Implementing the CACTVS/PubChem substructure keys

Here's the place to leave comments about my rather lengthy article on the problems I ran into while implementing the PubChem/CACTVS substructure keys, with background, pointers to the MACCS definitions, and other chunky nuggets of feature key wisdom.

subgraph enumeration

I've started a series on subgraph enumeration. In Part 1 I present a brute force enumeration algorithm, modify it to remove duplicates, and post-process the results to generate canonical SMARTS for each subgraph. In Part 2 I develop a new algorithm which is about 3.5 times faster.

Reordering SMILES atom order

I wrote a rather long essay about how to generate SMILES strings where the atoms are in arbitrary/user-defined order. The first two implementations use RDKit but in the last I couldn't work around an RDKit bug so I switched over to OpenBabel. (Edit: Greg commented here that the bug has been fixed in version control and will out as part of the Q4 2010 release.)

This is the place to leave questions and comments about what I wrote.

Ontologies of Algorithm Implementations

A place for you to leave comments about my essay Ontologies of Algorithm Implementations wherein I gave examples of how it's not simple to say "this data set was generated by algorithm X."

KNIME, Pipeline Pilot, and visual programming languages

I presented a talk at CUP 2010 in Santa Fe on KNIME, Pipeline Pilot and visual programming languages in general, with comparison to other visual programming languages and text-based toolkit approaches. I've broken the talk up into parts, which are published on my technical writings blog.

This is the place to leave comments on those writings. The relevant postings are:

• KNIME and beginners, where I walk through my problems trying to get heavy atom counts working in KNIME

Instrumenting the AST

Here is the place for you to leave comments on "Instrumenting the AST" wherein I describe an way to modify the AST for Python code in order to insert new code for things like line and branch tracing and ways to add tests which aren't otherwise easily possible.

Project hosting options?

This is a place to comment about my post "Project hosting options?"