Strain Filtering: Difference between revisions
(Created page with "This is Strain Filtering version 1.1. Please copy the code to your current directory. $ cp -r /mnt/nfs/home/sgu/code/ucsf . To run the code, you need RDKit. You can follow t...") |
Jgutierrez6 (talk | contribs) mNo edit summary |
||
| (14 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
This is Strain Filtering version 1.1. Please copy the code to your current directory. | This is Strain Filtering version 1.1 (20200218). Please copy the code to your current directory. | ||
$ cp -r /mnt/nfs/home/sgu/code/ | $ cp -r /mnt/nfs/home/sgu/code/strainfilter . | ||
To run the code, you need RDKit | Furthermore, if you don't want to include the strain from hydrogens, you can try this version: | ||
$ conda | $ cp -r /mnt/nfs/home/sgu/code/noh . | ||
To run the code, you need to install RDKit by following the instruction: 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 | $ 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. | 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>0 && $2<6.5 && $6<1.8' test2_Torsion_Strain.csv > filtered.csv | ||
This example uses | This example uses awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8. | ||
== Github Link == | |||
https://github.com/docking-org/ChemInfTools/tree/master/apps/strainfilter | |||
https://github.com/docking-org/ChemInfTools/tree/master/apps/noh | |||
Latest revision as of 19:44, 8 September 2022
This is Strain Filtering version 1.1 (20200218). Please copy the code to your current directory.
$ cp -r /mnt/nfs/home/sgu/code/strainfilter .
Furthermore, if you don't want to include the strain from hydrogens, you can try this version:
$ cp -r /mnt/nfs/home/sgu/code/noh .
To run the code, you need to install RDKit by following the instruction: 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>0 && $2<6.5 && $6<1.8' test2_Torsion_Strain.csv > filtered.csv
This example uses awk to output all the compounds with total strain energy <6.5 and every torsion energy <1.8.
Github Link
https://github.com/docking-org/ChemInfTools/tree/master/apps/strainfilter
https://github.com/docking-org/ChemInfTools/tree/master/apps/noh