Support Calculation in Fminer
in-silico toxicology gmbh blog
Fminer algorithms BBRC and LAST-PM can now be used for automatic support calculation. This post shows how to use it.
Types of Support in Chemical Datasets
The support of a pattern denotes the number of times it is contained in a chemical (also termed hits). The number of hits can be defined differently by counting unique or non-unique matches:
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Unique matches: a SMARTS may only match once on the same atoms.
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Non-unique matches: a SMARTS pattern may match more than once on the same atoms.
For example in a six-membered aromatic ring, the pattern “c:c:c:c:c:c” would have six unique, but twelve non-uniqe matches (since it has two non-unique matches on any six atoms). Fminer algorithms use the non-unique matching scheme.
Usage from the Command Line
Fminer may be called from ruby, python, java, and C++ as those APIs are integrated into the source and supported by the Makefile. For demonstration, we will use the standard front-end application.
Download and install the fminer2 package according to the BBRC instructions and LAST-PM instructions, respectively. Then run fminer from the main directory by setting the environment variable FMINER_NR_HITS first.
unset FMINER_LAZAR
export FMINER_SMARTS=1
export FMINER_P_VALUES=1
export FMINER_NR_HITS=1 # Switch on support
fminer/fminer libbbrc/libbbrc.so -f5 liblast/test/hamster_carcinogenicity.smi \
liblast/test/hamster_carcinogenicity.class
You will receive output such as the following:
- [ "[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]", 13.9894, [ 20018: '24', 20374: '24', 20682: '12', ... ]]
This denotes that the SMARTS pattern “[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]” matches e.g. 24 times on molecule 20018, and twelve times on molecule 20682 (you can check that from the .smi file). Please also see this post on how to check correctness of the hits.
Note: BBRC was used for demonstration, but LAST-PM supports the same functionality.
Integration into Opentox-Webservices
Calculating hits is also available as a web service within Opentox by passing the additional argument -d “nr_hits=true” to Fminer web services BBRC and LAST-PM. The support will be reported as numeric feature (as defined in the OpenTox ontology) and an integer value, compared to nominal feature and true/false (please read the post about calling BBRC and LAST-PM).
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