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<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
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<li class="toctree-l1"><a class="reference internal" href="getting_started/installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="getting_started/introduction.html">Graphein</a></li>
<li class="toctree-l1"><a class="reference internal" href="getting_started/usage.html">Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
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<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
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<li class="toctree-l1 has-children"><a class="reference internal" href="protein_notebooks.html">Protein</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="notebooks/residue_graphs.html">Graphein - Residue Graph Tutorial</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/atom_graph_tutorial.html">Graphein - Atom Graph Tutorial</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/alphafold_protein_graph_tutorial.html">Constructing Graphs from AlphaFold Protein Structure Database</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/higher_order_graphs.html">Secondary Structure Graphs & Chain Graphs</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/subgraphing_tutorial.html">Constructing Subgraphs in Graphein</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/protein_mesh_tutorial.html">Creating Protein Meshes in Graphein & 3D Visualisation</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/protein_graph_analytics.html">Protein Graph Analytics</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/interactive_plotly_example.html">Interactive Visualisation with Plotly</a></li>
</ul>
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<li class="toctree-l1 has-children"><a class="reference internal" href="molecule_notebooks.html">Molecules</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="notebooks/molecule_tutorial.html">Creating Molecular Graphs in Graphein</a></li>
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<li class="toctree-l1 has-children"><a class="reference internal" href="rna_notebooks.html">RNA Graphs</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" role="switch" type="checkbox"/><label for="toctree-checkbox-3"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="notebooks/rna_graph_tutorial.html">Graphein RNA Graph Construction Tutorial</a></li>
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<li class="toctree-l1 has-children"><a class="reference internal" href="ppi_notebooks.html">PPI Networks</a><input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" role="switch" type="checkbox"/><label for="toctree-checkbox-4"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="notebooks/ppi_tutorial.html">PPI Networks and Structural Interactomics</a></li>
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<li class="toctree-l1 has-children"><a class="reference internal" href="grn_notebooks.html">Gene Regulatory Networks</a><input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" role="switch" type="checkbox"/><label for="toctree-checkbox-5"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="notebooks/grn_tutorial.html">Gene Regulatory Network Tutorial</a></li>
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<p class="caption" role="heading"><span class="caption-text">Machine Learning</span></p>
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<li class="toctree-l1 has-children"><a class="reference internal" href="datasets.html">Datasets</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" role="switch" type="checkbox"/><label for="toctree-checkbox-6"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="notebooks/dataloader_tutorial.html">Graphein Protein Structure Dataloaders</a></li>
<li class="toctree-l2"><a class="reference internal" href="datasets/pscdb.html">PSCDB - Protein Structural Change Database</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/pscdb_baselines.html">PSCDB - Baselines</a></li>
<li class="toctree-l2"><a class="reference internal" href="datasets/ppisp.html">PPISP - Protein Protein Interaction Structure Prediction</a></li>
</ul>
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<p class="caption" role="heading"><span class="caption-text">API Reference</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/graphein.protein.html">graphein.protein</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/graphein.molecule.html">graphein.molecule</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/graphein.rna.html">graphein.rna</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/graphein.ppi.html">graphein.ppi</a></li>
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<h1 id="index">Index</h1>
<div class="genindex-jumpbox"><a href="#_"><strong>_</strong></a> | <a href="#A"><strong>A</strong></a> | <a href="#B"><strong>B</strong></a> | <a href="#C"><strong>C</strong></a> | <a href="#D"><strong>D</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#F"><strong>F</strong></a> | <a href="#G"><strong>G</strong></a> | <a href="#H"><strong>H</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#L"><strong>L</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#N"><strong>N</strong></a> | <a href="#O"><strong>O</strong></a> | <a href="#P"><strong>P</strong></a> | <a href="#Q"><strong>Q</strong></a> | <a href="#R"><strong>R</strong></a> | <a href="#S"><strong>S</strong></a> | <a href="#T"><strong>T</strong></a> | <a href="#V"><strong>V</strong></a> | <a href="#W"><strong>W</strong></a></div>
</section>
<section id="_" class="genindex-section">
<h2>_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.utils.ProteinGraphConfigurationError.__init__">__init__() (graphein.protein.utils.ProteinGraphConfigurationError method)</a>
</li>
</ul></td>
</tr></table>
</section>
<section id="A" class="genindex-section">
<h2>A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.aa_dipeptide_composition">aa_dipeptide_composition() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.AA_RING_ATOMS">AA_RING_ATOMS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.aa_spectrum">aa_spectrum() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.aaindex.aaindex1">aaindex1() (in module graphein.protein.features.nodes.aaindex)</a>
</li>
