Add MD dependencies, readme, and code coverage reporting

[sarahnlewis]

No description provided.

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Summary

Summary

Generated on:	01/24/2025 - 11:55:56
Parser:	Cobertura
Assemblies:	3
Classes:	17
Files:	17
Line coverage:	69% (1543 of 2234)
Covered lines:	1543
Uncovered lines:	691
Coverable lines:	2234
Total lines:	7526
Covered branches:	0
Total branches:	0
Method coverage:	Feature is only available for sponsors

Coverage

src.bioemu - 86.2%

Name	Line	Branch
src.bioemu	86.2%	****
init.py
chemgraph.py	100%
convert_chemgraph.py	85%
denoiser.py	96.8%
get_embeds.py	96%
md_utils.py	98.3%
models.py	94.1%
sample.py	54.2%
sde_lib.py	84.3%
shortcuts.py	100%
sidechain_relax.py	87.2%
so3_sde.py	81%
structure_module.py	99%
utils.py	90%

src.bioemu.openfold.np - 44%

Name	Line	Branch
src.bioemu.openfold.np	44%	****
protein.py	31.2%
residue_constants.py	60.7%

src.bioemu.openfold.utils - 50.1%

Name	Line	Branch
src.bioemu.openfold.utils	50.1%	****
rigid_utils.py	50.1%