Merge pull request #29 from drewnutt/master

fix mdpocket to allow for reading in list of pdb files

.gitignore

@@ -1,3 +1,5 @@
 nbproject
 *.o
 *_out
+.vscode
+src/qhull/bin/

INSTALL.txt

@@ -1,22 +1,4 @@
-// Fpocket brought to you by Vincent Le Guilloux & Peter Schmidtke
-//
-// GNU GPL
-// 
-// This file is part of the fpocket package.
-// 
-// fpocket is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-// 
-// fpocket is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-// GNU General Public License for more details.
-// 
-// You should have received a copy of the GNU General Public License
-// along with fpocket. If not, see <http://www.gnu.org/licenses/>.
-// 
+
 ===========================
 DEPENDENCIES              :
 ===========================

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Peter Schmidtke & Vincent Le Guilloux
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -41,6 +41,7 @@ sudo yum install netcdf-devel.x86_64
 
 Download the sources from github via the website or using git clone and then build and deploy fpocket using the following commands.
 
+#### Compiling on Linux
 
 ```
 git clone https://github.com/Discngine/fpocket.git
@@ -49,6 +50,18 @@ make
 sudo make install
 ```
 
+#### Compiling on Mac
+Install MacPorts https://www.macports.org/ for instance (needed for netcdf install)
+```
+sudo port install netcdf
+export LIBRARY_PATH=/opt/local/lib
+git clone https://github.com/Discngine/fpocket.git
+cd fpocket
+make ARCH=MACOSXX86_64
+sudo make install
+```
+
+
 
 End with an example of getting some data out of the system or using it for a little demo
 
@@ -66,6 +79,50 @@ fpocket should state when it's beginning to search pocket and also when it's end
 ## User Manual
 For now the user manual (still the one from fpocket 2.0) can be found in the doc folder. When I have some time to kill (or if somebody else has) we could add that here somewhere.
 
+## Frequent issues encountered
+### netcdf issues
+```
+cannot find -lnetcdf
+```
+mdpocket supports reading and writing NETCDF formatted files. In order to use this you need to install the netcdf development libraries on your system. 
+In centos this can be achieved like this : 
+```
+yum install -y epel-release #if the epel repo is not yet activated on your system
+yum install -y netcdf-devel
+
+```
+
+Run make again after installing this library. Mdpocket should build just fine now. 
+
+### stdc++ issues
+```
+cannot find -lstdc++
+```
+You need to install the stc++ static libraries to build fpocket & mdpocket. On centos 7.4 this can be done like this : 
+```
+yum install -y libstc++-static
+```
+
+### linking to molfile plugin issues
+If you observe an error similar to this one
+```
+ld: warning: ignoring file plugins/MACOSXX86/molfile/libmolfile_plugin.a, file was built for archive which is not the architecture being linked (x86_64): plugins/MACOSXX86/molfile/libmolfile_plugin.a
+Undefined symbols for architecture x86_64:
+  "_molfile_parm7plugin_init", referenced from:
+      _read_topology in topology.o
+  "_molfile_parm7plugin_register", referenced from:
+      _read_topology in topology.o
+ld: symbol(s) not found for architecture x86_64
+clang: error: linker command failed with exit code 1 (use -v to see invocation)
+make[1]: *** [bin/fpocket] Error 1
+make: *** [all] Error 2
+```
+then statically built libmolfile_plugin is not compatible with your machine. First check out that the ARCH variable set in the first line of the Makefile of fpocket actually reflects the architecture you want. For now I'm trying to support linux 64 bit systems and OSX 64 (LINUXAMD64) bit systems built with clang (MACOSXX86). So both should work out of the box. If they do not, you might need to build the molfile plugin for your architecture. All available system architectures for the molfile plugin can be found in the plugins folder tree : [plugins directory](https://github.com/Discngine/fpocket/tree/master/plugins). 
+Here you can find more information on how to build the molfile plugin on CentOS 7.4: 
+[compile molfile plugin on centos 7.4 - Discngine blog post](https://www.discngine.com/blog/2019/5/25/building-the-vmd-molfile-plugin-from-source-code)
+Once built, copy the architecture folder into the fpocket/plugins directory and make sure to declare this architecture in the ARCH variable in the Makefile. Finally run make again.
+If you manage to build for other architectures and it works, I'd be happy to accept PR's with the relevant plugin architectures as I cannot build all of them on my own ;).
+
 ## Contributing
 
 Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c63ec426) for details on our code of conduct, and the process for submitting pull requests to us.
@@ -79,7 +136,7 @@ Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c6
 