<li><a href="modules/graphein.rna.html#graphein.rna.edges.add_all_dotbracket_edges">add_all_dotbracket_edges() (in module graphein.rna.edges)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_aromatic_interactions">add_aromatic_interactions() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_aromatic_sulphur_interactions">add_aromatic_sulphur_interactions() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.edges.atomic.add_atom_bonds">add_atom_bonds() (in module graphein.molecule.edges.atomic)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.atomic.add_atomic_edges">add_atomic_edges() (in module graphein.protein.edges.atomic)</a>
</li>
<li><a href="modules/graphein.rna.html#graphein.rna.edges.add_base_pairing_interactions">add_base_pairing_interactions() (in module graphein.rna.edges)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.geometry.add_beta_carbon_vector">add_beta_carbon_vector() (in module graphein.protein.features.nodes.geometry)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.edges.add_biogrid_edges">add_biogrid_edges() (in module graphein.ppi.edges)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.graph_metadata.add_biogrid_metadata">add_biogrid_metadata() (in module graphein.ppi.graph_metadata)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.atomic.add_bond_order">add_bond_order() (in module graphein.protein.edges.atomic)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.edges.bonds.add_bond_type">add_bond_type() (in module graphein.molecule.features.edges.bonds)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_cation_pi_interactions">add_cation_pi_interactions() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.intramolecular.add_contacts_edge">add_contacts_edge() (in module graphein.protein.edges.intramolecular)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_delaunay_triangulation">add_delaunay_triangulation() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.edges.distance.add_distance_threshold">add_distance_threshold() (in module graphein.molecule.edges.distance)</a>
<ul>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_distance_threshold">(in module graphein.protein.edges.distance)</a>
</li>
</ul></li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_disulfide_interactions">add_disulfide_interactions() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.dssp.add_dssp_df">add_dssp_df() (in module graphein.protein.features.nodes.dssp)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.dssp.add_dssp_feature">add_dssp_feature() (in module graphein.protein.features.nodes.dssp)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.edges.distance.add_fully_connected_edges">add_fully_connected_edges() (in module graphein.molecule.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_hydrogen_bond_interactions">add_hydrogen_bond_interactions() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_hydrophobic_interactions">add_hydrophobic_interactions() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.grn.html#graphein.grn.edges.add_interacting_genes">add_interacting_genes() (in module graphein.grn.edges)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.edges.add_interacting_proteins">add_interacting_proteins() (in module graphein.ppi.edges)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_interacting_resis">add_interacting_resis() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_ionic_interactions">add_ionic_interactions() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.edges.distance.add_k_nn_edges">add_k_nn_edges() (in module graphein.molecule.edges.distance)</a>
<ul>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_k_nn_edges">(in module graphein.protein.edges.distance)</a>
</li>
</ul></li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.graphs.add_nodes_to_graph">add_nodes_to_graph() (in module graphein.molecule.graphs)</a>
<ul>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.add_nodes_to_graph">(in module graphein.protein.graphs)</a>
</li>
</ul></li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_peptide_bonds">add_peptide_bonds() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.rna.html#graphein.rna.edges.add_phosphodiester_bonds">add_phosphodiester_bonds() (in module graphein.rna.edges)</a>
</li>
<li><a href="modules/graphein.rna.html#graphein.rna.edges.add_pseudoknots">add_pseudoknots() (in module graphein.rna.edges)</a>
</li>
<li><a href="modules/graphein.grn.html#graphein.grn.edges.add_regnetwork_edges">add_regnetwork_edges() (in module graphein.grn.edges)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.atomic.add_ring_status">add_ring_status() (in module graphein.protein.edges.atomic)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.add_sequence_distance_edges">add_sequence_distance_edges() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.geometry.add_sequence_neighbour_vector">add_sequence_neighbour_vector() (in module graphein.protein.features.nodes.geometry)</a>
</li>
<li><a href="modules/graphein.grn.html#graphein.grn.features.node_features.add_sequence_to_nodes">add_sequence_to_nodes() (in module graphein.grn.features.node_features)</a>
<ul>
<li><a href="modules/graphein.ppi.html#graphein.ppi.features.node_features.add_sequence_to_nodes">(in module graphein.ppi.features.node_features)</a>
</li>
</ul></li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.geometry.add_sidechain_vector">add_sidechain_vector() (in module graphein.protein.features.nodes.geometry)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.graph_metadata.add_string_biogrid_metadata">add_string_biogrid_metadata() (in module graphein.ppi.graph_metadata)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.edges.add_string_edges">add_string_edges() (in module graphein.ppi.edges)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.graph_metadata.add_string_metadata">add_string_metadata() (in module graphein.ppi.graph_metadata)</a>
</li>
