Strain Filtering: Difference between revisions
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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 | 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 | $ 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. | This example uses awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8. | ||
Revision as of 03:10, 15 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
On our cluster, you may source my environment.
$ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh $ 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.