adding linux built molfileplugin

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

data/sample/5RGF.cif

@@ -3,7 +3,7 @@ data_5RGF
 _entry.id   5RGF 
 # 
 _audit_conform.dict_name       mmcif_pdbx.dic 
-_audit_conform.dict_version    5.330 
+_audit_conform.dict_version    5.342 
 _audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
 # 
 loop_
@@ -36,18 +36,19 @@ _audit_author.identifier_ORCID
 'Chica, R.A.'         5 ? 
 # 
 _citation.id                        primary 
-_citation.title                     'Evolution of an enzyme conformational ensembles guides the design of an efficient biocatalyst' 
-_citation.journal_abbrev            'To be published' 
-_citation.journal_volume            ? 
-_citation.page_first                ? 
-_citation.page_last                 ? 
-_citation.year                      ? 
-_citation.pdbx_database_id_PubMed   ? 
-_citation.pdbx_database_id_DOI      ? 
+_citation.title                     
+'Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.' 
+_citation.journal_abbrev            'Nat Commun' 
+_citation.journal_volume            11 
+_citation.page_first                4808 
+_citation.page_last                 4808 
+_citation.year                      2020 
+_citation.pdbx_database_id_PubMed   32968058 
+_citation.pdbx_database_id_DOI      10.1038/s41467-020-18619-x 
 _citation.journal_id_ASTM           ? 
-_citation.country                   ? 
-_citation.journal_id_ISSN           ? 
-_citation.journal_id_CSD            0353 
+_citation.country                   UK 
+_citation.journal_id_ISSN           2041-1723 
+_citation.journal_id_CSD            ? 
 _citation.book_publisher            ? 
 # 
 loop_
@@ -55,11 +56,15 @@ _citation_author.citation_id
 _citation_author.name 
 _citation_author.identifier_ORCID 
 _citation_author.ordinal 
-primary 'Broom, A.'           ? 1 
-primary 'Rakotoharisoa, R.V.' ? 2 
-primary 'Thompson, M.'        ? 3 
-primary 'Fraser, J.'          ? 4 
-primary 'Chica, R.A.'         ? 5 
+primary 'Broom, A.'           ?                   1 
+primary 'Rakotoharisoa, R.V.' ?                   2 
+primary 'Thompson, M.C.'      0000-0002-6099-2027 3 
+primary 'Zarifi, N.'          0000-0003-4748-7082 4 
+primary 'Nguyen, E.'          ?                   5 
+primary 'Mukhametzhanov, N.'  ?                   6 
+primary 'Liu, L.'             0000-0003-1283-1410 7 
+primary 'Fraser, J.S.'        0000-0002-5080-2859 8 
+primary 'Chica, R.A.'         0000-0003-3789-9841 9 
 # 
 _cell.entry_id           5RGF 
 _cell.length_a           76.410 
@@ -18221,11 +18226,15 @@ _pdbx_struct_oper_list.matrix[3][2]         0.0000000000
 _pdbx_struct_oper_list.matrix[3][3]         1.0000000000 
 _pdbx_struct_oper_list.vector[3]            0.0000000000 
 # 
-_pdbx_audit_revision_history.ordinal             1 
-_pdbx_audit_revision_history.data_content_type   'Structure model' 
-_pdbx_audit_revision_history.major_revision      1 
-_pdbx_audit_revision_history.minor_revision      0 
-_pdbx_audit_revision_history.revision_date       2020-07-22 
+loop_
+_pdbx_audit_revision_history.ordinal 
+_pdbx_audit_revision_history.data_content_type 
+_pdbx_audit_revision_history.major_revision 
+_pdbx_audit_revision_history.minor_revision 
+_pdbx_audit_revision_history.revision_date 
+1 'Structure model' 1 0 2020-07-22 
+2 'Structure model' 1 1 2020-12-02 
+3 'Structure model' 1 2 2021-05-12 
 # 
 _pdbx_audit_revision_details.ordinal             1 
 _pdbx_audit_revision_details.revision_ordinal    1 
@@ -18236,6 +18245,41 @@ _pdbx_audit_revision_details.description         ?
 _pdbx_audit_revision_details.details             ? 
 # 
 loop_
+_pdbx_audit_revision_group.ordinal 
+_pdbx_audit_revision_group.revision_ordinal 
+_pdbx_audit_revision_group.data_content_type 
+_pdbx_audit_revision_group.group 
+1 2 'Structure model' 'Database references' 
+2 3 'Structure model' 'Structure summary'   
+# 
+loop_
+_pdbx_audit_revision_category.ordinal 
+_pdbx_audit_revision_category.revision_ordinal 
+_pdbx_audit_revision_category.data_content_type 
+_pdbx_audit_revision_category.category 
+1 2 'Structure model' citation           
+2 2 'Structure model' citation_author    
+3 3 'Structure model' pdbx_deposit_group 
+# 
+loop_
+_pdbx_audit_revision_item.ordinal 
+_pdbx_audit_revision_item.revision_ordinal 
+_pdbx_audit_revision_item.data_content_type 
+_pdbx_audit_revision_item.item 
+1  2 'Structure model' '_citation.country'                 
+2  2 'Structure model' '_citation.journal_abbrev'          
+3  2 'Structure model' '_citation.journal_id_CSD'          
+4  2 'Structure model' '_citation.journal_id_ISSN'         
+5  2 'Structure model' '_citation.journal_volume'          
+6  2 'Structure model' '_citation.page_first'              
+7  2 'Structure model' '_citation.page_last'               
+8  2 'Structure model' '_citation.pdbx_database_id_DOI'    
+9  2 'Structure model' '_citation.pdbx_database_id_PubMed' 
+10 2 'Structure model' '_citation.title'                   
+11 2 'Structure model' '_citation.year'                    
+12 3 'Structure model' '_pdbx_deposit_group.group_type'    
+# 
+loop_
 _pdbx_refine_tls.pdbx_refine_id 
 _pdbx_refine_tls.id 
 _pdbx_refine_tls.details 
@@ -18489,6 +18533,7 @@ _pdbx_audit_support.ordinal                1
 _pdbx_deposit_group.group_title         'Crystal structures of HG-series of Kemp Eliminases at Room-temperature' 
 _pdbx_deposit_group.group_description   'Crystal structure of Kemp eliminase HG4 with bound transition state analogue, 277K' 
 _pdbx_deposit_group.group_id            G_1002148 
+_pdbx_deposit_group.group_type          undefined 
 # 
 _pdbx_entity_instance_feature.ordinal        1 
 _pdbx_entity_instance_feature.comp_id        6NT 

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

@@ -81,7 +81,8 @@ typedef struct s_pdb
     int n_xlig_atoms;   /**number of atoms in xlig array ( number of atoms of selected atom*/
     int natoms,			/**< Number of atoms */
             nhetatm,		/**< Number of HETATM */
-            natm_lig ;		/**< Number of ligand atoms */
+            natm_lig,       /**< Number of ligand atoms */
+            natoms_h ;		/**< Number of hydrogen atoms */
 
     float A, B, C, 			/**< Side lengths of the unit cell */
           alpha, beta, gamma ;	/**< Angle between B and C, A and C, A and C */
@@ -89,6 +90,8 @@ typedef struct s_pdb
     char header[M_PDB_BUF_LEN] ; /**< Header container*/
     char fname[M_PDB_FILE_NAME_LEN];    /**< File name container*/
     float avg_bfactor;  /**<overall average B factor*/
+    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
 }