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42 lines
2.3 KiB
Plaintext
42 lines
2.3 KiB
Plaintext
This directory contains scripts for carrying out the calculations and analyis from the publications:
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1) A. Vulpetti, U. Hommel, G. Landrum, R. Lewis and C. Dalvit, "Design and NMR-based screening of LEF,
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a library of chemical fragments with different Local Environment of Fluorine" J. Am. Chem. Soc. 131 (2009) 12949-12959. https://doi.org/10.1021/ja905207t
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2) A. Vulpetti, G. Landrum, S. Ruedisser, P. Erbel and C. Dalvit, "19F NMR Chemical Shift Prediction with
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Fluorine Fingerprint Descriptor" J. of Fluorine Chemistry (2010). https://doi.org/10.1016/j.jfluchem.2009.12.024
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The scripts require that the RDKit (www.rdkit.org) be installed and properly configured.
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The scripts assume that input db.sdf files only contain molecules having either CF or CF3 moieties.
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Commands to run:
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1) Generation of Fluorine Fingerprint (F-FP-L)
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------------------------------------------------------------------------------------------
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python CreateFps.py db.sdf db.layers.pkl > dupes.layers.txt
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2) Butina Clustering using Fluorine Fingerprint (F-FP-L)
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python ClusterFps.py db.layers.pkl > clusters.layers.txt
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3) Cliff Analysis using Fluorine Fingerprint Similarity vs a specified property in propField
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-------------------------------------------------------------------------------------------
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python DistancePlot.py db.sdf cliff.txt
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4) KNN prediction of a property specified in propField using F-FP-L (L= maximum path length in atoms)
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-------------------------------------------------------------------------------------------
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python DistancePredict.py --max=L+1 --sim="[0.9,0.8,0.7]" --nbrs=nbrs.txt training.sdf
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test.sdf prediction.txt
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In the event you use the scripts for publication please reference the original publications:
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1) A. Vulpetti, U. Hommel, G. Landrum, R. Lewis and C. Dalvit, "Design and NMR-based screening of LEF,
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a library of chemical fragments with different Local Environment of Fluorine" J. Am. Chem. Soc. 131 (2009) 12949-12959. https://doi.org/10.1021/ja905207t
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2) A. Vulpetti, G. Landrum, S. Ruedisser, P. Erbel and C. Dalvit, "19F NMR Chemical Shift Prediction with
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Fluorine Fingerprint Descriptor" J. of Fluorine Chemistry (2010). https://doi.org/10.1016/j.jfluchem.2009.12.024
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