GitHub - wcatykid/Graph-Based-Molecular-Synthesis: Synthesis of molecules from fragments into larger molecules using graph-based representations and techniques.

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Synthesis of molecules from fragments into larger molecules using graph-based representations and techniques.

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
example-fragments		example-fragments
obj		obj
.gitattributes		.gitattributes
.gitignore		.gitignore
Atom.cpp		Atom.cpp
Atom.h		Atom.h
AtomT.cpp		AtomT.cpp
AtomT.h		AtomT.h
Bond.cpp		Bond.cpp
Bond.h		Bond.h
ConnectableAtom.cpp		ConnectableAtom.cpp
ConnectableAtom.h		ConnectableAtom.h
Constants.cpp		Constants.cpp
Constants.h		Constants.h
EdgeAggregator.h		EdgeAggregator.h
EdgeAnnotation.h		EdgeAnnotation.h
EdgeDatabase.h		EdgeDatabase.h
FixedSortedList.h		FixedSortedList.h
FragmentEdgeMap.cpp		FragmentEdgeMap.cpp
FragmentEdgeMap.h		FragmentEdgeMap.h
IdFactory.cpp		IdFactory.cpp
IdFactory.h		IdFactory.h
Instantiator.cpp		Instantiator.cpp
Instantiator.h		Instantiator.h
LICENSE		LICENSE
LevelHashMap.h		LevelHashMap.h
LikeMoleculesContainer.h		LikeMoleculesContainer.h
Linker.cpp		Linker.cpp
Linker.h		Linker.h
LinkerConnectableAtom.cpp		LinkerConnectableAtom.cpp
LinkerConnectableAtom.h		LinkerConnectableAtom.h
Main.cpp		Main.cpp
Makefile		Makefile
MinimalMolecule.h		MinimalMolecule.h
Molecule.cpp		Molecule.cpp
Molecule.h		Molecule.h
MoleculeHashHypergraph.h		MoleculeHashHypergraph.h
OBWriter.cpp		OBWriter.cpp
OBWriter.h		OBWriter.h
Options.cpp		Options.cpp
Options.h		Options.h
README		README
README~		README~
Rigid.cpp		Rigid.cpp
Rigid.h		Rigid.h
RigidConnectableAtom.cpp		RigidConnectableAtom.cpp
RigidConnectableAtom.h		RigidConnectableAtom.h
SimpleFragmentGraph.h		SimpleFragmentGraph.h
SmiMinimalMolecule.h		SmiMinimalMolecule.h
Thread_Pool.h		Thread_Pool.h
TimedHashMap.cpp		TimedHashMap.cpp
TimedHashMap.h		TimedHashMap.h
TimedLikeValueContainer.cpp		TimedLikeValueContainer.cpp
TimedLikeValueContainer.h		TimedLikeValueContainer.h
Utilities.cpp		Utilities.cpp
Utilities.h		Utilities.h
Validator.cpp		Validator.cpp
Validator.h		Validator.h
bloom_filter.hpp		bloom_filter.hpp
compliantwriter.cpp		compliantwriter.cpp
convertToSMI.cpp		convertToSMI.cpp
l-test-linker1.sdf		l-test-linker1.sdf
l-test-linker2.sdf		l-test-linker2.sdf
obgen.cpp		obgen.cpp
obgen.h		obgen.h
r-test-rigid1.sdf		r-test-rigid1.sdf
r-test-rigid2.sdf		r-test-rigid2.sdf
script.cpp		script.cpp
synth		synth
synthobgen.cpp		synthobgen.cpp
zpipe.cpp		zpipe.cpp
zpipe.h		zpipe.h

Repository files navigation

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