintf(out, "%s/pocket%d_vert.pqr", out_path, i);
 
@@ -717,7 +742,7 @@ void write_pocket_mmcif(const char out[], s_pocket *pocket) {
             atom = atms[i];
 
             write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                    atom->res_name, atom->chain, atom->res_id,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
                     atom->pdb_insert, atom->x, atom->y, atom->z,
                     atom->dA, atom->a0, atom->abpa, atom->symbol,
                     atom->charge, atom->abpa_sourrounding_prob);

tests/reference_output/123abc_out/pocket10_atm.cif

@@ -0,0 +1,76 @@
+data_pocket10_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    10:
+0  - Pocket Score                      : 0.0405
+1  - Drug Score                        : 0.0230
+2  - Number of alpha spheres           :    57
+3  - Mean alpha-sphere radius          : 3.8604
+4  - Mean alpha-sphere Solvent Acc.    : 0.4592
+5  - Mean B-factor of pocket residues  : 0.2769
+6  - Hydrophobicity Score              : 40.0769
+7  - Polarity Score                    :     6
+8  - Amino Acid based volume Score     : 3.6154
+9  - Pocket volume (Monte Carlo)       : 433.1334
+10  -Pocket volume (convex hull)       : 76.0139
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 32.4571
+13 - Number of apolar alpha sphere     :    35
+14 - Proportion of apolar alpha sphere : 0.6140
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3335     C  CG2 ?  THR    Bxp 167 ?   23.611   41.302   32.855   0.00  0 394 B
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    3399     C  CD1 ?  ILE    Bxp 176 ?   22.413   39.457   35.570   0.00  0 403 B
+ATOM    3397     C  CG1 ?  ILE    Bxp 176 ?   21.483   40.079   36.568   0.00  0 403 B
+ATOM    3345     C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM    3378     C   CB ?  PHE    Bxp 174 ?   18.390   43.943   35.478   0.00  0 401 B
+ATOM    3332     O    O ?  THR    Bxp 167 ?   21.633   44.211   32.694  -1.07  0 394 B
+ATOM    3735     C   CA ?  SER    Bxp 219 ?   24.536   33.701   35.059   0.00  0 446 B
+ATOM    3729     O    O ?  LEU    Bxp 218 ?   23.720   35.415   36.830   0.00  0 445 B
+ATOM    1239     C   CB ?  ALA    Axp 168 ?   21.952   31.542   32.252   0.00  0 395 A
+ATOM    3454     O    O ?  SER    Bxp 183 ?   12.618   40.049   35.823  -1.07  0 410 B
+ATOM    3488     O  OD1 ?  ASN    Bxp 187 ?   12.383   40.631   32.241  -1.07  0 414 B
+ATOM    3380     C  CD1 ?  PHE    Bxp 174 ?   16.492   43.534   33.887   0.00  0 401 B
+ATOM    3460     O    O ?  LEU    Bxp 184 ?   14.089   37.175   34.255  -3.21  0 411 B
+ATOM    3458     C   CA ?  LEU    Bxp 184 ?   14.473   38.083   36.400   0.00  0 411 B
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    1241     C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM    3760     C   CB ?  TYR    Bxp 222 ?   18.259   32.959   38.062   0.00  0 449 B
+ATOM    3756     N    N ?  TYR    Bxp 222 ?   20.251   33.164   39.466  -1.09  0 449 B
+ATOM    3398     C  CG2 ?  ILE    Bxp 176 ?   21.928   38.594   38.565   0.00  0 403 B
+ATOM    3463     C  CD1 ?  LEU    Bxp 184 ?   17.369   37.208   38.932   0.00  0 411 B
+ATOM    3737     O    O ?  SER    Bxp 219 ?   23.395   31.686   35.276  -1.07  0 446 B
+ATOM    3728     C    C ?  LEU    Bxp 218 ?   24.912   35.395   36.613   0.00  0 445 B
+ATOM    3730     C   CB ?  LEU    Bxp 218 ?   25.994   37.693   36.437   0.00  0 445 B
+ATOM    3738     C   CB ?  SER    Bxp 219 ?   25.152   33.376   33.704   0.00  0 446 B
+ATOM    3346     C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM    3464     C  CD2 ?  LEU    Bxp 184 ?   17.512   38.953   37.066   0.00  0 411 B
+ATOM    3734     N    N ?  SER    Bxp 219 ?   25.438   34.466   35.848  -1.09  0 446 B
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    3461     C   CB ?  LEU    Bxp 184 ?   15.552   37.271   37.155   0.00  0 411 B
+ATOM    1250     N    N ?  ALA    Axp 170 ?   17.224   33.325   33.516  -4.79  0 397 A
+ATOM    1255     N    N ?  GLY    Axp 171 ?   17.151   30.558   34.884  -1.09  0 398 A
+ATOM    1237     C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+# 

