OEBuildLoops¶

Attention

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

These functions build missing loops and tails in protein structures. They return false if any of the loops or tails cannot be built, but it will return with as many built loops and tails 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 proprietary 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/proprietary structures to this database if desired, again using the desktop application. The options class allows different behaviors for the loop builder.

Note

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

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. The function calls OEOmega to generate possible conformations for tails.

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.