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) and
OEMakeDesignUnitOptions
(opts) arguments,
respectively. 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
OEMakeDesignUnitOptions
class