tests/reference_output/123abc_out/pocket10_env_atm.cif

@@ -0,0 +1,91 @@
+data_pocket10_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1236     C   CA ?  ALA    Axp 168 ?   21.345   31.742   30.855   0.00  0 395 A
+ATOM    1237     C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    1239     C   CB ?  ALA    Axp 168 ?   21.952   31.542   32.252   0.00  0 395 A
+ATOM    1240     N    N ?  HIS    Axp 169 ?   19.130   32.633   31.043   0.00  0 396 A
+ATOM    1241     C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM    1242     C    C ?  HIS    Axp 169 ?   17.124   32.937   32.241   0.00  0 396 A
+ATOM    1244     C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM    1245     C   CG ?  HIS    Axp 169 ?   16.104   34.797   30.229   0.00  0 396 A
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    1249     N  NE2 ?  HIS    Axp 169 ?   14.590   36.367   30.529   0.00  0 396 A
+ATOM    1250     N    N ?  ALA    Axp 170 ?   17.224   33.325   33.516  -4.79  0 397 A
+ATOM    1251     C   CA ?  ALA    Axp 170 ?   16.342   32.830   34.571   0.00  0 397 A
+ATOM    1252     C    C ?  ALA    Axp 170 ?   16.105   31.311   34.539   0.00  0 397 A
+ATOM    1254     C   CB ?  ALA    Axp 170 ?   15.038   33.564   34.528   0.00  0 397 A
+ATOM    1255     N    N ?  GLY    Axp 171 ?   17.151   30.558   34.884  -1.09  0 398 A
+ATOM    3331     C    C ?  THR    Bxp 167 ?   22.771   43.904   32.327   0.00  0 394 B
+ATOM    3332     O    O ?  THR    Bxp 167 ?   21.633   44.211   32.694  -1.07  0 394 B
+ATOM    3333     C   CB ?  THR    Bxp 167 ?   23.958   42.338   33.911   0.00  0 394 B
+ATOM    3335     C  CG2 ?  THR    Bxp 167 ?   23.611   41.302   32.855   0.00  0 394 B
+ATOM    3338     C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    3341     N    N ?  HIS    Bxp 169 ?   19.743   43.280   29.949   0.00  0 396 B
+ATOM    3342     C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM    3345     C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM    3346     C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM    3347     N  ND1 ?  HIS    Bxp 169 ?   15.399   41.864   29.978  -2.19  0 396 B
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    3349     C  CE1 ?  HIS    Bxp 169 ?   14.459   40.980   29.690   0.00  0 396 B
+ATOM    3350     N  NE2 ?  HIS    Bxp 169 ?   14.959   39.769   29.859   0.00  0 396 B
+ATOM    3374     N    N ?  PHE    Bxp 174 ?   19.806   45.500   34.237   0.00  0 401 B
+ATOM    3375     C   CA ?  PHE    Bxp 174 ?   19.360   45.109   35.564   0.00  0 401 B
+ATOM    3377     O    O ?  PHE    Bxp 174 ?   21.500   44.304   36.088   0.00  0 401 B
+ATOM    3378     C   CB ?  PHE    Bxp 174 ?   18.390   43.943   35.478   0.00  0 401 B
+ATOM    3379     C   CG ?  PHE    Bxp 174 ?   17.076   44.325   34.855   0.00  0 401 B
+ATOM    3380     C  CD1 ?  PHE    Bxp 174 ?   16.492   43.534   33.887   0.00  0 401 B
+ATOM    3382     C  CE1 ?  PHE    Bxp 174 ?   15.273   43.909   33.319   0.00  0 401 B
+ATOM    3396     C   CB ?  ILE    Bxp 176 ?   21.966   39.989   38.044   0.00  0 403 B
+ATOM    3397     C  CG1 ?  ILE    Bxp 176 ?   21.483   40.079   36.568   0.00  0 403 B
+ATOM    3398     C  CG2 ?  ILE    Bxp 176 ?   21.928   38.594   38.565   0.00  0 403 B
+ATOM    3399     C  CD1 ?  ILE    Bxp 176 ?   22.413   39.457   35.570   0.00  0 403 B
+ATOM    3453     C    C ?  SER    Bxp 183 ?   12.616   39.571   36.930   0.00  0 410 B
+ATOM    3454     O    O ?  SER    Bxp 183 ?   12.618   40.049   35.823  -1.07  0 410 B
+ATOM    3457     N    N ?  LEU    Bxp 184 ?   13.478   38.624   37.304   0.00  0 411 B
+ATOM    3458     C   CA ?  LEU    Bxp 184 ?   14.473   38.083   36.400   0.00  0 411 B
+ATOM    3459     C    C ?  LEU    Bxp 184 ?   13.764   37.165   35.433   0.00  0 411 B
+ATOM    3460     O    O ?  LEU    Bxp 184 ?   14.089   37.175   34.255  -3.21  0 411 B
+ATOM    3461     C   CB ?  LEU    Bxp 184 ?   15.552   37.271   37.155   0.00  0 411 B
+ATOM    3462     C   CG ?  LEU    Bxp 184 ?   16.587   38.098   37.951   0.00  0 411 B
+ATOM    3463     C  CD1 ?  LEU    Bxp 184 ?   17.369   37.208   38.932   0.00  0 411 B
+ATOM    3464     C  CD2 ?  LEU    Bxp 184 ?   17.512   38.953   37.066   0.00  0 411 B
+ATOM    3488     O  OD1 ?  ASN    Bxp 187 ?   12.383   40.631   32.241  -1.07  0 414 B
+ATOM    3727     C   CA ?  LEU    Bxp 218 ?   25.851   36.423   37.264   0.00  0 445 B
+ATOM    3728     C    C ?  LEU    Bxp 218 ?   24.912   35.395   36.613   0.00  0 445 B
+ATOM    3729     O    O ?  LEU    Bxp 218 ?   23.720   35.415   36.830   0.00  0 445 B
+ATOM    3730     C   CB ?  LEU    Bxp 218 ?   25.994   37.693   36.437   0.00  0 445 B
+ATOM    3734     N    N ?  SER    Bxp 219 ?   25.438   34.466   35.848  -1.09  0 446 B
+ATOM    3735     C   CA ?  SER    Bxp 219 ?   24.536   33.701   35.059   0.00  0 446 B
+ATOM    3736     C    C ?  SER    Bxp 219 ?   24.150   32.474   35.811   0.00  0 446 B
+ATOM    3737     O    O ?  SER    Bxp 219 ?   23.395   31.686   35.276  -1.07  0 446 B
+ATOM    3738     C   CB ?  SER    Bxp 219 ?   25.152   33.376   33.704   0.00  0 446 B
+ATOM    3751     C    C ?  VAL    Bxp 221 ?   21.031   32.982   40.538   0.00  0 448 B
+ATOM    3753     C   CB ?  VAL    Bxp 221 ?   22.559   35.077   40.397   0.00  0 448 B
+ATOM    3756     N    N ?  TYR    Bxp 222 ?   20.251   33.164   39.466  -1.09  0 449 B
+ATOM    3757     C   CA ?  TYR    Bxp 222 ?   18.886   32.708   39.432   0.00  0 449 B
+ATOM    3760     C   CB ?  TYR    Bxp 222 ?   18.259   32.959   38.062   0.00  0 449 B
+ATOM    3761     C   CG ?  TYR    Bxp 222 ?   16.811   32.522   38.032   0.00  0 449 B
+ATOM    3762     C  CD1 ?  TYR    Bxp 222 ?   15.795   33.459   38.329   0.00  0 449 B
+ATOM    3768     N    N ?  GLU    Bxp 223 ?   19.652   30.471   39.123   0.00  0 450 B
+ATOM    3773     C   CG ?  GLU    Bxp 223 ?   20.865   28.953   37.013   0.00  0 450 B
+ATOM    3776     O  OE2 ?  GLU    Bxp 223 ?   21.549   28.266   34.820   0.00  0 450 B
+#

