Strain Filtering: Difference between revisions

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  $ conda activate my-rdkit-env
  $ 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:
Currently, the code can handle db2/db2.gz and mol2 inputs. For example:
  $ python3 Torsion_Strain.py test1.db2.gz
  $ python Torsion_Strain.py test1.db2.gz
  $ python3 Torsion_Strain.py test2.mol2
  $ python 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.
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 thresholds to filter compounds. e.g.
You may be interested in column 2 (total strain energy) and column 6 (the maximum dihedral torsion energy), from which you can choose different thresholds 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}'
  $ awk -F"," '$2<6.5&&$6<1.8' test2_Torsion_Strain.csv
This example uses csvkit and awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8.
This example uses awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8.

Revision as of 09:39, 13 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

Currently, the code can handle db2/db2.gz and mol2 inputs. For example:

$ python Torsion_Strain.py test1.db2.gz
$ python 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 6 (the maximum dihedral torsion energy), from which you can choose different thresholds to filter compounds. e.g.

$ awk -F"," '$2<6.5&&$6<1.8' test2_Torsion_Strain.csv

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