pharmit Activity
Open-source online virtual screening tools for large databases
Status: Beta
Brought to you by:
dkoes
Activity for pharmit
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David Koes committed [409f54] on Code
Add features requested by Amedeo Caflisch
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pharmit released /README.txt
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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update interaction points to get cation pi
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Bug fix
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script fixes
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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Add building of shapedb executable
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The command you posted is identifying all the features on the ligand. If want only the interaction features you need to also specify the receptor. If you want some consensus pharmacophore derived from multiple ligands, you need to use some other software as pharmit doesn't do that.
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AndyLi created ticket #11
How to generate pharmacophore model based on common features？
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OK，I use commandline make libraries，thank you!
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Port 11111 is what startlibbuild.py listens on by default. These instructions are for if you want to host your own library building service. Are you sure this is what you want to do? It is much simpler to build the libraries directly using the commandline if you are the only one who needs to make libraries.
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How to use the online database creation service
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Looks like you are missing the boost system library or are linking against a different version than you compiled headers with.
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Vito S. created ticket #9
Error on make
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Failed to build pharmit
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this is good news, build success,I solved the previous problems： vim /etc/profile add two lines: LD_LIBRARY_PATH=/usr/lib export LD_LIBRARY_PATH source /etc/profile ./pharmit USAGE: pharmit [options] --cmd command [pharma, dbcreate, dbcreateserverdir, dbsearch, server] OPTIONS: -cmd=<string> - command [pharma, dbcreate, dbcreateserverdir, dbsearch, server] -dbdir=<string> - database directory(s) -dbinfo=<string> - [dbcreateserverdir] JSON file describing database subset -extra-info - Output additional...
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use command: make -j12 success create Executable ’pharmit‘ but But an error occurred at runtime： ./pharmit: error while loading shared libraries: libcgicc.so.3: cannot open shared object file: No such file or directory
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Failed to build pharmit
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thank you，I will try to reinstall other dependent components, and continue to give feedback later
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Your openbabel installation is missing maeparser and coordgen, which are notorious both in their absence and presence for causing build problems. Try configuring cmake with -DWITH_MAEPARSER=0 -DWITH_COORDGEN=0 or otherwise modifying cmake to not require these superfluous libraries.
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Compiling pharmit failed About OpenBabel3 configuration
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Build with newer compilers
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comment
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Make 1.0 default radius; sphere quality diffs
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Fix radius update problem
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Fix body position
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Fix bug with very small libraries
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As it turns out, I never added build support for the server binary to the cmake files. This has been fixed as well.
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Sorry, these instructions weren't updated with the move to the cmake git clone http://git.code.sf.net/p/smina/code smina cd smina mkdir build cd build cmake .. make -j8 cp libsmina.a /usr/local/lib/
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Will created ticket #6
Install Instructions for minimisation server do not work.
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pg
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gulp
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fix chrome
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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David Wright posted a comment on ticket #5
Great - thanks for the quick response
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You need to set SMINA_DIR to the correct location when running cmake.
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Compilation failing due to missing header file
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Fix stupid bug I introduced trying to be clever.
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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init
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tolerance
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tolerance
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more tolerance
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Unmmap user supplied databases
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fix ligand parsing
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fix colorscheme
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refine label style
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show resi
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update readme
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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update packages, implement hover, bindingsite style
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(untested) fixes for 20.04 compilation
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add https
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update help w/benchmark info
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Update ligand fetching to use new PDB interface
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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fix php errors
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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Strip non-ASCII characters from user supplied SDF files.
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Better checking of too lage queries.
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Update shared_ptr ref in main
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Don't put time consuming code in critical section
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Increase robustness.
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Script for removing removed libraries
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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example of sending data to pharmit
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noshapeindex
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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noshapeindex
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covid
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MCULE ultimate
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install readme updates
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print backtrace on segfault
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ob3 cmake
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Fix python3 issue
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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mcule link
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update text
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visual tweak
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Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
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Python3 fixes and more robust bond order handling
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python3 fix
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Be more robust to bad databases.
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Update README
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Use variable for lemon library
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Updated README with ubuntu install instructions
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Update README
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Python3 compat, remove scan for file existance
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python3 conversion
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David Koes committed [a12931]
initial conversion to python3
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Improved cmake
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David Koes committed [141c75]
better cmake, openbabel 3.0
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describe smiles format
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dialog for contributed with search functionality
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more doc
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more instructions
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