tests/reference_output/123abc_out/pocket10_vert.pqr

@@ -0,0 +1,59 @@
+ATOM      1    O STP    10      21.702  37.817  31.893    0.00     4.09
+ATOM      2    C STP    10      19.673  40.504  33.491    0.00     3.60
+ATOM      3    C STP    10      19.762  41.204  33.656    0.00     3.56
+ATOM      4    O STP    10      19.774  41.436  33.555    0.00     3.45
+ATOM      5    O STP    10      19.888  41.310  33.676    0.00     3.53
+ATOM      6    O STP    10      20.810  34.601  34.374    0.00     3.89
+ATOM      7    O STP    10      22.171  36.269  33.386    0.00     3.87
+ATOM      8    O STP    10      15.383  40.306  33.837    0.00     3.41
+ATOM      9    O STP    10      15.487  40.276  33.991    0.00     3.41
+ATOM     10    O STP    10      15.519  40.241  33.611    0.00     3.44
+ATOM     11    C STP    10      19.399  38.571  32.764    0.00     4.21
+ATOM     12    O STP    10      19.631  37.930  32.444    0.00     4.45
+ATOM     13    C STP    10      19.282  37.676  32.828    0.00     4.53
+ATOM     14    O STP    10      20.160  35.844  37.073    0.00     3.59
+ATOM     15    C STP    10      20.138  35.856  37.103    0.00     3.58
+ATOM     16    C STP    10      20.119  35.880  36.964    0.00     3.63
+ATOM     17    O STP    10      20.785  34.426  34.531    0.00     3.86
+ATOM     18    C STP    10      24.048  36.964  33.366    0.00     3.71
+ATOM     19    C STP    10      23.766  36.842  33.568    0.00     3.56
+ATOM     20    C STP    10      23.470  37.040  32.145    0.00     4.32
+ATOM     21    C STP    10      22.938  36.606  32.779    0.00     4.02
+ATOM     22    C STP    10      24.363  37.273  32.697    0.00     4.10
+ATOM     23    C STP    10      24.101  36.997  33.214    0.00     3.80
+ATOM     24    C STP    10      17.002  40.176  33.584    0.00     3.41
+ATOM     25    C STP    10      17.136  40.046  33.708    0.00     3.55
+ATOM     26    C STP    10      16.167  40.018  33.979    0.00     3.53
+ATOM     27    C STP    10      16.305  39.958  33.848    0.00     3.58
+ATOM     28    C STP    10      19.086  39.525  33.553    0.00     3.89
+ATOM     29    C STP    10      19.053  38.731  33.178    0.00     4.19
+ATOM     30    C STP    10      18.646  40.617  34.047    0.00     3.63
+ATOM     31    C STP    10      18.847  40.579  34.038    0.00     3.69
+ATOM     32    C STP    10      20.140  36.950  36.141    0.00     3.43
+ATOM     33    C STP    10      20.148  36.427  35.991    0.00     3.81
+ATOM     34    C STP    10      19.995  36.133  36.373    0.00     3.82
+ATOM     35    C STP    10      19.906  35.986  36.229    0.00     3.90
+ATOM     36    C STP    10      24.433  36.790  33.463    0.00     3.48
+ATOM     37    C STP    10      24.463  36.791  33.428    0.00     3.49
+ATOM     38    C STP    10      17.930  37.771  33.253    0.00     4.01
+ATOM     39    C STP    10      19.259  37.654  32.729    0.00     4.47
+ATOM     40    C STP    10      19.138  37.660  32.994    0.00     4.54
+ATOM     41    C STP    10      19.116  37.654  33.024    0.00     4.54
+ATOM     42    C STP    10      19.115  37.662  33.021    0.00     4.54
+ATOM     43    C STP    10      18.498  35.757  35.907    0.00     3.54
+ATOM     44    O STP    10      18.041  37.280  33.428    0.00     4.04
+ATOM     45    C STP    10      18.664  37.361  33.249    0.00     4.29
+ATOM     46    O STP    10      17.586  36.737  34.326    0.00     3.53
+ATOM     47    C STP    10      18.506  35.744  35.825    0.00     3.58
+ATOM     48    C STP    10      19.301  37.188  33.471    0.00     4.39
+ATOM     49    O STP    10      19.927  36.095  35.154    0.00     4.20
+ATOM     50    O STP    10      19.807  35.859  35.537    0.00     4.14
+ATOM     51    O STP    10      19.624  36.886  33.557    0.00     4.29
+ATOM     52    O STP    10      20.418  35.977  34.266    0.00     4.22
+ATOM     53    O STP    10      20.780  34.426  34.534    0.00     3.86
+ATOM     54    O STP    10      20.507  34.155  35.241    0.00     3.80
+ATOM     55    O STP    10      20.041  32.362  35.203    0.00     3.42
+ATOM     56    O STP    10      20.690  34.424  34.197    0.00     3.70
+ATOM     57    O STP    10      20.804  34.600  34.377    0.00     3.90
+TER
+END

tests/reference_output/123abc_out/pocket11_atm.cif

@@ -0,0 +1,63 @@
+data_pocket11_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    11:
+0  - Pocket Score                      : 0.0388
+1  - Drug Score                        : 0.0007
+2  - Number of alpha spheres           :    30
+3  - Mean alpha-sphere radius          : 3.6177
+4  - Mean alpha-sphere Solvent Acc.    : 0.4151
+5  - Mean B-factor of pocket residues  : 0.1046
+6  - Hydrophobicity Score              : 17.4167
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 3.8333
+9  - Pocket volume (Monte Carlo)       : 157.8834
+10  -Pocket volume (convex hull)       : 11.3291
+11 - Charge Score                      :    -1
+12 - Local hydrophobic density Score   : 5.0000
+13 - Number of apolar alpha sphere     :     6
+14 - Proportion of apolar alpha sphere : 0.2000
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    1405     C  CD2 ?  PHE    Axp 189 ?   10.703   31.452   22.157   0.00  0 416 A
+ATOM    1435     O    O ?  SER    Axp 193 ?   11.879   32.960   15.552  -3.21  0 420 A
+ATOM    1407     C  CE2 ?  PHE    Axp 189 ?   11.966   31.656   22.739   0.00  0 416 A
+ATOM    996      O    O ?  ARG    Axp 135 ?   13.454   28.096   20.320  -4.69  0 362 A
+ATOM    1436     C   CB ?  SER    Axp 193 ?    9.997   34.149   17.982   0.00  0 420 A
+ATOM    1329     N    N ?  ALA    Axp 180 ?   14.229   35.929   18.757  -1.09  0 407 A
+ATOM    1327     O  OG1 ?  THR    Axp 179 ?   17.108   33.330   21.134  -2.14  0 406 A
+ATOM    1290     C   CD ?  PRO    Axp 175 ?   18.295   29.738   22.438   0.00  0 402 A
+ATOM    1323     C   CA ?  THR    Axp 179 ?   16.193   34.623   19.411   0.00  0 406 A
+ATOM    1437     O   OG ?  SER    Axp 193 ?    9.317   33.077   18.605   0.00  0 420 A
+ATOM    1289     C   CG ?  PRO    Axp 175 ?   18.737   29.443   21.033   0.00  0 402 A
+ATOM    1312     C   CB ?  TRP    Axp 178 ?   18.807   31.481   17.128   0.00  0 405 A
+ATOM    1005     C   CA ?  ASP    Axp 136 ?   14.988   26.627   18.681   0.00  0 363 A
+ATOM    1311     O    O ?  TRP    Axp 178 ?   16.495   33.261   16.896  -2.14  0 405 A
+ATOM    1471     C   CB ?  ALA    Axp 197 ?   14.926   31.065   14.885   0.00  0 424 A
+ATOM    1355     O   OG ?  SER    Axp 183 ?   10.954   35.267   20.964   0.00  0 410 A
+ATOM    1012     N    N ?  LEU    Axp 137 ?   14.970   26.942   16.300   0.00  0 364 A
+ATOM    1444     O  OD1 ?  ASP    Axp 194 ?   10.115   28.834   16.531   0.00  0 421 A
+ATOM    995      C    C ?  ARG    Axp 135 ?   12.856   27.406   19.519   0.00  0 362 A
+ATOM    994      C   CA ?  ARG    Axp 135 ?   11.309   27.407   19.509   0.00  0 362 A
+ATOM    1328     C  CG2 ?  THR    Axp 179 ?   15.235   34.657   21.794   0.00  0 406 A
+# 

