feat: add apo features

[yusuf1759]

• Add apo features and masking
• trim apo to inference seqres
• add multi-protein, multi-ligand support via dictionaries
• TL;DR version of dataloader for recommended dataloader inputs and fitting masks for loss calculations

[github-actions]

Coverage report

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File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core/index
system.py
utils.py
src/plinder/core/loader
__init__.py
dataset.py
featurizer.py
transforms.py
utils.py					115-130, 166-182
src/plinder/core/scores
clusters.py
index.py
ligand.py
links.py
protein.py
src/plinder/core/split
plot.py
utils.py
src/plinder/core/structure
atoms.py					393
diffdock_utils.py
structure.py					202
vendored.py					895
src/plinder/core/utils
config.py
cpl.py
dataclass.py
dec.py
gcs.py
unpack.py
src/plinder/eval/docking
write_scores.py
Project Total

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