deploy: 69643ba

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 2dc36450a846ca42bb9c1649ae6bc8fe
+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:class:: PreProcessedDataset(splits, transform: List[Callable] = None, shuffle=True, pre_transform=False)
+

_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])
+

_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.PreProcessedDataset
+   moleculib.assembly.dataset.ChromaDataset
+
+
+Module Contents
+---------------
+
+.. py:class:: PreProcessedDataset(splits, transform: List[Callable] = None, shuffle=True, pre_transform=False)
+
+.. 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.MoleculeDatum
+   moleculib.assembly.datum.ProteinDatum
+   moleculib.assembly.datum.AssemblyDatum
+
+
+Module Contents
+---------------
+
+.. py:class:: MoleculeDatum(atom_token: numpy.ndarray, atom_coord: numpy.ndarray, atom_mask: numpy.ndarray, bonds: numpy.ndarray, **kwargs)
+
+   .. py:method:: empty()
+
+
+   .. py:method:: to_atom_array()
+
+
+   .. py:method:: to_sdf_str()
+
+
+   .. py:method:: plot(view, viewer=None, color=None)
+
+
+.. py:class:: ProteinDatum(idcode: str, resolution: float, sequence: biotite.sequence.ProteinSequence, residue_token: numpy.ndarray, residue_index: numpy.ndarray, residue_mask: numpy.ndarray, chain_token: numpy.ndarray, atom_token: numpy.ndarray, atom_coord: numpy.ndarray, atom_mask: numpy.ndarray, **kwargs)
+
+   Incorporates protein data to MolecularDatum
+   and reshapes atom arrays to residue-based representation
+
+
+   .. py:method:: separate_chains(datum)
+      :staticmethod:
+
+
+
+   .. py:method:: empty()
+      :classmethod:
+
+
+
+   .. py:method:: replace(**kwargs)
+
+
+   .. py:method:: from_filepath(filepath, format=None, idcode=None, chain_id=None, chain=None, model=1)
+      :classmethod:
+
+
+
+   .. py:method:: fetch_pdb_id(id, format='pdb', chain=None, model=None, save_path=None)
+      :classmethod:
+
+
+
+   .. py:method:: set(**kwargs)
+
+
+   .. py:method:: from_atom_array(atom_array, header)
+      :classmethod:
+
+
+      Reshapes atom array to residue-indexed representation to
+      build a protein datum.
+
+
+
+   .. py:method:: apply_bonds(f)
+
+
+   .. py:method:: apply_angles(f)
+
+
+   .. py:method:: apply_dihedrals(f)
+
+
+   .. py:method:: to_dict(attrs=None)
+
+
+   .. py:method:: numpy()
+
+
+   .. py:method:: to_pdb_str()
+
+
+   .. py:method:: plot(view, viewer=None, sphere=False, ribbon=True, sidechain=True, color='spectrum', colors=None)
+
+
+   .. py:method:: align_to(other, window=None)
+
+      Aligns the current protein datum to another protein datum based on CA atoms.
+
+
+
+   .. py:method:: save_mmcif(filepath)
+
+      Saves the protein datum to an mmcif file.
+
+
+
+   .. py:method:: to_dict()
+
+
+   .. py:method:: from_dict(dict_)
+      :classmethod:
+
+
+
+.. py:class:: AssemblyDatum(idcode: str = None, protein_data: List[moleculib.protein.datum.ProteinDatum] = None, molecule_data: List[moleculib.molecule.datum.MoleculeDatum] = None)
+
+   Bases: :py:obj:`simple_pytree.Pytree`
+
+
+   .. 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.MetricsPipe
+   moleculib.assembly.metrics.DescribeChemistry
+   moleculib.assembly.metrics.ProteinMetric
+   moleculib.assembly.metrics.AssemblyDatum
+   moleculib.assembly.metrics.AssemblyMetric
+   moleculib.assembly.metrics.ApplyMetricsToProtein
+
+
+Module Contents
+---------------
+
+.. py:class:: MetricsPipe(metrics_list: List[Callable])
+
+.. py:class:: DescribeChemistry
+
+   Bases: :py:obj:`ProteinTransform`
+
+
+   Augments ProteinDatum with bonds_list and angles_list a list of atomic indexes connected by bonds and angles
+   that should have invariant behavior according to chemistry
+   Note that indexing is performed at atom level, that is, as residue_dim atom_dim -> (residue_dim atom_dim)
+
+
+   .. py:method:: transform(datum)
+
+      Takes as input an individual data point, processes
+      the values in it and returns a new ProteinDatum
+
+
+
+.. py:class:: ProteinMetric
+
+.. py:class:: AssemblyDatum(idcode: str = None, protein_data: List[moleculib.protein.datum.ProteinDatum] = None, molecule_data: List[moleculib.molecule.datum.MoleculeDatum] = None)
+
+   Bases: :py:obj:`simple_pytree.Pytree`
+
+
+   .. 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:
+
+
+
+.. 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`
+
+