Free ligand module - Githubissues

EPiCs-group / obelix

An automated workflow for generation & analysis of bidentate ligand containing complexes

https://epics-group.github.io/obelix/

GNU General Public License v3.0

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Free ligand module #14

Closed akalikadien closed 1 year ago

akalikadien commented 1 year ago

Added functionality for extracting free ligand from M-L complex using molecular_graph
Added FreeLigand class with example, allows for calculating DFT descriptors on a free ligand
Modified DFTExtractor to allow a free ligand to be passed as an input
Made molecular_graph more robust and now also enabled O donor atoms
fixed descriptor extraction in DFTExtractor class for O donor atoms and different endings of lone pair occupancy section in log file

akalikadien commented 1 year ago

Keep in mind that this PR changes the default behavior of _buried_volume_quadrant_analysis. The default radius used for quadrant/octant buried volume (BV) analysis is now 7A instead of 3.5A.