OEMakeDesignUnits

Attention

This API is currently available in C++ and Python.

OESystem::OEIterBase<OEBio::OEDesignUnit> *
  OEMakeDesignUnits(const OEChem::OEMolBase &structure,
                    const OESpruce::OEStructureMetadata &metadata=OESpruce::OEStructureMetadata(),
                    const OESpruce::OEMakeDesignUnitOptions &opts=OESpruce::OEMakeDesignUnitOptions(),
                    const std::string siteResidue="")
OESystem::OEIterBase<OEBio::OEDesignUnit> *
  OEMakeDesignUnits(const OEChem::OEMolBase &structure,
                    const OESystem::OESkewGrid &electronDensity,
                    const OESpruce::OEStructureMetadata &metadata=OESpruce::OEStructureMetadata(),
                    const OESpruce::OEMakeDesignUnitOptions &opts=OESpruce::OEMakeDesignUnitOptions(),
                    const std::string siteResidue="")
OESystem::OEIterBase<OEBio::OEDesignUnit> *
  OEMakeDesignUnits(const OEChem::OEMolBase &structure,
                    const OEBio::OEDesignUnit &designUnitReference,
                    const OESpruce::OEStructureMetadata &metadata=OESpruce::OEStructureMetadata(),
                    const OESpruce::OEMakeDesignUnitOptions &opts=OESpruce::OEMakeDesignUnitOptions()
                    const std::string siteResidue="")
OESystem::OEIterBase<OEBio::OEDesignUnit> *
  OEMakeDesignUnits(const OEChem::OEMolBase &structure,
                    const OESystem::OESkewGrid &electronDensity,
                    const OEBio::OEDesignUnit &designUnitReference,
                    const OESpruce::OEStructureMetadata &metadata=OESpruce::OEStructureMetadata(),
                    const OESpruce::OEMakeDesignUnitOptions &opts=OESpruce::OEMakeDesignUnitOptions(),
                    const std::string siteResidue="")

Return an iterator over all OEDesignUnit objects that can be produced from the input OEMolBase structure. A reference structure to be used for biounit extraction and structural superposition can be passed in through the designUnitReference argument, while information regarding the experimental data as well as basic options for constructing the design units themselves can be provided through the OEStructureMetadata (metadata), OESkewGrid (electronDensity) and OEMakeDesignUnitOptions (opts) arguments, respectively. The input option of providing a electron density map can be used to calculate Iridium score. For more information about the Iridium score, see Iridium chapter of that toolkit. The OEStructureMetadata class stores constants for use with OEFieldMeta. These attributes (e.g. symmetry) are used to construct DUs. There is an input option to specify a binding site using a single residue specification if apo (or holo). The format is “name:num:insert code:chainid”, e.g. “ASP:25: :A” indicating Aspartic acid 25 in chain A. Note: A blank/whitespace character is used for the insert code, which is a typical use case.

Note

This function will return an iterator over OEDesignUnit pointers, where the system’s molecules have been binned into categories given by the OEDesignUnitComponents namespace. Although an OEDesignUnitComponents_Metals category exists, depending on the proximity of the metal to the design unit’s binding site, the metal may be contained in either the OEDesignUnitComponents_Cofactors category if it falls within a cutoff to the binding site, or in the OEDesignUnitComponents_Metals category if not.

Code Example

See also