tests/reference_output/123abc_out/pocket11_env_atm.cif

@@ -0,0 +1,64 @@
+data_pocket11_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    993      N    N ?  ARG    Axp 135 ?   10.598   26.723   18.417   0.00  0 362 A
+ATOM    994      C   CA ?  ARG    Axp 135 ?   11.309   27.407   19.509   0.00  0 362 A
+ATOM    995      C    C ?  ARG    Axp 135 ?   12.856   27.406   19.519   0.00  0 362 A
+ATOM    996      O    O ?  ARG    Axp 135 ?   13.454   28.096   20.320  -4.69  0 362 A
+ATOM    997      C   CB ?  ARG    Axp 135 ?   10.850   26.919   20.881   0.00  0 362 A
+ATOM    1004     N    N ?  ASP    Axp 136 ?   13.515   26.641   18.666   0.00  0 363 A
+ATOM    1005     C   CA ?  ASP    Axp 136 ?   14.988   26.627   18.681   0.00  0 363 A
+ATOM    1006     C    C ?  ASP    Axp 136 ?   15.413   26.185   17.291   0.00  0 363 A
+ATOM    1008     C   CB ?  ASP    Axp 136 ?   15.490   25.673   19.755   0.00  0 363 A
+ATOM    1009     C   CG ?  ASP    Axp 136 ?   16.996   25.759   19.996   0.00  0 363 A
+ATOM    1010     O  OD1 ?  ASP    Axp 136 ?   17.712   26.739   19.639   0.00  0 363 A
+ATOM    1012     N    N ?  LEU    Axp 137 ?   14.970   26.942   16.300   0.00  0 364 A
+ATOM    1014     C    C ?  LEU    Axp 137 ?   16.652   27.030   14.689   0.00  0 364 A
+ATOM    1015     O    O ?  LEU    Axp 137 ?   16.968   28.209   14.932   0.00  0 364 A
+ATOM    1280     C  CD2 ?  PHE    Axp 174 ?   15.409   30.643   25.623   0.00  0 401 A
+ATOM    1287     O    O ?  PRO    Axp 175 ?   19.472   32.424   20.666   0.00  0 402 A
+ATOM    1289     C   CG ?  PRO    Axp 175 ?   18.737   29.443   21.033   0.00  0 402 A
+ATOM    1290     C   CD ?  PRO    Axp 175 ?   18.295   29.738   22.438   0.00  0 402 A
+ATOM    1309     C   CA ?  TRP    Axp 178 ?   18.854   33.025   17.137   0.00  0 405 A
+ATOM    1310     C    C ?  TRP    Axp 178 ?   17.481   33.558   17.564   0.00  0 405 A
+ATOM    1311     O    O ?  TRP    Axp 178 ?   16.495   33.261   16.896  -2.14  0 405 A
+ATOM    1312     C   CB ?  TRP    Axp 178 ?   18.807   31.481   17.128   0.00  0 405 A
+ATOM    1322     N    N ?  THR    Axp 179 ?   17.421   34.347   18.657   0.00  0 406 A
+ATOM    1323     C   CA ?  THR    Axp 179 ?   16.193   34.623   19.411   0.00  0 406 A
+ATOM    1324     C    C ?  THR    Axp 179 ?   15.545   35.958   19.044   0.00  0 406 A
+ATOM    1326     C   CB ?  THR    Axp 179 ?   16.508   34.581   20.893   0.00  0 406 A
+ATOM    1327     O  OG1 ?  THR    Axp 179 ?   17.108   33.330   21.134  -2.14  0 406 A
+ATOM    1328     C  CG2 ?  THR    Axp 179 ?   15.235   34.657   21.794   0.00  0 406 A
+ATOM    1329     N    N ?  ALA    Axp 180 ?   14.229   35.929   18.757  -1.09  0 407 A
+ATOM    1333     C   CB ?  ALA    Axp 180 ?   12.155   36.812   17.751   0.00  0 407 A
+ATOM    1354     C   CB ?  SER    Axp 183 ?   11.829   35.508   22.060   0.00  0 410 A
+ATOM    1355     O   OG ?  SER    Axp 183 ?   10.954   35.267   20.964   0.00  0 410 A
+ATOM    1405     C  CD2 ?  PHE    Axp 189 ?   10.703   31.452   22.157   0.00  0 416 A
+ATOM    1407     C  CE2 ?  PHE    Axp 189 ?   11.966   31.656   22.739   0.00  0 416 A
+ATOM    1408     C   CZ ?  PHE    Axp 189 ?   12.053   32.229   24.016   0.00  0 416 A
+ATOM    1433     C   CA ?  SER    Axp 193 ?    9.893   34.090   16.472   0.00  0 420 A
+ATOM    1434     C    C ?  SER    Axp 193 ?   10.658   32.899   15.802   0.00  0 420 A
+ATOM    1435     O    O ?  SER    Axp 193 ?   11.879   32.960   15.552  -3.21  0 420 A
+ATOM    1436     C   CB ?  SER    Axp 193 ?    9.997   34.149   17.982   0.00  0 420 A
+ATOM    1437     O   OG ?  SER    Axp 193 ?    9.317   33.077   18.605   0.00  0 420 A
+ATOM    1438     N    N ?  ASP    Axp 194 ?    9.907   31.853   15.450   0.00  0 421 A
+ATOM    1439     C   CA ?  ASP    Axp 194 ?   10.435   30.800   14.622   0.00  0 421 A
+ATOM    1444     O  OD1 ?  ASP    Axp 194 ?   10.115   28.834   16.531   0.00  0 421 A
+ATOM    1471     C   CB ?  ALA    Axp 197 ?   14.926   31.065   14.885   0.00  0 424 A
+#

