1. Andrew Dalke
  2. fmcs

Commits

Author Commit Message Date Builds
dalke
Added --version
dalke
Removed "ignore aromaticity" options because it doesn't work. Matches must be transitive. Otherwise, an aromatic can match a single and can match a double, even if a single can't match a double. This makes the MCS dependent on what is used as the reference structure.
dalke
Added tag fmcs-1.0b2 for changeset 8fbeea079fa9
dalke
Added an option to match the valences
Tags
fmcs-1.0b2
dalke
Better error reporting. If there's no MCS then report the sizes at "0 0 0" instead of "-1 -1 -1"
dalke
Fixed bug in how I generated the bond closure symbol when there were 10 or more unclosed closures.
dalke
Strange. My "slow" test is no longer slow.
dalke
renamed "indicies" to the correct "indices"
dalke
Wrong argument order. Now fixed.
dalke
Changed to version 1.0b2
dalke
User-defined atom classes, via an SD tag. Options to save structures/substructures from the MCS
dalke
more cleanups because of small errors found during manual testing.
dalke
All sorts of information about using the benchmark program
dalke
Added help strings. Changed the Indigo options from "fold_hydrogens" to "fold-hydrogens"
dalke
Legal issues; added license notice
dalke
Program I used to normalize the structures for the ChEMBL-based benchmarks
dalke
How I made the ChEMBL benchmarks.
dalke
chmod +x and add /usr/bin/env python so this can run on the command-line.
dalke
Whoo-hoo! I've got benchmarks and timings!
dalke
Smoothed out a couple of edges found during actual use.
dalke
Various restructurings to add progress/verbose information
dalke
Process the ChEMBL-13 data set to make the input files used for the ChEMBL-based MCS benchmarks.
dalke
Added a "subset" option to make a new structure file based on the subset of atoms needed for an MCS benchmark file. This required changes to the SMILES/SDF records so I can get access to the low-level records.
dalke
Fixed code so it handles .gz filenames. Fixed error handling reporting.
dalke
Ooops. Never supported the --num-tests option. Had hard-coded "at most 10"
dalke
Keep track of the total atom/bond match sizes
dalke
Change the name to 'timestamp'
dalke
Added lazy SMILES loading. Added RNG seed. Added timestamp
dalke
Changed the directive name from 'Load' to 'File'
dalke
Changed the directive name from 'Load' to 'File'
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