Add features requested by Amedeo Caflisch
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
update interaction points to get cation pi
Bug fix
script fixes
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
Add building of shapedb executable
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.
How to generate pharmacophore model based on common features?
OK,I use commandline make libraries,thank you!
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.
How to use the online database creation service
Looks like you are missing the boost system library or are linking against a different version than you compiled headers with.
Error on make
Failed to build pharmit
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...
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
Failed to build pharmit
thank you,I will try to reinstall other dependent components, and continue to give feedback later
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.
Compiling pharmit failed About OpenBabel3 configuration
Build with newer compilers
comment
Make 1.0 default radius; sphere quality diffs
Fix radius update problem
Fix body position
Fix bug with very small libraries
As it turns out, I never added build support for the server binary to the cmake files. This has been fixed as well.
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/
Install Instructions for minimisation server do not work.
pg
gulp
fix chrome
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
Great - thanks for the quick response
You need to set SMINA_DIR to the correct location when running cmake.
Compilation failing due to missing header file
Fix stupid bug I introduced trying to be clever.
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
init
tolerance
tolerance
more tolerance
Unmmap user supplied databases
fix ligand parsing
fix colorscheme
refine label style
show resi
update readme
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
update packages, implement hover, bindingsite style
(untested) fixes for 20.04 compilation
add https
update help w/benchmark info
Update ligand fetching to use new PDB interface
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
fix php errors
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
Strip non-ASCII characters from user supplied SDF files.
Better checking of too lage queries.
Update shared_ptr ref in main
Don't put time consuming code in critical section
Increase robustness.
Script for removing removed libraries
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
example of sending data to pharmit
noshapeindex
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
noshapeindex
covid
MCULE ultimate
install readme updates
print backtrace on segfault
ob3 cmake
Fix python3 issue
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
mcule link
update text
visual tweak
Merge branch 'master' of ssh://git.code.sf.net/p/pharmit/code
Python3 fixes and more robust bond order handling
python3 fix
Be more robust to bad databases.
Update README
Use variable for lemon library
Updated README with ubuntu install instructions
Update README
Python3 compat, remove scan for file existance
python3 conversion
initial conversion to python3
Improved cmake
better cmake, openbabel 3.0
describe smiles format
dialog for contributed with search functionality
more doc
more instructions