deploy: c335c1a

.buildinfo

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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: e4704fbb189cc4c497c04e6ee89de3e7
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/autoapi/index.rst.txt

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+API Reference
+=============
+
+This page contains auto-generated API reference documentation [#f1]_.
+
+.. toctree::
+   :titlesonly:
+
+   /autoapi/moleculib/index
+
+.. [#f1] Created with `sphinx-autoapi <https://github.com/readthedocs/sphinx-autoapi>`_

_sources/autoapi/moleculib/abstract/dataset/index.rst.txt

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+moleculib.abstract.dataset
+==========================
+
+.. py:module:: moleculib.abstract.dataset
+
+
+Classes
+-------
+
+.. autoapisummary::
+
+   moleculib.abstract.dataset.Dataset
+   moleculib.abstract.dataset.PreProcessedDataset
+
+
+Module Contents
+---------------
+
+.. py:class:: Dataset(transform: List[Callable] = None)
+
+   .. py:attribute:: transform
+      :value: None
+
+
+
+.. py:class:: PreProcessedDataset(splits, transform: List[Callable] = None, shuffle=True, pre_transform=False)
+
+   .. py:attribute:: splits
+
+
+   .. py:attribute:: transform
+      :value: None
+
+
+

_sources/autoapi/moleculib/abstract/index.rst.txt

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+moleculib.abstract
+==================
+
+.. py:module:: moleculib.abstract
+
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   /autoapi/moleculib/abstract/dataset/index
+   /autoapi/moleculib/abstract/metrics/index
+   /autoapi/moleculib/abstract/transform/index
+
+

_sources/autoapi/moleculib/abstract/metrics/index.rst.txt

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+moleculib.abstract.metrics
+==========================
+
+.. py:module:: moleculib.abstract.metrics
+
+
+Classes
+-------
+
+.. autoapisummary::
+
+   moleculib.abstract.metrics.MetricsPipe
+
+
+Module Contents
+---------------
+
+.. py:class:: MetricsPipe(metrics_list: List[Callable])
+
+   .. py:attribute:: metrics_list
+
+

_sources/autoapi/moleculib/abstract/transform/index.rst.txt

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+moleculib.abstract.transform
+============================
+
+.. py:module:: moleculib.abstract.transform
+
+

_sources/autoapi/moleculib/assembly/dataset/index.rst.txt

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+moleculib.assembly.dataset
+==========================
+
+.. py:module:: moleculib.assembly.dataset
+
+
+Classes
+-------
+
+.. autoapisummary::
+
+   moleculib.assembly.dataset.ChromaDataset
+
+
+Module Contents
+---------------
+
+.. py:class:: ChromaDataset(base_path, transform: List[Callable] = None, shuffle=True, reduced=False)
+
+   Bases: :py:obj:`moleculib.abstract.dataset.PreProcessedDataset`
+
+

_sources/autoapi/moleculib/assembly/datum/index.rst.txt

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+moleculib.assembly.datum
+========================
+
+.. py:module:: moleculib.assembly.datum
+
+
+Classes
+-------
+
+.. autoapisummary::
+
+   moleculib.assembly.datum.AssemblyDatum
+
+
+Module Contents
+---------------
+
+.. py:class:: AssemblyDatum(idcode: str = None, protein_data: List[moleculib.protein.datum.ProteinDatum] = None, molecule_data: List[moleculib.molecule.datum.MoleculeDatum] = None)
+
+   .. py:attribute:: idcode
+      :value: None
+
+
+
+   .. py:attribute:: protein_data
+      :value: None
+
+
+
+   .. py:attribute:: molecule_data
+      :value: None
+
+
+
+   .. py:method:: from_datalist()
+
+
+   .. py:method:: filter_proteins(keep=None, drop=None)
+
+      indices to keep or drop
+
+
+
+   .. py:method:: plot(view, viewer=None, protein_style=dict(), molecule_style=dict())
+
+
+   .. py:method:: from_filepath(filepath, idcode=None)
+      :classmethod:
+
+
+
+   .. py:method:: fetch_pdb_id(idcode, save_path=None)
+      :classmethod:
+
+
+

