TODOlist.txt

Improve the API:
1. Need to find a way to have hierarchical Classes for example Molecule.Descriptors.

2. Hosecode for NMR in progress. 

Some examples to implement in the development stage:
Look at the python getstart rdkit page for a list of missing functionnalities.
(http://www.rdkit.org/docs/GettingStartedInPython.html)

Status : 15/10/2015 guillaume godin

Done Molecule.AllDescriptors like function to generate all of descriptors

Done create a empty molecule (but this is a workaround!)

Done Reading and Writing Molecules: DONE, ok, we don't need to implement files readers for the moment, need to be done in Nodejs
Reading sets of molecules: need to do that (not a priority) need to be done in Nodejs

Done Writing molecules: DONE, we don't need to implement files writers for the moment
Writing sets of molecules: need to do that (not a priority)

In progress: Looping over Atoms and Bonds: Done  (addAtom, addBond)

Ring Information: Done

Done Modifying molecules: MolOps functions

IN Progress (thegodone) Working with 2D molecules: GenerateDepictionMatching2DStructure, GenerateDepictionMatching3DStructure

IN Progress (thegodone) Working with 3D Molecules: AlignMolConformers,GetConformerRMS

Done Preserving Molecules: MolToBinary

Done Drawing Molecules: Drawing2D (done), remark MolsToGridImage can be interesting need to check for interaction with visualizer ?

Done: Substructure Searching: HasSubstructMatch, GetSubstructMatches.

Stereochemistry in substructure matches: need to test

Not implemented Chemical Transformations: DeleteSubstructs, ReplaceSubstructs, ReplaceSidechains, ReplaceCore, GetMolFrags, can be interesting for HoseCode.

Done Murcko Decomposition

Not implemented Maximum Common Substructure: FindMCS, smartsString,

Done Fingerprinting and Molecular Similarity: FingerprintMol done, FingerprintSimilarity done,MACCS done

Done Atom Pairs and Topological Torsions: GetAtomPairFingerprint 

Done Morgan Fingerprints (Circular Fingerprints): GetMorganFingerprint done, GetMorganFingerprintAsBitVect done

to do: Picking Diverse Molecules Using Fingerprints: to do not a priority

Done (partially for AtomContribution): Generating Similarity Maps Using Fingerprints

Done Descriptors, option can we add more descriptors obabel, cdk, Padel

Done Visualization of Descriptors

to do: Chemical Reactions: very interesting!

to do: BRICS Implementation: very interesting!

to do: Chemical Features and Pharmacophores: very interesting!

to do: 2D Pharmacophore Fingerprints: idem

to do: Molecular Fragments

Done: Database functionnalities: indexedDB interaction... (http://blog.gmane.org/gmane.science.chemistry.rdkit.user/month=20140301 like for ORCALE)

Inchi: to do not a priority

Avalon: to do not a priority