update for osx

Documentation stuff missing

.dockerignore

@@ -0,0 +1 @@
+*.o

.gitignore

@@ -5,3 +5,4 @@ src/qhull/bin/
 src/qhull/lib/libqhullstatic_r.a
 src/qhull/lib/libqhullstatic.a
 *.pyc
+vmd/plugins

Dockerfile-debian-slim

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

Dockerfile-molfile-debug

@@ -0,0 +1,29 @@
+FROM ubuntu:latest
+RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PLUGINDIR=compiled
+RUN apt update -y && apt install -y vim gdb 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 vmd /vmd
+WORKDIR /vmd/plugins
+RUN make LINUXAMD64 && make distrib
+
+COPY makefile /opt/fpocket/
+COPY src /opt/fpocket/src
+COPY data/sample /opt/fpocket/sample
+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 cp -r /vmd/plugins/molfile_plugin/compiled/LINUXAMD64/molfile/* plugins/LINUXAMD64/molfile/
+#RUN make && make install && make clean
+USER fpocket
+WORKDIR /tmp
+CMD ["fpocket"]

README.md

@@ -18,6 +18,8 @@ The documentation below here is just a quick & rough overview.
 
 ## What's new compared to fpocket 2.0 (old sourceforge repo)
 __fpocket__: 
+- fpocket now supports mmCIF as input and output format together with the classical PDB format
+- support was added to define / delete and handle protein chains or sets of them to enable characterization of protein protein binding epitopes
 - is now able to consider explicit pockets when you want to calculate properties for a known binding site
 - cli changed a bit
 - pocket flexibility using temperature factors is better considered (less very flexible pockets on very solvent exposed areas)
@@ -179,7 +181,7 @@ Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c6
 
 * **Peter Schmidtke** - *Initial work* - [pschmidtke](https://github.com/pschmidtke)
 * **Vincent Le Guilloux** - *Initial work* - [leguilv](https://github.com/leguilv)
-* **Mael Shorkar** - *Chain handling* - [leguilv](https://github.com/shorkarmael)
+* **Mael Shorkar** - *Chain handling, MMCIF support* - [shorkarmael](https://github.com/shorkarmael)
 
 
 ## License

headers/pertable.h

@@ -28,6 +28,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 float pte_get_vdw_ray(const char *symbol) ;
 float pte_get_mass(const char *symbol) ;
 float pte_get_enegativity(const char *symbol) ;
+float pte_get_enegativity_from_number(int atomicnumber) ;
+char *pte_get_element_from_number(int atomicnumber);
 int is_valid_element(const char *str, int ignore_case) ;
 int element_in_std_res(char *res_name);
 int element_in_nucl_acid(char *res_name);

headers/rpdb.h

@@ -89,6 +89,8 @@ typedef struct s_pdb
     char header[M_PDB_BUF_LEN] ; /**< Header container*/
     char fname[M_PDB_FILE_NAME_LEN];    /**< File name container*/
     float avg_bfactor;  /**<overall average B factor*/
+    int model_flag; /**<flag set to 1 if a particular model / conformation was read*/
+    int model_number; /**<number of the model read in*/
 
 } s_pdb ;
 

makefile

@@ -1,6 +1,7 @@
 #------------------------------------------------------------
 # Makefile.
 #------------------------------------------------------------
+#ARCH	    = MACOSXX86_64
 ARCH	    = LINUXAMD64
 export ARCH
 
@@ -12,8 +13,11 @@ PATH_HEADER = headers/
 PATH_BIN    = bin/
 PATH_MAN    = man/
 PATH_QHULL  = src/qhull/src
+PATH_LIB	= $(PLUGINDIR)/$(ARCH)/molfile/
 
 BINDIR  = /usr/local/bin/
+LIBDIR  = /usr/local/lib/
+
 MANDIR  = /usr/local/man/man8/
 
 
@@ -48,7 +52,8 @@ QCFLAGS     = -O -g -pg -ansi
 
 LGSL        = -L$(PATH_GSL)lib -lgsl -lgslcblas 
 LFLAGS	    = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/libmolfile_plugin.a -lstdc++
-NETCDFFLAGS	= -lnetcdf
+NETCDFFLAGS	= 
+#-lnetcdf
 
