BioPandas / BioPandas/biopandas

Add function for structural alignments via least-squares fit

Open
#5 4 comments 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
Python
Stars
756
Forks
119
Avg merge
23h 8m
Merged PRs (30d)
2

Description

A `staticmethod` least-squares superposition. We could call it `align` and implement it with similar parameters as the [rmsd](https://github.com/rasbt/biopandas/blob/master/biopandas/pdb/pandas_pdb.py#L118) function. In addition, it would be nice to have a `substructure` parameter for substructure alignment -- maybe accepting an iterable of residue numbers here.

Contributor guide

Open the contributing guide

Research direction

Start with the rmsd function in biopandas/pdb/pandas_pdb.py and compare its parameters with the proposed align interface. Define how least-squares superposition and residue-number substructure selection should behave, then verify that the resulting alignment handles the requested full-structure and substructure cases.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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