OEPrepareFastROCSMolΒΆ

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 a OEShapeDatabase object from a 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 also recommended to call OEPRECompress on the oemolostream before writing out to OEB. This will cause conformers to be stored in “PRE-compressed” form. This alleviates the need to Gzip the OEB file as well as it is also recommended to store the molecule in uncompressed form to improve 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.

If OEB file-size is the chief concern, a further reduction in file-size can be achieved by using a OEMCMolType::HalfFloatCartesian molecule to store reference coordinates and torsions as 16-bit floating point. To do this, make a copy of the output molecule from OEPrepareFastROCSMol like the following:

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

Currently, 16-bit floating point has been measured to have a %12 file size savings while only costing 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.