Difference between revisions of "Strain Filtering"

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This is Strain Filtering version 1.1. Please copy the code to your current directory.
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This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.
  $ cp -r /mnt/nfs/home/sgu/code/ucsf .
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  $ cp -r /mnt/nfs/home/sgu/code/strainfilter .
  
 
To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html
 
To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html

Revision as of 20:34, 11 February 2020

This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.

$ cp -r /mnt/nfs/home/sgu/code/strainfilter .

To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html

$ conda create -c rdkit -n my-rdkit-env rdkit
$ conda activate my-rdkit-env

Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:

$ python3 Torsion_Strain.py test1.db2.gz
$ python3 Torsion_Strain.py test2.mol2

The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.

You may be interested in column 2 (total strain energy) and column 11 (the maximum dihedral torsion energy), from which you can choose different levels to filter compounds, e.g.

$ csvcut -c 1,2,11 test2_Torsion_Strain.csv | awk -F"," '$2<6.5&&$3<1.8 {print $1" "$2" "$3}'

This example uses csvkit and awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8.