 ## License
 
-This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
 
 ## Acknowledgments
 

data/sample/mdpocket/input.txt

@@ -0,0 +1,10 @@
+2yex.pdb
+3ot3.pdb
+3pa3.pdb
+3pa4.pdb
+3tki.pdb
+4hyi.pdb
+4rvk.pdb
+5opb.pdb
+5opu.pdb
+5oq5.pdb

data/sample/mdpocket/mdpout_dens_iso_8.pdb

@@ -0,0 +1,184 @@
+ATOM      1  C   PTH     1      -8.641   4.782   5.052  0.00  0.00
+ATOM      2  C   PTH     1      -8.641   4.782   6.052  0.00  0.00
+ATOM      3  C   PTH     1      -8.641   5.782   6.052  0.00  0.00
+ATOM      4  C   PTH     1      -7.641   4.782   5.052  0.00  0.00
+ATOM      5  C   PTH     1      -7.641   4.782   6.052  0.00  0.00
+ATOM      6  C   PTH     1      -7.641   5.782   3.052  0.00  0.00
+ATOM      7  C   PTH     1      -7.641   5.782   4.052  0.00  0.00
+ATOM      8  C   PTH     1      -7.641   5.782   6.052  0.00  0.00
+ATOM      9  C   PTH     1      -7.641   6.782   7.052  0.00  0.00
+ATOM     10  C   PTH     1      -6.641   4.782   3.052  0.00  0.00
+ATOM     11  C   PTH     1      -6.641   4.782   4.052  0.00  0.00
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+ATOM     38  C   PTH     1       0.359  11.782 -15.948  0.00  0.00
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+ATOM    173  C   PTH     1      12.359  22.782  -1.948  0.00  0.00
+ATOM    174  C   PTH     1      12.359  22.782  -0.948  0.00  0.00
+ATOM    175  C   PTH     1      12.359  22.782   0.052  0.00  0.00
+ATOM    176  C   PTH     1      12.359  23.782  -0.948  0.00  0.00
+ATOM    177  C   PTH     1      13.359  13.782  27.052  0.00  0.00
+ATOM    178  C   PTH     1      13.359  13.782  28.052  0.00  0.00
+ATOM    179  C   PTH     1      13.359  22.782  -0.948  0.00  0.00
+ATOM    180  C   PTH     1      14.359  17.782  -7.948  0.00  0.00
+ATOM    181  C   PTH     1      15.359  16.782  -8.948  0.00  0.00
+ATOM    182  C   PTH     1      15.359  16.782  -7.948  0.00  0.00
+ATOM    183  C   PTH     1      15.359  17.782  -8.948  0.00  0.00
+ATOM    184  C   PTH     1      15.359  17.782  -7.948  0.00  0.00

data/sample/mdpocket/time.txt

@@ -0,0 +1,10 @@
+0.215480
+0.271399
+0.217237
+0.212487
+0.221198
+0.217482
+0.234323
+0.224301
+0.218361
+0.211592

makefile

@@ -2,10 +2,10 @@
 # Makefile.
 #------------------------------------------------------------
 ARCH	    = LINUXAMD64
+export ARCH
 
 PLUGINDIR   = plugins
 
-PATH_GSL    = /home/user/gsl/
 PATH_OBJ    = obj/
 PATH_SRC    = src/
 PATH_HEADER = headers/
@@ -22,23 +22,33 @@ TPOCKET	    = tpocket
 DPOCKET	    = dpocket
 MDPOCKET    = mdpocket
 CHECK	    = pcheck
-MYPROGS	    = $(PATH_BIN)$(FPOCKET) $(PATH_BIN)$(TPOCKET) $(PATH_BIN)$(DPOCKET) $(PATH_BIN)$(MDPOCKET)
+PROGFPOCKET	    = $(PATH_BIN)$(FPOCKET) $(PATH_BIN)$(TPOCKET) $(PATH_BIN)$(DPOCKET) $(PATH_BIN)$(MDPOCKET)
+PROGMDPOCKET    = $(PATH_BIN)$(MDPOCKET)
 
-CC          = gcc
-CCQHULL	    = gcc
-LINKER      = gcc
-LINKERQHULL = gcc
+ifeq ($(CXX),g++)
+  CC          = gcc
+  CCQHULL	    = gcc
+  LINKER      = LD_LIBRARY_PATH=$(PLUGINDIR)/$(ARCH)/molfile gcc
+  LINKERQHULL = gcc
+else 
+  CCQHULL	    = clang
+  CC          = clang
+  LINKER      = LD_LIBRARY_PATH=$(PLUGINDIR)/$(ARCH)/molfile clang
+  LINKERQHULL = clang
+endif
 
