I’ve just uploaded my Perl scripts from Summer ’07, when I was doing my MSc. dissertation on a possible new method for predicting the pharmacologically important property logP in a large database of potential drug candidate molecules.  These descriptions aren’t great, a more in-depth explanation of how they were used will be forthcoming, just in case there are any budding computational chemists out there who would like some Perl examples specifically geared to their field.  The CSV parsing routines are probably the most useful, as they can be easily adapted to different data structures and don’t require any external programs.

CSVparser – Contains all the CSV parsing functionality that I needed.
colappend – Appends a new column from a specified input file to an existing CSV file.
XEDcompoundfilter – Removes lines from an XED output file where there is no data, and also according to an optional blocklist of SMILES strings (used to remove outliers).
XEDparser – Parses an XED output file in a variety of ways to generate the required CSV file.
XEDrunner – Handles the conversion of SMILES string files to XEDEX input files, runs them through the XEDEX program and then the SDF conversion program to produce readable SDF files.

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