oe_conversion_hurdles.txt

OpenEye conversion hurdles:

For PDBCHEM schema:
- IUPAC Naming: No open source alternative. Free academic of http://www.xemistry.com/academic maybe?
- RingSystem Determination from OE has no strict equivalent 
- XLogP only on CDK (Cinfony). Other logP implementations exist.
- Not all fingerprints, but RDKit has some
- Fragmentation -> use molblocks
- Conformer generation: RDKit, Frog2 (GPL)
- normalized ratios (NPRs) of principal moments of inertia (PMI) requires re-implementation, but doable

For CREDOVI:
	General: 
		- OEB convenience features will need to be emulated/worked around somehow (see below). Maybe some sort of pickle?
		- Performance concerns?
		
	For preparepdbs:
		- Calculation of surface areas needs replacement. MMTK / PyMOL? CDK/Cinfony? Reimplementation?

	For ligand surfareas:
		- Calculation of surface areas needs replacement. MMTK / PyMOL? CDK/Cinfony? Reimplementation?
	For ligand molstrings:
		- USRCAT is currently OpenEye dependent, but could be transformable.
		- OEB column will need to be dropped
		
		
OEB Useful Features:
- Pre-processed ligand list
- Secondary Structure
- Reliable AddMols