rdkit/rdkit — pull request #205 by ptosco (2014-01-27 18:19:26+00:00)
Title: Re-prepared SDF/SMILES files of the MMFF validation suite + a fix

- removed a spurious #ifdef [...] #endif from
Code/ForceField/MMFF/testMMFFForceField.h
- re-prepared the SDF files from their MOL2 counterparts present in the
original MMFF validation suites. For this purpose a C++ program was
written which only uses information in MOL2 files and in .fc files
provided by Halgren. The C++ program does not depend on RDKit.
- re-prepared the SMILES files from their SDF counterparts using
a Python script which calls MolToSmiles()
- found an issue which affects 2 files in the test suite, namely
ERULE_05 and PO02A (only the hypervalent notation). The issue is
connected with removal of hydrogens bonded to phosphorous and
appears to be fixed by the modifications in Code/GraphMol/AddHs.cpp
and Code/GraphMol/SmilesParse/SmilesWrite.cpp. This issue is
independent of the changes ini the SDF files; indeed, it has
always been present, and had been previously addressed by
manual correction of the two SMILES strings