OEExtractBioUnitsΒΆ

Attention

PRELIMINARY-IMAGE This is a preliminary API until 2019.Apr and may be improved based on user feedback. It is currently available in C++ and Python.

OESystem::OEIterBase<OEChem::OEMolBase>* OEExtractBioUnits(const OEChem::OEMolBase& extractProtein)

OESystem::OEIterBase<OEChem::OEMolBase>* OEExtractBioUnits(const OEChem::OEMolBase& extractProtein,
                                                           unsigned maxAtoms,
                                                           bool preferAuthor)

OESystem::OEIterBase<OEChem::OEMolBase>* OEExtractBioUnits(const OEChem::OEMolBase& extractProtein,
                                                           const OEChem::OEMolBase& refProtein)

OESystem::OEIterBase<OEChem::OEMolBase>* OEExtractBioUnits(const OEChem::OEMolBase& extractProtein,
                                                           const OEChem::OEMolBase& refProtein,
                                                           int minScore, bool superpose)

Extracts BUs using either the PDB remarks when a single OEMolBase is provided, or a sequence alignment to a reference if two OEMolBases are provided. The OEExtractBioUnits overload with a reference OEMolBase will take a minimum score, as well as a flag to instruct the function to superimpose the biological units to the reference in place as optional inputs. Alternatively, the overload for extracting BUs from the remarks will take an optional flag to prefer the PDB author (or software) headers, and the max number of atoms allowed per extracted BU. This function returns an iterator of OEMolBase objects, one for each of the BUs.

Parameters :

extractProtein
The protein from which the BUs will be extracted.
refProtein
The reference protein that will be used for sequence alignment.
minScore
The minimum score that determines a successful sequence alignment (default = 200 ).
superpose
If true (default = false ), the function will perform an in-place superposition of the output proteins to the protein given in refProtein.
maxAtoms
The maximum number of atoms for a single BU when extracting from PDB header remarks (default = 50000 ).
preferAuthor
If true (the default), then biounits without author remarks will be ignored.