 CGSL        = -DMD_NOT_USE_GSL -I$(PATH_GSL)include
 COS         = -DM_OS_LINUX
 CDEBUG      = -DMNO_MEM_DEBUG
 CWARN       = -Wall -Wextra -Wwrite-strings -Wstrict-prototypes
 
-CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile #$(CGSL)
+CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
 QCFLAGS     = -O -g -pg -ansi
 
 LGSL        = -L$(PATH_GSL)lib -lgsl -lgslcblas 
-LFLAGS	    = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/libmolfile_plugin.a -lnetcdf -lstdc++
+LFLAGS	    = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/libmolfile_plugin.a -lstdc++
+NETCDFFLAGS	= -lnetcdf
+
 #
 #------------------------------------------------------------
 # BINARIES OBJECTS 
@@ -46,7 +56,7 @@ LFLAGS	    = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/lib
 #QOBJS = $(PATH_QHULL)/src/qvoronoi/qvoronoi.o $(PATH_QHULL)/src/qconvex/qconvex.o
 
 QOBJS = $(PATH_QHULL)/libqhull/geom2.o $(PATH_QHULL)/libqhull/geom.o $(PATH_QHULL)/libqhull/global.o \
-        $(PATH_QHULL)/libqhull/io.o $(PATH_QHULL)/libqhull/io.h $(PATH_QHULL)/libqhull/libqhull.o \
+        $(PATH_QHULL)/libqhull/io.o $(PATH_QHULL)/libqhull/libqhull.o \
         $(PATH_QHULL)/libqhull/mem.o $(PATH_QHULL)/libqhull/merge.o $(PATH_QHULL)/libqhull/poly2.o \
         $(PATH_QHULL)/libqhull/poly.o $(PATH_QHULL)/libqhull/qset.o \
         $(PATH_QHULL)/libqhull/random.o $(PATH_QHULL)/libqhull/rboxlib.o \
@@ -54,6 +64,16 @@ QOBJS = $(PATH_QHULL)/libqhull/geom2.o $(PATH_QHULL)/libqhull/geom.o $(PATH_QHUL
         $(PATH_QHULL)/libqhull/usermem.o \
         $(PATH_QHULL)/libqhull/userprintf.o $(PATH_QHULL)/libqhull/userprintf_rbox.o $(PATH_QHULL)/qvoronoi/qvoronoi.o $(PATH_QHULL)/qconvex/qconvex.o
 
+
+# QOBJS = $(PATH_QHULL)/libqhull/geom2.o $(PATH_QHULL)/libqhull/geom.o $(PATH_QHULL)/libqhull/global.o \
+#         $(PATH_QHULL)/libqhull/io.o $(PATH_QHULL)/libqhull/io.h $(PATH_QHULL)/libqhull/libqhull.o \
+#         $(PATH_QHULL)/libqhull/mem.o $(PATH_QHULL)/libqhull/merge.o $(PATH_QHULL)/libqhull/poly2.o \
+#         $(PATH_QHULL)/libqhull/poly.o $(PATH_QHULL)/libqhull/qset.o \
+#         $(PATH_QHULL)/libqhull/random.o $(PATH_QHULL)/libqhull/rboxlib.o \
+#         $(PATH_QHULL)/libqhull/stat.o $(PATH_QHULL)/libqhull/user.o \
+#         $(PATH_QHULL)/libqhull/usermem.o \
+#         $(PATH_QHULL)/libqhull/userprintf.o $(PATH_QHULL)/libqhull/userprintf_rbox.o $(PATH_QHULL)/qvoronoi/qvoronoi.o $(PATH_QHULL)/qconvex/qconvex.o
+
 CHOBJ = $(PATH_OBJ)check.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
 		$(PATH_OBJ)utils.o $(PATH_OBJ)pertable.o $(PATH_OBJ)memhandler.o \
 		$(PATH_OBJ)voronoi.o $(PATH_OBJ)sort.o $(PATH_OBJ)calc.o \
@@ -131,7 +151,10 @@ $(PATH_OBJ)%.o: $(PATH_SRC)%.cpp
 all: 
 	make qhull
 	make fpocket
-fpocket: $(MYPROGS) # $(PATH_BIN)$(CHECK)
+	make mdpocket
+fpocket: qhull 	$(PROGFPOCKET) # $(PATH_BIN)$(CHECK)
+mdpocket: qhull $(PROGMDPOCKET)
+
 
 qhull:
 	cd src/qhull/ && make
@@ -149,7 +172,7 @@ $(PATH_BIN)$(DPOCKET): $(DPOBJ) $(QOBJS)
 	$(LINKER) $^ -o $@ $(LFLAGS)
 
