Switch from OpenBabel to RDKit#135

Closed

rwest wants to merge 30 commits into

ReactionMechanismGenerator:masterfrom

rwest:rdkit

Commits on Jul 17, 2013

Fixed drawing of multiple rings in a molecule. Fused rings still broken.

Victor Lambert
authored and
Victor Lambert
committed

Commits on Jul 18, 2013

Fixed multiple ring drawing again (fused rings still broken).
Victor Lambert
committed

Commits on Jul 24, 2013

Improved fused ring drawing for one or two common atoms.
Victor Lambert
committed

Commits on Jul 25, 2013

use rdkit drawing
Victor Lambert
committed

Commits on Jul 26, 2013

Use rdkit to draw, excess code removed.
Victor Lambert
committed

Commits on Jul 29, 2013

Cleaned up comments to reflect changes.
Victor Lambert
committed
Merge rdkit into molDraw
Victor Lambert
committed
Fix spin multiplicity calc in from rdkitmol.
Victor Lambert
committed

Commits on Jul 30, 2013

Use rdkit instead of OB. Add from functions.
Victor Lambert
committed
Adds kekulization for fromRDKitMol.
Victor Lambert
committed
Removed OpenBabel dependence from writing gaussian input files.
rwest
committed
Removed OpenBabel dependence from writing mopac input files.
rwest
committed

Commits on Jul 31, 2013

Remove CML from example input file.
rwest
committed
Tweak the molecule drawing - make bonds a little shorter.
rwest
committed
Get the qm.molecule.rd_build to use the molecule.toRDKitMol method.
rwest
committed
Remove unnecessary imports.
Victor Lambert
committed
Remove unnecessary SMILEwriter code.
Victor Lambert
committed
Remove references to CML in rmg input file.
Victor Lambert
committed
Remove openbabel in favor of RDkit for database loading.
Victor Lambert
committed
Remove unnecessary openbabel code.
Victor Lambert
committed

Commits on Aug 1, 2013

Raise ValueError if you try to parse an invalid SMILES string.
rwest
committed