background / intent

For a set of molecules, DataWarrior¹ can generate conformers (Chemistry -> Generate Conformers). While exploring these variations, which includes the interconversion of stereogenic centers, the conformers are assigned an energy. These results can either be saved in DataWarrior's native .dwar format, or exported by DataWarrior in a tabulator separated text file (File -> Save Special -> Textfile).

The aim of this project is to provide quick access to each isomers' conformer of lowest assigned energy in a form further work with DataWarrior is possible.

intended use

The included script best_conformer.py requires a working installation of Python. For a greater portability, only modules provided by Python's standard library are used. There are no additional dependencies.

Copy the script into the same folder which contains DataWarrior's .txt export of the conformers and run

python3 best_conformers.py input.txt > output.txt

which is going to work on your input data and redirect (>) the results from the command line into a new permanent record. Both input and output filename can be of your choice; to use a file extension .txt however facilitates the subsequent import of the results into DataWarrior by Ctrl + O. Else you can copy-paste the content of the results into DataWarrior via the computer's clipboard memory and Edit -> Paste Special -> New From Data With Header Row in DataWarrior.

reference data

Sub folder test_data contains a test library of random molecules generated by DataWarrior, Random_Molecules.dwar which was used to generate conformers (file conformers.dwar, and subsequent export conformers.txt, respectively). File results.txt is the permanent record applying the Python script.

some internal

The script reads the first line of DataWarrior's .txt file and – assuming it is the table's header – queries the columns to identify which one contains the structure ID, the tag about the isomers, and the assigned energy. Subsequent lines are read to check if the combination of structure ID and isomer tag ("a key") already is a new one; if this is the case, the the whole line (including the assigned energy) is saved in a temporary dictionary.

For entries with an already known combination of structure ID and isomer tag, the energy already known is compared with the new value from the list's new line read. The entry in the dictionary is updated – by the line's complete content, including conformation and energy – if the energy reported by the line is lower.

content

.
├── best_conformer.py
├── LICENSE
├── README.md
├── README.org
└── test_data
    ├── conformers.dwar
    ├── conformers.txt
    ├── Random_Molecules.dwar
    └── results.txt

2 directories, 8 files

Footnotes

Footnotes

1. https://openmolecules.org/datawarrior/index.html ↩