 $(PATH_BIN)$(MDPOCKET): $(MDPOBJ) $(QOBJS)
-	$(LINKER) $^ -o $@ $(LFLAGS)
+	$(LINKER) $^ -o $@ $(LFLAGS) $(NETCDFFLAGS)
 
 install:
 	mkdir -p $(BINDIR)
@@ -173,7 +196,7 @@ clean:
 	rm -f $(PATH_BIN)$(TPOCKET)
 	rm -f $(PATH_BIN)$(DPOCKET)
 	rm -f $(PATH_BIN)$(MDPOCKET)
-	cd src/qhull && make clean
+	cd src/qhull && make clean && rm lib/libqhull*.a
 
 uninstall:
 	rm -f $(PATH_BIN)$(FPOCKET) $(BINDIR)$(FPOCKET)

mdpout_descriptors.txt

@@ -1 +0,0 @@
-snapshot pock_volume pock_asa pock_pol_asa pock_apol_asa pock_asa22 pock_pol_asa22 pock_apol_asa22 nb_AS mean_as_ray mean_as_solv_acc apol_as_prop mean_loc_hyd_dens hydrophobicity_score volume_score polarity_score charge_score prop_polar_atm as_density as_max_dst ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL

plugins/LINUXAMD64/molfile/libmolfile_plugin.h

@@ -51,11 +51,6 @@ 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_netcdfplugin_init(void);
-extern int molfile_netcdfplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_netcdfplugin_fini(void);
-
 extern int molfile_dlpolyplugin_init(void);
 extern int molfile_dlpolyplugin_register(void *, vmdplugin_register_cb);
 extern int molfile_dlpolyplugin_fini(void);
@@ -206,6 +201,15 @@ 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_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);
+extern int molfile_netcdfplugin_init(void);
+extern int molfile_netcdfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_netcdfplugin_fini(void);
 
 #define MOLFILE_INIT_ALL \
     molfile_abinitplugin_init(); \
@@ -223,7 +227,6 @@ extern int molfile_maeffplugin_fini(void);
     molfile_crdplugin_init(); \
     molfile_cubeplugin_init(); \
     molfile_dcdplugin_init(); \
-    molfile_netcdfplugin_init(); \
     molfile_dlpolyplugin_init(); \
     molfile_dsn6plugin_init(); \
     molfile_dxplugin_init(); \
@@ -274,6 +277,9 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_init(); \
     molfile_dtrplugin_init(); \
     molfile_maeffplugin_init(); \
+    molfile_vtfplugin_init(); \
+    molfile_webpdbplugin_init(); \
+    molfile_netcdfplugin_init(); \
 
 #define MOLFILE_REGISTER_ALL(v, cb) \
     molfile_abinitplugin_register(v, cb); \
@@ -291,7 +297,6 @@ extern int molfile_maeffplugin_fini(void);
     molfile_crdplugin_register(v, cb); \
     molfile_cubeplugin_register(v, cb); \
     molfile_dcdplugin_register(v, cb); \
-    molfile_netcdfplugin_register(v, cb); \
     molfile_dlpolyplugin_register(v, cb); \
     molfile_dsn6plugin_register(v, cb); \
     molfile_dxplugin_register(v, cb); \
@@ -342,6 +347,9 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_register(v, cb); \
     molfile_dtrplugin_register(v, cb); \
     molfile_maeffplugin_register(v, cb); \
+    molfile_vtfplugin_register(v, cb); \
+    molfile_webpdbplugin_register(v, cb); \
+    molfile_netcdfplugin_register(v, cb); \
 
 #define MOLFILE_FINI_ALL \
     molfile_abinitplugin_fini(); \
@@ -359,7 +367,6 @@ extern int molfile_maeffplugin_fini(void);
     molfile_crdplugin_fini(); \
     molfile_cubeplugin_fini(); \
     molfile_dcdplugin_fini(); \
-    molfile_netcdfplugin_fini(); \
     molfile_dlpolyplugin_fini(); \
     molfile_dsn6plugin_fini(); \
     molfile_dxplugin_fini(); \
@@ -410,6 +417,9 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_fini(); \
     molfile_dtrplugin_fini(); \
     molfile_maeffplugin_fini(); \
+    molfile_vtfplugin_fini(); \
+    molfile_webpdbplugin_fini(); \
+    molfile_netcdfplugin_fini(); \
 
 #ifdef __cplusplus
 }