OESplitMolComplexSetupΒΆ

This namespace encodes symbolic constants used as bit-masks to indicate which parameters are created when the OEConfigureSplitMolComplexOptions function is called to configure command-line options.

All

The combination of following constants:

CovBondTreatment

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the splitting of covalent ligand bonds by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -covalentbondtreatment
    Type : string
    Allow list : false
    Default : hydrogen
    Simple : false
    Required : false
    Legal values : hydrogen rgroup none
    Brief : Covalent bond treatment
    Detail
        Add hydrogens, add Rgroups or do nothing when a covalent bond is broken

CovCofactor

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the treatment of covalent cofactors by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -covalentcofactor
    Aliases : -covcofact
    Type : bool
    Allow list : false
    Default : false
    Simple : false
    Required : false
    Brief : Split covalent cofactors
    Detail
        Identify and separate covalently bound cofactors

CovLig

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the treatment of covalent ligands by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -covalentligand
    Aliases : -covlig
    Type : bool
    Allow list : false
    Default : false
    Simple : true
    Required : false
    Brief : Split covalent ligands
    Detail
        Identify and separate covalently bound ligands

LigFilter

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the ligand filter used by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -ligandfilter
    Type : string
    Allow list : false
    Default : ligand
    Simple : false
    Required : false
    Legal values : protein ligand water saccharide cofactor cofactor_and_ligand
                   metal counter_ion prot_complex peptide dna_rna nucleotide
                   covalent solution misc unknown
                   underdefined site1 surface_waters1 model1 chainA anything nothing
    Brief : Ligand filter category
    Detail
        Return molecules from this category as the ligand

LigName

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the identification of ligands by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -ligandname
    Aliases : -ligname
    Type : string
    Allow list : false
    Default : (parameter does not have a default)
    Simple : true
    Required : false
    Brief : Ligand name
    Detail
        Select ligand having this residue name

MaxSiteDist

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the identification of binding sites by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -maxsitedistance
    Type : double
    Allow list : false
    Default : 8.0
    Simple : false
    Required : false
    Legal ranges :
        9999.9 to 1.0
    Brief : Maximum distance to be associated with the binding site

MaxSurfDist

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the identification of surface waters by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -maxsurfacedistance
    Type : double
    Allow list : false
    Default : 5.0
    Simple : false
    Required : false
    Legal ranges :
        9999.9 to 1.0
    Brief : Maximum distance to be associated with the protein surface
    Detail
        Used when surface waters are selected

ModelNum

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the selection filters used by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -modelnum
    Type : unsigned
    Allow list : false
    Default : 1
    Simple : false
    Required : false
    Legal ranges :
        999 to 0
    Brief : Select this NMR model number
    Detail
        Molecules that are not marked as models are treated as model 1.
        Model 0 selects all models.

Note

It may be necessary to remove the input flavor OEIFlavor_PDB_ENDM to read all models (see the splitmolcomplex example for how to do this). In most situations, this parameter should be set to either 0 (allow all models to be selected) or 1 (the default). The reason for this is that the site counter, which the parameter -bindingsitenum selects based on, does not reset for each model and therefore site and model are not independent. A good example of where this can be used is with a PDB biological assembly file: setting the -modelnum parameter to 0 (use all models), allows a binding site spanning symmetry related proteins marked as different models to be recognized.

ProtFilter

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the protein filter used by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -proteinfilter
    Type : string
    Allow list : false
    Default : prot_complex
    Simple : false
    Required : false
    Legal values : protein ligand water saccharide cofactor cofactor_and_ligand
                   metal counter_ion prot_complex peptide dna_rna nucleotide
                   covalent solution misc unknown
                   underdefined site1 surface_waters1 model1 chainA anything nothing
    Brief : Protein filter category
    Detail
        Return molecules from this category as the protein

SeparateRes

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the whether individual protein residues are separated before selection by OESplitMolComplex and OEGetMolComplexComponents. This is commonly used to return just binding-site residues.

Contents of parameter -separateresidues
    Type : bool
    Allow list : false
    Default : false
    Simple : true
    Required : false
    Brief : Separate individual residues before selection
    Detail
        Used to return just those residues near the binding site

SiteNum

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the selection filters used by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -bindingsitenum
    Aliases : -sitenum
    Type : unsigned
    Allow list : false
    Default : 1
    Simple : false
    Required : false
    Legal ranges :
        999 to 0
    Brief : Select this binding site
    Detail
        Specifying site 0 means select ALL sites

SurfWat

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the treatment of surface waters by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -surfacewaters
    Aliases : -surfwat
    Type : bool
    Allow list : false
    Default : false
    Simple : true
    Required : false
    Brief : Select surface waters
    Detail
        Waters near the surface of the protein rather than just near the binding site

WatFilter

Passing this constant to the OEConfigureSplitMolComplexOptions function results in generating the following default interface to configure the water filter used by OESplitMolComplex and OEGetMolComplexComponents.

Contents of parameter -waterfilter
    Type : string
    Allow list : false
    Default : water
    Simple : false
    Required : false
    Legal values : protein ligand water saccharide cofactor cofactor_and_ligand
                   metal counter_ion prot_complex peptide dna_rna nucleotide
                   covalent solution misc unknown
                   underdefined site1 surface_waters1 model1 chainA anything nothing
    Brief : Water filter category
    Detail
        Return molecules from this category as water