tests/reference_output/123abc_out/pocket11_vert.pqr

@@ -0,0 +1,32 @@
+ATOM      1    O STP    11      12.898  31.662  19.017    0.00     3.84
+ATOM      2    O STP    11      13.150  32.247  19.120    0.00     3.85
+ATOM      3    O STP    11      15.088  30.679  21.810    0.00     3.40
+ATOM      4    O STP    11      14.161  31.633  19.836    0.00     3.64
+ATOM      5    O STP    11      13.387  31.848  19.044    0.00     3.96
+ATOM      6    O STP    11      13.175  32.231  19.116    0.00     3.86
+ATOM      7    O STP    11      12.808  31.604  18.987    0.00     3.81
+ATOM      8    O STP    11      12.873  31.765  19.036    0.00     3.81
+ATOM      9    C STP    11      12.557  32.462  19.477    0.00     3.41
+ATOM     10    O STP    11      12.931  31.991  19.076    0.00     3.80
+ATOM     11    C STP    11      16.028  30.026  18.804    0.00     3.56
+ATOM     12    O STP    11      13.473  31.801  18.968    0.00     3.94
+ATOM     13    O STP    11      13.537  32.512  18.591    0.00     3.49
+ATOM     14    O STP    11      15.773  30.122  18.478    0.00     3.59
+ATOM     15    O STP    11      14.671  31.353  19.355    0.00     3.61
+ATOM     16    O STP    11      15.838  30.562  19.199    0.00     3.61
+ATOM     17    O STP    11      15.915  30.373  18.983    0.00     3.61
+ATOM     18    O STP    11      16.143  30.691  19.153    0.00     3.44
+ATOM     19    O STP    11      13.668  31.316  18.409    0.00     3.75
+ATOM     20    O STP    11      15.536  30.118  18.260    0.00     3.56
+ATOM     21    C STP    11      15.745  30.047  18.174    0.00     3.54
+ATOM     22    O STP    11      12.904  32.687  19.451    0.00     3.57
+ATOM     23    C STP    11      15.940  29.800  17.882    0.00     3.41
+ATOM     24    O STP    11      12.225  30.961  18.523    0.00     3.60
+ATOM     25    O STP    11      12.987  30.452  17.753    0.00     3.52
+ATOM     26    O STP    11      12.997  30.420  17.738    0.00     3.50
+ATOM     27    O STP    11      11.766  30.743  19.000    0.00     3.41
+ATOM     28    O STP    11      11.834  30.739  18.825    0.00     3.44
+ATOM     29    C STP    11      13.290  32.673  19.656    0.00     3.51
+ATOM     30    C STP    11      14.144  31.854  20.011    0.00     3.50
+TER
+END

tests/reference_output/123abc_out/pocket12_atm.cif

@@ -0,0 +1,61 @@
+data_pocket12_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    12:
+0  - Pocket Score                      : 0.0380
+1  - Drug Score                        : 0.0004
+2  - Number of alpha spheres           :    22
+3  - Mean alpha-sphere radius          : 4.0091
+4  - Mean alpha-sphere Solvent Acc.    : 0.5656
+5  - Mean B-factor of pocket residues  : 0.1891
+6  - Hydrophobicity Score              : 14.1667
+7  - Polarity Score                    :     7
+8  - Amino Acid based volume Score     : 4.4167
+9  - Pocket volume (Monte Carlo)       : 288.4808
+10  -Pocket volume (convex hull)       : 19.5893
+11 - Charge Score                      :     1
+12 - Local hydrophobic density Score   : 1.0000
+13 - Number of apolar alpha sphere     :     2
+14 - Proportion of apolar alpha sphere : 0.0909
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    3271     O   OG ?  SER    Bxp 158 ?   19.353   51.914   34.201  -4.02  0 385 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    3383     C  CE2 ?  PHE    Bxp 174 ?   15.221   45.900   34.664   0.00  0 401 B
+ATOM    3094     O    O ?  ARG    Bxp 135 ?   14.784   48.309   40.445  -7.50  0 362 B
+ATOM    3097     C   CD ?  ARG    Bxp 135 ?   10.822   49.558   37.921   0.00  0 362 B
+ATOM    3504     C  CE2 ?  PHE    Bxp 189 ?   12.691   45.021   38.263   0.00  0 416 B
+ATOM    3368     O    O ?  LYS    Bxp 173 ?   18.932   47.542   34.352  -3.62  0 400 B
+ATOM    3109     O  OD2 ?  ASP    Bxp 136 ?   19.063   51.084   39.753  -0.40  0 363 B
+ATOM    3258     N    N ?  LEU    Bxp 157 ?   20.869   54.873   37.697   0.00  0 384 B
+ATOM    3095     C   CB ?  ARG    Bxp 135 ?   12.276   49.729   39.764   0.00  0 362 B
+ATOM    3084     O    O ?  HIS    Bxp 134 ?   12.372   52.048   41.332  -1.07  0 361 B
+ATOM    3381     C  CD2 ?  PHE    Bxp 174 ?   16.430   45.506   35.243   0.00  0 401 B
+ATOM    3270     C   CB ?  SER    Bxp 158 ?   20.116   50.947   34.907   0.00  0 385 B
+ATOM    3326     C  CE2 ?  TYR    Bxp 166 ?   21.152   49.314   38.053   0.00  0 393 B
+ATOM    3391     C   CD ?  PRO    Bxp 175 ?   19.172   45.854   38.445   0.00  0 402 B
+ATOM    3106     C   CB ?  ASP    Bxp 136 ?   17.005   50.806   40.933   0.00  0 363 B
+ATOM    3107     C   CG ?  ASP    Bxp 136 ?   18.465   50.434   40.626   0.00  0 363 B
+# 

