A package of Python objects for parsing and interacting with Alphafold models.
Project description
AlphafoldModel is a package to parse Alphafold PDB structures and PAE Matrices into interactive Python objects.
The package contains the following classes:
AlphafoldModel
: Parses the Alphafold model PDB file alongside its JSON PAE matrix into an interactive Python object. It allows declarative queries for a model's local PAE and plDDT metrics.ModelPDB
:ModelPDB
is the base class that carries the PDB parsing functionalities as well as residue-based nearest-neighbour search methods.ModelPAE
:ModelPAE
is the base class that carries the PAE parsing functionalities forAlphafoldModel
.LoadedKDTree
:LoadedKDTree
is a wrapper class which provides an interface over thescipy.spatial.KDTree
class to instead store and return arbitrary objects with coordinate information.
Explore the source file in:
src/AlphafoldModel/alphafoldmodel
Installing
pip install alphafoldmodel
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