OEPrepareFastROCSMol

bool OEPrepareFastROCSMol(OEChem::OEMCMolBase &mol)
bool OEPrepareFastROCSMol(OEChem::OEMCMolBase &mol,
                          const OEShape::OEColorForceField &cff)

Prepares the molecule mol to improve the performance of loading the molecule into memory as an OEShapeDatabase object from an OEFormat.OEB file. The following steps are taken to improve the performance of OEShapeDatabase.Open by as much as 10-fold:

  • Sets the energy of each conformer to 0.0 to avoid writing it to OEB.

  • Suppresses hydrogens and reorders reference conformers for compression.

  • Pre-calculates color atoms.

  • Pre-calculates self-color and self-shape terms for all conformers.

It is recommended to call OEPRECompress on the oemolostream before writing out to OEB. This will store conformers in “PRE-compressed” form therefore alleviating the need to Gzip the OEB file and consequently improving the performance of OEMolDatabase.Open. In general, calling OEPrepareFastROCSMol and OEPRECompress will result in a smaller OEB file than the default OEB.GZ output from OMEGA.

Additionally, if OEB file size is of chief concern a further reduction in file size can be achieved by using an OEMCMolType.HalfFloatCartesian molecule, which stores reference coordinates and torsions in half floating point precision (16-bit). The following code snippet demonstrates how to cast the resultant molecule from OEPrepareFastROCSMol to use half precision:

OEPrepareFastROCSMol(mol);
OEMol halfMol(mol, OEMCMolType::HalfFloatCartesian);
OEWriteMolecule(ofs, halfMol);

OEPrepareFastROCSMol(mol)
halfMol = OEMol(mol, OEMCMolType_HalfFloatCartesian)
OEWriteMolecule(ofs, halfMol)

16-bit floating point will give a file size saving of approximately 12% with a tradeoff of about 7% more performance when loading the OEB from disk into memory.

Note

By default, OEPrepareFastROCSMol will cache color atoms and self color terms for the OEColorFFType.ImplicitMillsDean color force field. The second overload that takes a OEColorForceField can be used to override this default.