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)
Code¶
Download code
See also
OEGetMolComplexComponents
functionOESplitMolComplexOptions object
OEConfigureSplitMolComplexOptions
functionOESplitMolComplexSetup
function