 #
 #------------------------------------------------------------
@@ -180,6 +185,7 @@ install:
 	cp $(PATH_BIN)$(DPOCKET) $(BINDIR)
 	cp $(PATH_BIN)$(MDPOCKET) $(BINDIR)
 	cp $(PATH_MAN)* $(MANDIR)
+	cp $(PATH_LIB)* $(LIBDIR)
 
 check:
 	./$(PATH_BIN)$(CHECK)

plugins/LINUXAMD64/molfile/libmolfile_plugin.h

@@ -207,6 +207,9 @@ extern int molfile_maeffplugin_fini(void);
 extern int molfile_orcaplugin_init(void);
 extern int molfile_orcaplugin_register(void *, vmdplugin_register_cb);
 extern int molfile_orcaplugin_fini(void);
+extern int molfile_qcschemaplugin_init(void);
+extern int molfile_qcschemaplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_qcschemaplugin_fini(void);
 
 #define MOLFILE_INIT_ALL \
     molfile_abinitplugin_init(); \
@@ -276,6 +279,7 @@ extern int molfile_orcaplugin_fini(void);
     molfile_dtrplugin_init(); \
     molfile_maeffplugin_init(); \
     molfile_orcaplugin_init(); \
+    molfile_qcschemaplugin_init(); \
 
 #define MOLFILE_REGISTER_ALL(v, cb) \
     molfile_abinitplugin_register(v, cb); \
@@ -345,6 +349,7 @@ extern int molfile_orcaplugin_fini(void);
     molfile_dtrplugin_register(v, cb); \
     molfile_maeffplugin_register(v, cb); \
     molfile_orcaplugin_register(v, cb); \
+    molfile_qcschemaplugin_register(v, cb); \
 
 #define MOLFILE_FINI_ALL \
     molfile_abinitplugin_fini(); \
@@ -414,6 +419,7 @@ extern int molfile_orcaplugin_fini(void);
     molfile_dtrplugin_fini(); \
     molfile_maeffplugin_fini(); \
     molfile_orcaplugin_fini(); \
+    molfile_qcschemaplugin_fini(); \
 
 #ifdef __cplusplus
 }

plugins/MACOSXX86_64/molfile/libmolfile_plugin.h

@@ -204,6 +204,15 @@ 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);
+extern int molfile_netcdfplugin_init(void);
+extern int molfile_netcdfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_netcdfplugin_fini(void);
+extern int molfile_vtfplugin_init(void);
+extern int molfile_vtfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vtfplugin_fini(void);
+extern int molfile_webpdbplugin_init(void);
+extern int molfile_webpdbplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_webpdbplugin_fini(void);
 
 #define MOLFILE_INIT_ALL \
     molfile_abinitplugin_init(); \
@@ -272,6 +281,9 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_init(); \
     molfile_dtrplugin_init(); \
     molfile_maeffplugin_init(); \
+    molfile_netcdfplugin_init(); \
+    molfile_vtfplugin_init(); \
+    molfile_webpdbplugin_init(); \
 
 #define MOLFILE_REGISTER_ALL(v, cb) \
     molfile_abinitplugin_register(v, cb); \
@@ -340,6 +352,9 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_register(v, cb); \
     molfile_dtrplugin_register(v, cb); \
     molfile_maeffplugin_register(v, cb); \
+    molfile_netcdfplugin_register(v, cb); \
+    molfile_vtfplugin_register(v, cb); \
+    molfile_webpdbplugin_register(v, cb); \
 
 #define MOLFILE_FINI_ALL \
     molfile_abinitplugin_fini(); \
@@ -408,6 +423,9 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_fini(); \
     molfile_dtrplugin_fini(); \
     molfile_maeffplugin_fini(); \
+    molfile_netcdfplugin_fini(); \
+    molfile_vtfplugin_fini(); \
+    molfile_webpdbplugin_fini(); \
 
 #ifdef __cplusplus
 }