Required changes for CDK 1.5.3
Using CDK version 1.5.3 (on separate branch to avoid collisions with Pablo)
Resolving CDK 1.5.3 API changes
More CDK API changes.
IteratingMDLReader/IteratingSDFReader
Verifying correctness of hash code.
Avoid name clash with the CDK hash code implementation.
Using the CDK hash code implementation.
Using the CDK generator to compare reconstruction.
Improved error message when parsing SMILES - show what the input was.
Using the CDK hash implementation to suggest metabolites for transport/exchange.
MnxRef conversion - note we only add metabolites to which we find reactions for. Currently loading of the Structures is turned off - using the new SMILES Parser should make things fast enough.
Using custom fork of CDK until required classes are available in the main branch.
Use custom CDK fork with SMILES and MDL patches - this class can be removed once CDK is up to date.
Move Beam utility to where it is needed (annotation module) and renamed to avoid confusion with names.
Using improved SMILES parser.
Catch exceptions when converting molecular formula.
No need to atom-type - the implicit hydrogens are now loaded from MDL/SMILES correctly.
Removing commented out code.
With new SMILES code we can now load all the information and read the Metingear reconstruction in relatively quick time.