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