OEBuildSingleLoopΒΆ

Attention

PRELIMINARY-IMAGE This is a preliminary API until Spring 2021 and may be improved based on user feedback. It is currently available in C++ and Python.

This function functions builds a specified missing loop in a protein structures. The function returns false if the loop cannot be built. The function requires a loop database be provided in the options class. Using the loopdb_builder application it is possible to build your own database for a given target family, or a set of propritary structure. OpenEye provides a database built of the structures in the entire PDB repository at the time of toolkit release. The datastamps are noted in the info table and logged during loop building. It is possible to append local/propriatary structures to this database if desired, again using the desktop application. The options classes allows different behaviors for the loop builder.

Note

Explicit hydrogens are not added to the structure during the build processes.

bool OEBuildSingleLoop(OEChem::OEMCMolBase& outputMol,
                            const OEChem::OEMolBase& inputMol,
                            const std::string fasta,
                            const OEChem::OEResidue& cTerminalAttachment,
                            const OEChem::OEResidue& nTerminalAttachment,
                            const OESidechainBuilderOptions& scOpts=OESidechainBuilderOptions(),
                            const OELoopBuilderOptions& lOpts=OELoopBuilderOptions());

The function takes an empty multi-conformer molecule which will contain the protein with the looop built if the function is successful. Multiple conformers of the loop will be returned based on the passed options, the results are sorted by a force field energy score. The remaining arguments are, the molecule with the gap, the loop protein sequence in 1-letter codes as a string (e.g. “PVHTAL”), and the c- and n-terminal attachtment (or anchor) residues. The function also takes options classes for the loop building, and side-chain re-building, in case the loop in the database is not a 100% identity match.