OEBuildSidechains¶

Attention

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

These functions build out partial sidechains using a rotamer library. The rotamer chosen is the one with the best interaction energy with the surrounding environment without taking solvent effects into account. If multiple sidechains are built that interact with one another, the energy chosen is the best collective interaction energy. The functions will return false if a sidechain can not be built due to clashes, but will still return a structure with all the ones it could build.

Note

Explicit hydrogens are not added to the structure during the build processes, therefore no partial charges are assigned.

bool OEBuildSidechains(OEChem::OEMolBase &mol,
                       const OESpruce::OESidechainBuilderOptions& opts=OESpruce::OESidechainBuilderOptions())

This function takes a molecule and builds any partial sidechain of standard protein residues determined using the OEGetPartialResidues function. An options class defining a rotamer library from the OERotamerLibrary namespace can be set, otherwise the default library from that namespace is chosen. Additionally, in the options the number of rotamers used can be reduced by picking a rotamer coverage below the default 100%. The percentage is calculated cumulatively, so the most probably rotamer is tested first, up to the rotamer that takes it above the percentage limit. The options class also defines the behavior of removing water molecules that clash with the built sidechain.

bool OEBuildSidechains(OEChem::OEMolBase &mol,
                       const std::vector<OEChem::OEResidue> residues,
                       const OESpruce::OESidechainBuilderOptions& opts=OESpruce::OESidechainBuilderOptions())

This function works identically to the above function, but only builds the residues identified in the vector residues.