GitHub - GrtAndPwrflTrtl/chemistry

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
biology		biology
build/CMakeFiles		build/CMakeFiles
openbabel-2.3.2		openbabel-2.3.2
Atom.cpp		Atom.cpp
Atom.h		Atom.h
AtomT.cpp		AtomT.cpp
AtomT.h		AtomT.h
Bond.cpp		Bond.cpp
Bond.h		Bond.h
Constants.cpp		Constants.cpp
Constants.h		Constants.h
EdgeAggregator.h		EdgeAggregator.h
EdgeAnnotation.h		EdgeAnnotation.h
FragmentGraph.cpp		FragmentGraph.cpp
FragmentGraph.h		FragmentGraph.h
FragmentGraphNode.cpp		FragmentGraphNode.cpp
FragmentGraphNode.h		FragmentGraphNode.h
FragmentSubNode.cpp		FragmentSubNode.cpp
FragmentSubNode.h		FragmentSubNode.h
HyperEdge.h		HyperEdge.h
HyperEdgeMultiMap.h		HyperEdgeMultiMap.h
HyperGraph.h		HyperGraph.h
HyperNode.h		HyperNode.h
IdFactory.cpp		IdFactory.cpp
IdFactory.h		IdFactory.h
Instantiator.cpp		Instantiator.cpp
Instantiator.h		Instantiator.h
Linker.cpp		Linker.cpp
Linker.h		Linker.h
LinkerFragmentSubNode.cpp		LinkerFragmentSubNode.cpp
LinkerFragmentSubNode.h		LinkerFragmentSubNode.h
Main.cpp		Main.cpp
Makefile		Makefile
Molecule.cpp		Molecule.cpp
Molecule.h		Molecule.h
OBWriter.cpp		OBWriter.cpp
OBWriter.h		OBWriter.h
Options.cpp		Options.cpp
Options.h		Options.h
PebblerHyperEdge.h		PebblerHyperEdge.h
PebblerHyperGraph.h		PebblerHyperGraph.h
PebblerHyperNode.h		PebblerHyperNode.h
README		README
Rigid.cpp		Rigid.cpp
Rigid.h		Rigid.h
RigidFragmentSubNode.cpp		RigidFragmentSubNode.cpp
RigidFragmentSubNode.h		RigidFragmentSubNode.h
Rigid_backup.cpp		Rigid_backup.cpp
ScrubAndExportSMI_logfile.txt		ScrubAndExportSMI_logfile.txt
Thread_Pool.h		Thread_Pool.h
Utilities.cpp		Utilities.cpp
Utilities.h		Utilities.h
Validator.cpp		Validator.cpp
Validator.h		Validator.h
obgen.cpp		obgen.cpp
obgen.h		obgen.h
script.cpp		script.cpp
timer.cpp		timer.cpp

Repository files navigation

To run:

   ./synth <linker-files> <rigid-files> -v <validation-file> -o <output-file> -tc <real-value>

*  rigid files must be prefixed with r and linkers with l .
*  -tc is Tanimoto coefficient [0, 1] where usually 0.95 is accepted as a strong enough coefficient. Default value is 0.95.


Files:

Molecule.cpp : main molecule class implementation. This includes the functions to combine two molecules together.

A molecule consists of atoms (Atom.*) and bonds (Bond.*)

AtomT : parsing and representation of the specific type for an atom: <atom>.<atom-type>

Instantiator.* : Main routine for creating all combinations of molecules and adding to the hypergraph.

Linker.* : parsing and representation of linkers. Note, linkers are molecules in the hypergraph, but are NOT output as combined molecules.

Rigid.cpp : parsing and representation of rigids. Rigids are molecules in the hypergraph, but are NOT output as combined molecules. 


obgen.* : Borrowed code from the obgen application. Provides an interface for us in this application.

OBWriter.* : Outputs the synthesized molecules to the given output file.


Unused currently, but necessary to acquire paths by which molecules are created:

HyperEdgeMultiMap.h
EdgeAggregator.h
EdgeAnnotation.h