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README
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README
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Compiling:
The following libraries are required: modify the Makefile to update path accordingly.
* openbabel (we used 2.3.2) http://sourceforge.net/projects/openbabel/?source=typ_redirect
* gsl (1.16) http://www.linuxfromscratch.org/blfs/view/svn/general/gsl.html
* gslcblas
* z
NOTE: Openbabel.2.3.2 should be compiled from source code. (You might need to remove the generic instalation of OpenBabel to prevent path conflict)
Object Files:
All object files are compiled and places in the ./obj directory. 'make clean' will empty this folder.
NOTE:before executing the esynth file, export LD_LIBRARY_PATH
example:
export LD_LIBRARY_PATH=${HOME}/apps/openbabel-2.3.2-install/lib/
export LD_LIBRARY_PATH[to /gsl/lib]
Executable:
'make' will create the esynth application.
All output of SMI molecules are dumped into the output directory (synth_output_dir). Each file will contain 250000 SMI molecules and wil
l be compressed using the zlib compression algorithm.
Running (input):
./esynth is the executable.
Comamand-line arguments are specified with a prefix '-' and may include the following:
* -serial : specified serial execution
* -threaded : specifies a threaded execution; do not use.
* -odir <directory> specifies the name of the directory where output will be placed (./<directory>); default is ./esynth_output_dir
* -tc <value> defines the tanimoto coefficient as a value between 0 and 1; default is 0.95.
* -smi-only ; species all molecules are to be handled as SMI objects.
* -nopen ; specifies OpenBabel will not be used except for the first input from the SDF files and the resulting output in SMI format.
* -prob-level ; specifies what level to begin pruning molecules for probability purposes.
* -lip ; Allows the user to turn on Lipinski compliance of molecules (Lipinski compliance defaults to off).
A typical run: ./esynth -nopen -serial -smi-only <linkers sdfs> <rigid sdfs>
Sample: ./esynth -nopen -serial -smi-only -prob-level 2 l-test-linker1.sdf l-test-linker2.sdf r-test-rigid1.sdf r-test-rigid2.sdf
All data files (*.sdf) must exist in the same directory as the executable.
Example run:
go to test directory located in example-fragments in esynth [esynth/example-fragments/test]
PATH_TO_esynth/esynth `cat list` -nopen
This is the simplest run, options can be added as explained above. The output smi molecules are in synth_output_dir