Split a Macro-molecular Complex Into Fragments

A program that extracts and filters components of a protein structure, returning individual fragments.

An example command that returns just the ligands for all binding sites would be:

prompt> python splitmolcomplexfrags.py -waterfilter nothing -proteinfilter nothing -bindingsitenum 0 input.pdb output.sdf

Help is available for all the supported OESplitMolComplexOptions parameters:

prompt> python splitmolcomplexfrags.py --help all

Complete parameter list
 Display options :
   -verbose : If true, return more verbose output

 SplitMolComplex options :
   -bindingsitenum : Select this binding site
   -covalentbondtreatment : Covalent bond treatment
   -covalentligand : Split covalent ligands
   -ligandfilter : Ligand filter category
   -ligandname : Ligand name
   -maxsitedistance : Maximum distance to be associated with the binding site
   -maxsurfacedistance : Maximum distance to be associated with the protein
                         surface
   -modelnum : Select this NMR model number
   -proteinfilter : Protein filter category
   -separateresidues : Separate individual residues before selection
   -surfacewaters : Select surface waters
   -waterfilter : Water filter category

 input/output options :
   -in : Input molecule (usually a pdb file)
   -out : Output molecule (usually an oeb)