tests/reference_output/123abc_out/pocket12_env_atm.cif

@@ -0,0 +1,58 @@
+data_pocket12_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    3084     O    O ?  HIS    Bxp 134 ?   12.372   52.048   41.332  -1.07  0 361 B
+ATOM    3092     C   CA ?  ARG    Bxp 135 ?   12.705   49.230   41.141   0.00  0 362 B
+ATOM    3093     C    C ?  ARG    Bxp 135 ?   14.235   49.115   41.170   0.00  0 362 B
+ATOM    3094     O    O ?  ARG    Bxp 135 ?   14.784   48.309   40.445  -7.50  0 362 B
+ATOM    3095     C   CB ?  ARG    Bxp 135 ?   12.276   49.729   39.764   0.00  0 362 B
+ATOM    3096     C   CG ?  ARG    Bxp 135 ?   10.987   49.132   39.313   0.00  0 362 B
+ATOM    3097     C   CD ?  ARG    Bxp 135 ?   10.822   49.558   37.921   0.00  0 362 B
+ATOM    3098     N   NE ?  ARG    Bxp 135 ?    9.837   48.697   37.316  -3.28  0 362 B
+ATOM    3099     C   CZ ?  ARG    Bxp 135 ?    9.680   48.564   36.008   0.00  0 362 B
+ATOM    3100     N  NH1 ?  ARG    Bxp 135 ?   10.479   49.242   35.166   0.00  0 362 B
+ATOM    3102     N    N ?  ASP    Bxp 136 ?   14.929   49.943   41.933   0.00  0 363 B
+ATOM    3103     C   CA ?  ASP    Bxp 136 ?   16.383   49.878   41.974   0.00  0 363 B
+ATOM    3106     C   CB ?  ASP    Bxp 136 ?   17.005   50.806   40.933   0.00  0 363 B
+ATOM    3107     C   CG ?  ASP    Bxp 136 ?   18.465   50.434   40.626   0.00  0 363 B
+ATOM    3108     O  OD1 ?  ASP    Bxp 136 ?   19.011   49.469   41.230  -2.14  0 363 B
+ATOM    3109     O  OD2 ?  ASP    Bxp 136 ?   19.063   51.084   39.753  -0.40  0 363 B
+ATOM    3240     C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    3254     N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM    3256     C    C ?  GLY    Bxp 156 ?   20.360   55.778   36.866   0.00  0 383 B
+ATOM    3258     N    N ?  LEU    Bxp 157 ?   20.869   54.873   37.697   0.00  0 384 B
+ATOM    3266     N    N ?  SER    Bxp 158 ?   21.413   52.688   36.129   0.00  0 385 B
+ATOM    3267     C   CA ?  SER    Bxp 158 ?   21.516   51.514   35.236   0.00  0 385 B
+ATOM    3270     C   CB ?  SER    Bxp 158 ?   20.116   50.947   34.907   0.00  0 385 B
+ATOM    3271     O   OG ?  SER    Bxp 158 ?   19.353   51.914   34.201  -4.02  0 385 B
+ATOM    3324     C  CD2 ?  TYR    Bxp 166 ?   21.644   48.614   37.025   0.00  0 393 B
+ATOM    3326     C  CE2 ?  TYR    Bxp 166 ?   21.152   49.314   38.053   0.00  0 393 B
+ATOM    3368     O    O ?  LYS    Bxp 173 ?   18.932   47.542   34.352  -3.62  0 400 B
+ATOM    3375     C   CA ?  PHE    Bxp 174 ?   19.360   45.109   35.564   0.00  0 401 B
+ATOM    3381     C  CD2 ?  PHE    Bxp 174 ?   16.430   45.506   35.243   0.00  0 401 B
+ATOM    3383     C  CE2 ?  PHE    Bxp 174 ?   15.221   45.900   34.664   0.00  0 401 B
+ATOM    3390     C   CG ?  PRO    Bxp 175 ?   19.698   46.334   39.774   0.00  0 402 B
+ATOM    3391     C   CD ?  PRO    Bxp 175 ?   19.172   45.854   38.445   0.00  0 402 B
+ATOM    3502     C  CD2 ?  PHE    Bxp 189 ?   11.410   45.318   38.790   0.00  0 416 B
+ATOM    3504     C  CE2 ?  PHE    Bxp 189 ?   12.691   45.021   38.263   0.00  0 416 B
+ATOM    3505     C   CZ ?  PHE    Bxp 189 ?   12.791   44.477   36.970   0.00  0 416 B
+#

tests/reference_output/123abc_out/pocket12_vert.pqr

@@ -0,0 +1,24 @@
+ATOM      1    O STP    12      15.798  53.375  36.448    0.00     4.45
+ATOM      2    C STP    12      13.890  48.091  37.059    0.00     3.51
+ATOM      3    O STP    12      15.723  50.129  36.349    0.00     4.58
+ATOM      4    O STP    12      16.096  50.102  36.606    0.00     4.44
+ATOM      5    O STP    12      15.901  52.536  36.959    0.00     4.46
+ATOM      6    O STP    12      16.813  53.016  37.079    0.00     3.99
+ATOM      7    O STP    12      18.001  53.059  37.147    0.00     3.44
+ATOM      8    C STP    12      14.176  48.608  36.866    0.00     3.64
+ATOM      9    O STP    12      12.896  52.943  37.474    0.00     3.99
+ATOM     10    O STP    12      16.135  49.273  36.737    0.00     4.06
+ATOM     11    O STP    12      17.906  49.419  37.009    0.00     3.41
+ATOM     12    O STP    12      16.145  50.097  36.607    0.00     4.40
+ATOM     13    O STP    12      17.037  48.850  37.404    0.00     3.82
+ATOM     14    O STP    12      16.872  48.623  37.320    0.00     3.77
+ATOM     15    O STP    12      17.737  48.872  37.372    0.00     3.51
+ATOM     16    O STP    12      15.994  50.263  36.624    0.00     4.46
+ATOM     17    O STP    12      15.478  50.742  36.523    0.00     4.67
+ATOM     18    O STP    12      15.879  52.513  36.955    0.00     4.47
+ATOM     19    O STP    12      14.645  52.046  38.693    0.00     3.48
+ATOM     20    O STP    12      15.903  52.532  37.000    0.00     4.43
+ATOM     21    O STP    12      16.777  49.342  37.774    0.00     3.49
+ATOM     22    O STP    12      17.097  48.804  37.592    0.00     3.71
+TER
+END