_sources/autoapi/moleculib/assembly/index.rst.txt

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+moleculib.assembly
+==================
+
+.. py:module:: moleculib.assembly
+
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   /autoapi/moleculib/assembly/dataset/index
+   /autoapi/moleculib/assembly/datum/index
+   /autoapi/moleculib/assembly/metrics/index
+   /autoapi/moleculib/assembly/transform/index
+
+

_sources/autoapi/moleculib/assembly/metrics/index.rst.txt

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+moleculib.assembly.metrics
+==========================
+
+.. py:module:: moleculib.assembly.metrics
+
+
+Classes
+-------
+
+.. autoapisummary::
+
+   moleculib.assembly.metrics.AssemblyMetric
+   moleculib.assembly.metrics.ApplyMetricsToProtein
+
+
+Module Contents
+---------------
+
+.. py:class:: AssemblyMetric
+
+   .. py:method:: transform(datum: moleculib.assembly.datum.AssemblyDatum) -> moleculib.assembly.datum.AssemblyDatum
+      :abstractmethod:
+
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+
+.. py:class:: ApplyMetricsToProtein(protein_metrics: List[moleculib.protein.metrics.ProteinMetric])
+
+   Bases: :py:obj:`AssemblyMetric`
+
+
+   .. py:attribute:: protein_metrics
+
+

_sources/autoapi/moleculib/assembly/transform/index.rst.txt

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+moleculib.assembly.transform
+============================
+
+.. py:module:: moleculib.assembly.transform
+
+
+Classes
+-------
+
+.. autoapisummary::
+
+   moleculib.assembly.transform.AssemblyTransform
+   moleculib.assembly.transform.ApplyToProteins
+   moleculib.assembly.transform.ComplexPad
+   moleculib.assembly.transform.FilterProteinChains
+   moleculib.assembly.transform.StackProteins
+   moleculib.assembly.transform.UnstackProteins
+
+
+Module Contents
+---------------
+
+.. py:class:: AssemblyTransform
+
+   Abstract class for transformation of ProteinDatum datapoints
+
+
+   .. py:method:: transform(datum: moleculib.assembly.datum.AssemblyDatum) -> moleculib.assembly.datum.AssemblyDatum
+      :abstractmethod:
+
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+
+.. py:class:: ApplyToProteins(protein_transform: List[moleculib.protein.transform.ProteinTransform])
+
+   Bases: :py:obj:`AssemblyTransform`
+
+
+   Abstract class for transformation of ProteinDatum datapoints
+
+
+   .. py:attribute:: protein_transform
+
+
+   .. py:method:: transform(datum)
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+
+.. py:class:: ComplexPad(num_chains)
+
+   Bases: :py:obj:`AssemblyTransform`
+
+
+   Abstract class for transformation of ProteinDatum datapoints
+
+
+   .. py:attribute:: num_chains
+
+
+   .. py:method:: transform(datum)
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+
+.. py:class:: FilterProteinChains(num_chains)
+
+   Bases: :py:obj:`AssemblyTransform`
+
+
+   Abstract class for transformation of ProteinDatum datapoints
+
+
+   .. py:attribute:: num_chains
+
+
+   .. py:method:: transform(datum)
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+
+.. py:class:: StackProteins
+
+   Bases: :py:obj:`AssemblyTransform`
+
+
+   Abstract class for transformation of ProteinDatum datapoints
+
+
+   .. py:method:: transform(datum)
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+
+.. py:class:: UnstackProteins
+
+   Bases: :py:obj:`AssemblyTransform`
+
+
+   Abstract class for transformation of ProteinDatum datapoints
+
+
+   .. py:method:: transform(datum)
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+