OEBuildLoopsΒΆ

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.

These functions build missing loops in protein structures. They return false if any of the loops cannot be built, but it will return with as many built loops as possible. The functions require 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 OEBuildLoops(OEChem::OEMolBase& mol,
                       const OESidechainBuilderOptions& scOpts=OESidechainBuilderOptions(),
                       const OELoopBuilderOptions& lOpts=OELoopBuilderOptions())

This function takes a molecule and builds any missing loops that can be detected based on the information in the PDB header metadata. The function also takes options classes for the loop building, but also for the side-chain re-building, in case the loop in the database is not a 100% identity match.

bool OEBuildLoops(OEChem::OEMolBase& mol,
                       const OEStructureMetadata& data,
                       const OESidechainBuilderOptions& scOpts=OESidechainBuilderOptions(),
                       const OELoopBuilderOptions& lOpts=OELoopBuilderOptions())

This function works identically to the above function, only metadata is explicitly provided containing information about the sequence, so gaps can be detected.