tests/reference_output/123abc_out/pocket13_atm.cif

@@ -0,0 +1,74 @@
+data_pocket13_atm
+# 
+loop_
+_struct.pdbx_descriptor
+This is a mmcif format file writen by the programm fpocket.                 
+It represents the atoms contacted by the voronoi vertices of the pocket.  
+                                                                           
+Information about the pocket    13:
+0  - Pocket Score                      : 0.0342
+1  - Drug Score                        : 0.3180
+2  - Number of alpha spheres           :    51
+3  - Mean alpha-sphere radius          : 3.7908
+4  - Mean alpha-sphere Solvent Acc.    : 0.4415
+5  - Mean B-factor of pocket residues  : 0.1092
+6  - Hydrophobicity Score              : 59.0769
+7  - Polarity Score                    :     0
+8  - Amino Acid based volume Score     : 3.6154
+9  - Pocket volume (Monte Carlo)       : 411.4784
+10  -Pocket volume (convex hull)       : 39.2787
+11 - Charge Score                      :     0
+12 - Local hydrophobic density Score   : 37.1163
+13 - Number of apolar alpha sphere     :    43
+14 - Proportion of apolar alpha sphere : 0.8431
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    7064     N    N ?  VAL    Dxp 111 ?   48.340   24.744   22.841   0.00  0 338 D
+ATOM    7069     C  CG1 ?  VAL    Dxp 111 ?   50.065   24.177   20.697   0.00  0 338 D
+ATOM    7068     C   CB ?  VAL    Dxp 111 ?   49.531   23.019   21.320   0.00  0 338 D
+ATOM    7063     C   CB ?  ALA    Dxp 110 ?   45.905   26.806   22.761   0.00  0 337 D
+ATOM    8096     C  CG1 ?  VAL    Dxp 241 ?   40.339   21.749   29.386   0.00  0 468 D
+ATOM    7780     O    O ?  LEU    Dxp 202 ?   42.550   24.062   33.744   0.00  0 429 D
+ATOM    7784     C  CD2 ?  LEU    Dxp 202 ?   42.820   19.922   32.429   0.00  0 429 D
+ATOM    7814     C  CG2 ?  ILE    Dxp 205 ?   46.612   24.182   31.921   0.00  0 432 D
+ATOM    7081     O    O ?  LEU    Dxp 113 ?   47.597   21.725   29.219  -1.07  0 340 D
+ATOM    7086     N    N ?  LEU    Dxp 114 ?   47.359   21.989   26.988   0.00  0 341 D
+ATOM    7087     C   CA ?  LEU    Dxp 114 ?   46.823   20.670   26.737   0.00  0 341 D
+ATOM    7080     C    C ?  LEU    Dxp 113 ?   47.767   22.386   28.183   0.00  0 340 D
+ATOM    7062     O    O ?  ALA    Dxp 110 ?   47.080   24.204   24.629  -3.21  0 337 D
+ATOM    7093     C  CD2 ?  LEU    Dxp 114 ?   45.275   20.097   23.190   0.00  0 341 D
+ATOM    8079     C   CG ?  PRO    Dxp 238 ?   40.497   24.257   24.472   0.00  0 465 D
+ATOM    7061     C    C ?  ALA    Dxp 110 ?   47.472   25.051   23.811   0.00  0 337 D
+ATOM    8080     C   CD ?  PRO    Dxp 238 ?   40.408   25.135   25.676   0.00  0 465 D
+ATOM    8067     O    O ?  GLY    Dxp 236 ?   40.728   28.470   25.473  -1.21  0 463 D
+ATOM    7060     C   CA ?  ALA    Dxp 110 ?   46.959   26.484   23.905   0.00  0 337 D
+ATOM    7084     C  CD1 ?  LEU    Dxp 113 ?   46.418   27.158   28.740   0.00  0 340 D
+ATOM    7817     C   CA ?  ALA    Dxp 206 ?   43.249   27.236   31.702   0.00  0 433 D
+ATOM    7819     O    O ?  ALA    Dxp 206 ?   43.166   29.530   31.087  -4.69  0 433 D
+ATOM    8069     C   CA ?  CYS    Dxp 237 ?   39.173   27.291   27.413   0.00  0 464 D
+ATOM    7118     C   CB ?  ALA    Dxp 117 ?   45.712   18.926   30.827   0.00  0 344 D
+ATOM    7820     C   CB ?  ALA    Dxp 206 ?   41.725   26.810   31.590   0.00  0 433 D
+ATOM    8073     S   SG ?  CYS    Dxp 237 ?   38.662   25.215   29.286   0.00  0 464 D
+ATOM    7816     N    N ?  ALA    Dxp 206 ?   43.950   26.440   32.723   0.00  0 433 D
+ATOM    7065     C   CA ?  VAL    Dxp 111 ?   48.863   23.360   22.717   0.00  0 338 D
+ATOM    7082     C   CB ?  LEU    Dxp 113 ?   47.325   24.825   28.299   0.00  0 340 D
+ATOM    8097     C  CG2 ?  VAL    Dxp 241 ?   40.590   21.066   26.854   0.00  0 468 D
+ATOM    7092     C  CD1 ?  LEU    Dxp 114 ?   44.050   19.857   25.449   0.00  0 341 D
+ATOM    8308     C  CE1 ?  PHE    Dxp 266 ?   42.431   17.800   28.875   0.00  0 493 D
+# 

tests/reference_output/123abc_out/pocket13_env_atm.cif

@@ -0,0 +1,70 @@
+data_pocket13_env_atm
+# 
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_asym_id
+ATOM    7059     N    N ?  ALA    Dxp 110 ?   48.007   27.461   23.893  -1.09  0 337 D
+ATOM    7060     C   CA ?  ALA    Dxp 110 ?   46.959   26.484   23.905   0.00  0 337 D
+ATOM    7061     C    C ?  ALA    Dxp 110 ?   47.472   25.051   23.811   0.00  0 337 D
+ATOM    7062     O    O ?  ALA    Dxp 110 ?   47.080   24.204   24.629  -3.21  0 337 D
+ATOM    7063     C   CB ?  ALA    Dxp 110 ?   45.905   26.806   22.761   0.00  0 337 D
+ATOM    7064     N    N ?  VAL    Dxp 111 ?   48.340   24.744   22.841   0.00  0 338 D
+ATOM    7065     C   CA ?  VAL    Dxp 111 ?   48.863   23.360   22.717   0.00  0 338 D
+ATOM    7068     C   CB ?  VAL    Dxp 111 ?   49.531   23.019   21.320   0.00  0 338 D
+ATOM    7069     C  CG1 ?  VAL    Dxp 111 ?   50.065   24.177   20.697   0.00  0 338 D
+ATOM    7079     C   CA ?  LEU    Dxp 113 ?   48.430   23.739   28.221   0.00  0 340 D
+ATOM    7080     C    C ?  LEU    Dxp 113 ?   47.767   22.386   28.183   0.00  0 340 D
+ATOM    7081     O    O ?  LEU    Dxp 113 ?   47.597   21.725   29.219  -1.07  0 340 D
+ATOM    7082     C   CB ?  LEU    Dxp 113 ?   47.325   24.825   28.299   0.00  0 340 D
+ATOM    7083     C   CG ?  LEU    Dxp 113 ?   47.664   26.335   28.429   0.00  0 340 D
+ATOM    7084     C  CD1 ?  LEU    Dxp 113 ?   46.418   27.158   28.740   0.00  0 340 D
+ATOM    7086     N    N ?  LEU    Dxp 114 ?   47.359   21.989   26.988   0.00  0 341 D
+ATOM    7087     C   CA ?  LEU    Dxp 114 ?   46.823   20.670   26.737   0.00  0 341 D
+ATOM    7090     C   CB ?  LEU    Dxp 114 ?   46.375   20.660   25.286   0.00  0 341 D
+ATOM    7091     C   CG ?  LEU    Dxp 114 ?   45.386   19.662   24.699   0.00  0 341 D
+ATOM    7092     C  CD1 ?  LEU    Dxp 114 ?   44.050   19.857   25.449   0.00  0 341 D
+ATOM    7093     C  CD2 ?  LEU    Dxp 114 ?   45.275   20.097   23.190   0.00  0 341 D
+ATOM    7118     C   CB ?  ALA    Dxp 117 ?   45.712   18.926   30.827   0.00  0 344 D
+ATOM    7778     C   CA ?  LEU    Dxp 202 ?   42.652   21.867   34.762   0.00  0 429 D
+ATOM    7779     C    C ?  LEU    Dxp 202 ?   42.175   23.314   34.680   0.00  0 429 D
+ATOM    7780     O    O ?  LEU    Dxp 202 ?   42.550   24.062   33.744   0.00  0 429 D
+ATOM    7781     C   CB ?  LEU    Dxp 202 ?   41.521   21.052   34.137   0.00  0 429 D
+ATOM    7784     C  CD2 ?  LEU    Dxp 202 ?   42.820   19.922   32.429   0.00  0 429 D
+ATOM    7810     C    C ?  ILE    Dxp 205 ?   45.268   26.571   32.956   0.00  0 432 D
+ATOM    7812     C   CB ?  ILE    Dxp 205 ?   46.098   24.078   33.335   0.00  0 432 D
+ATOM    7814     C  CG2 ?  ILE    Dxp 205 ?   46.612   24.182   31.921   0.00  0 432 D
+ATOM    7816     N    N ?  ALA    Dxp 206 ?   43.950   26.440   32.723   0.00  0 433 D
+ATOM    7817     C   CA ?  ALA    Dxp 206 ?   43.249   27.236   31.702   0.00  0 433 D
+ATOM    7818     C    C ?  ALA    Dxp 206 ?   43.351   28.736   31.982   0.00  0 433 D
+ATOM    7819     O    O ?  ALA    Dxp 206 ?   43.166   29.530   31.087  -4.69  0 433 D
+ATOM    7820     C   CB ?  ALA    Dxp 206 ?   41.725   26.810   31.590   0.00  0 433 D
+ATOM    8066     C    C ?  GLY    Dxp 236 ?   39.903   29.189   26.105   0.00  0 463 D
+ATOM    8067     O    O ?  GLY    Dxp 236 ?   40.728   28.470   25.473  -1.21  0 463 D
+ATOM    8068     N    N ?  CYS    Dxp 237 ?   39.113   28.714   27.084   0.00  0 464 D
+ATOM    8069     C   CA ?  CYS    Dxp 237 ?   39.173   27.291   27.413   0.00  0 464 D
+ATOM    8072     C   CB ?  CYS    Dxp 237 ?   38.727   27.002   28.857   0.00  0 464 D
+ATOM    8073     S   SG ?  CYS    Dxp 237 ?   38.662   25.215   29.286   0.00  0 464 D
+ATOM    8074     N    N ?  PRO    Dxp 238 ?   38.989   25.529   25.691   0.00  0 465 D
+ATOM    8079     C   CG ?  PRO    Dxp 238 ?   40.497   24.257   24.472   0.00  0 465 D
+ATOM    8080     C   CD ?  PRO    Dxp 238 ?   40.408   25.135   25.676   0.00  0 465 D
+ATOM    8095     C   CB ?  VAL    Dxp 241 ?   39.605   21.580   27.947   0.00  0 468 D
+ATOM    8096     C  CG1 ?  VAL    Dxp 241 ?   40.339   21.749   29.386   0.00  0 468 D
+ATOM    8097     C  CG2 ?  VAL    Dxp 241 ?   40.590   21.066   26.854   0.00  0 468 D
+ATOM    8306     C  CD1 ?  PHE    Dxp 266 ?   43.156   16.946   28.042   0.00  0 493 D
+ATOM    8308     C  CE1 ?  PHE    Dxp 266 ?   42.431   17.800   28.875   0.00  0 493 D
+ATOM    8310     C   CZ ?  PHE    Dxp 266 ?   42.081   17.395   30.126   0.00  0 493 D
+#

tests/reference_output/123abc_out/pocket13_vert.pqr

@@ -0,0 +1,53 @@
+ATOM      1    C STP    13      46.059  24.382  19.261    0.00     4.26
+ATOM      2    C STP    13      43.573  22.870  30.504    0.00     3.60
+ATOM      3    C STP    13      43.984  22.433  29.906    0.00     3.75
+ATOM      4    O STP    13      43.952  22.288  28.531    0.00     3.75
+ATOM      5    O STP    13      43.955  22.851  28.597    0.00     3.86
+ATOM      6    C STP    13      43.827  23.601  22.719    0.00     3.82
+ATOM      7    C STP    13      45.118  23.290  19.762    0.00     4.69
+ATOM      8    C STP    13      45.149  23.388  21.337    0.00     3.78
+ATOM      9    C STP    13      44.874  23.447  21.846    0.00     3.63
+ATOM     10    C STP    13      43.793  26.502  25.724    0.00     3.65
+ATOM     11    C STP    13      43.786  25.191  24.960    0.00     3.45
+ATOM     12    C STP    13      43.895  25.524  25.355    0.00     3.52
+ATOM     13    O STP    13      42.903  27.502  28.148    0.00     3.58
+ATOM     14    C STP    13      43.879  26.514  26.051    0.00     3.75
+ATOM     15    C STP    13      44.061  25.792  26.172    0.00     3.74
+ATOM     16    C STP    13      42.795  26.738  28.029    0.00     3.72
+ATOM     17    C STP    13      43.975  21.875  29.579    0.00     3.64
+ATOM     18    C STP    13      43.957  21.481  28.872    0.00     3.66
+ATOM     19    C STP    13      42.130  24.737  28.746    0.00     3.54
+ATOM     20    C STP    13      43.487  23.966  29.665    0.00     3.86
+ATOM     21    C STP    13      43.458  23.963  30.068    0.00     3.66
+ATOM     22    C STP    13      43.369  23.803  30.112    0.00     3.73
+ATOM     23    O STP    13      43.391  23.850  30.163    0.00     3.68
+ATOM     24    O STP    13      42.594  27.525  28.277    0.00     3.50
+ATOM     25    O STP    13      42.505  27.578  28.306    0.00     3.46
+ATOM     26    C STP    13      42.795  26.735  28.032    0.00     3.72
+ATOM     27    C STP    13      42.802  26.839  28.057    0.00     3.69
+ATOM     28    C STP    13      42.795  26.746  28.033    0.00     3.71
+ATOM     29    C STP    13      45.471  23.095  20.260    0.00     4.20
+ATOM     30    O STP    13      43.876  23.748  26.816    0.00     3.91
+ATOM     31    C STP    13      44.046  25.266  26.548    0.00     3.74
+ATOM     32    C STP    13      43.944  22.937  28.572    0.00     3.88
+ATOM     33    C STP    13      43.723  23.220  27.954    0.00     3.96
+ATOM     34    C STP    13      43.497  23.681  27.807    0.00     4.03
+ATOM     35    C STP    13      43.694  23.535  27.272    0.00     3.99
+ATOM     36    C STP    13      43.249  24.512  28.561    0.00     4.10
+ATOM     37    C STP    13      43.261  24.584  28.537    0.00     4.08
+ATOM     38    C STP    13      43.457  24.225  29.088    0.00     3.99
+ATOM     39    C STP    13      43.380  24.593  28.735    0.00     3.98
+ATOM     40    C STP    13      43.972  23.122  29.275    0.00     3.89
+ATOM     41    C STP    13      43.957  22.936  28.651    0.00     3.88
+ATOM     42    C STP    13      43.579  24.045  29.361    0.00     3.97
+ATOM     43    C STP    13      43.373  23.252  26.343    0.00     3.58
+ATOM     44    C STP    13      43.788  23.106  24.178    0.00     3.50
+ATOM     45    C STP    13      43.744  23.515  26.179    0.00     3.74
+ATOM     46    C STP    13      43.710  23.456  26.998    0.00     3.93
+ATOM     47    O STP    13      43.820  23.548  26.634    0.00     3.88
+ATOM     48    C STP    13      43.834  22.399  28.195    0.00     3.75
+ATOM     49    C STP    13      43.828  22.419  28.181    0.00     3.75
+ATOM     50    C STP    13      43.887  21.298  28.775    0.00     3.63
+ATOM     51    C STP    13      43.778  21.088  28.773    0.00     3.55
+TER
+END