<li><a href="modules/graphein.grn.html#graphein.grn.edges.add_trrust_edges">add_trrust_edges() (in module graphein.grn.edges)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.visualisation.add_vector_to_plot">add_vector_to_plot() (in module graphein.protein.visualisation)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.utils.aggregate_graph_feature_over_chains">aggregate_graph_feature_over_chains() (in module graphein.protein.features.utils)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALL_BOND_TYPES">ALL_BOND_TYPES (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALL_BOND_TYPES_TO_CHANNEL">ALL_BOND_TYPES_TO_CHANNEL (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.all_composition_descriptors">all_composition_descriptors() (in module graphein.protein.features.sequence.propy)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.all_ctd_descriptors">all_ctd_descriptors() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.all_distribution_descriptors">all_distribution_descriptors() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALL_STEREO_TO_CHANNEL">ALL_STEREO_TO_CHANNEL (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALL_STEREO_TYPES">ALL_STEREO_TYPES (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.all_transition_descriptors">all_transition_descriptors() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALLOWED_BOND_TYPE_TO_CHANNEL">ALLOWED_BOND_TYPE_TO_CHANNEL (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALLOWED_BOND_TYPES">ALLOWED_BOND_TYPES (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALLOWED_DEGREES">ALLOWED_DEGREES (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALLOWED_HYBRIDIZATIONS">ALLOWED_HYBRIDIZATIONS (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALLOWED_NUM_H">ALLOWED_NUM_H (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.ALLOWED_VALENCES">ALLOWED_VALENCES (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.amino_acid_composition">amino_acid_composition() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.amino_acid.amino_acid_one_hot">amino_acid_one_hot() (in module graphein.protein.features.nodes.amino_acid)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.AMINO_ACIDS">AMINO_ACIDS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.annotate_edge_metadata">annotate_edge_metadata() (in module graphein.utils.utils)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.annotate_graph_metadata">annotate_graph_metadata() (in module graphein.utils.utils)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.annotate_node_features">annotate_node_features() (in module graphein.utils.utils)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.annotate_node_metadata">annotate_node_metadata() (in module graphein.utils.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.AROMATIC_RESIS">AROMATIC_RESIS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.dssp.asa">asa() (in module graphein.protein.features.nodes.dssp)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.atomic.assign_bond_states_to_dataframe">assign_bond_states_to_dataframe() (in module graphein.protein.edges.atomic)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.atomic.assign_covalent_radii_to_dataframe">assign_covalent_radii_to_dataframe() (in module graphein.protein.edges.atomic)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.assign_node_id_to_dataframe">assign_node_id_to_dataframe() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.visualisation.asteroid_plot">asteroid_plot() (in module graphein.protein.visualisation)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.nodes.atom_type.atom_type_one_hot">atom_type_one_hot() (in module graphein.molecule.features.nodes.atom_type)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.nodes.atom_type.atomic_mass">atomic_mass() (in module graphein.molecule.features.nodes.atom_type)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_all">autocorrelation_geary_all() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_av_flexibility">autocorrelation_geary_av_flexibility() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_free_energy">autocorrelation_geary_free_energy() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_hydrophobicity">autocorrelation_geary_hydrophobicity() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_mutability">autocorrelation_geary_mutability() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_polarizability">autocorrelation_geary_polarizability() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_residue_asa">autocorrelation_geary_residue_asa() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_residue_vol">autocorrelation_geary_residue_vol() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_geary_steric">autocorrelation_geary_steric() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_all">autocorrelation_moran_all() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_av_flexibility">autocorrelation_moran_av_flexibility() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_free_energy">autocorrelation_moran_free_energy() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_hydrophobicity">autocorrelation_moran_hydrophobicity() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_mutability">autocorrelation_moran_mutability() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_polarizability">autocorrelation_moran_polarizability() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_residue_asa">autocorrelation_moran_residue_asa() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_residue_vol">autocorrelation_moran_residue_vol() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_moran_steric">autocorrelation_moran_steric() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_all">autocorrelation_normalized_moreau_broto_all() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_av_flexibility">autocorrelation_normalized_moreau_broto_av_flexibility() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_free_energy">autocorrelation_normalized_moreau_broto_free_energy() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_hydrophobicity">autocorrelation_normalized_moreau_broto_hydrophobicity() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_mutability">autocorrelation_normalized_moreau_broto_mutability() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_polarizability">autocorrelation_normalized_moreau_broto_polarizability() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_residue_asa">autocorrelation_normalized_moreau_broto_residue_asa() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_residue_vol">autocorrelation_normalized_moreau_broto_residue_vol() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_normalized_moreau_broto_steric">autocorrelation_normalized_moreau_broto_steric() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.autocorrelation_total">autocorrelation_total() (in module graphein.protein.features.sequence.propy)</a>
</li>
</ul></td>
</tr></table>
</section>
<section id="B" class="genindex-section">
<h2>B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.BACKBONE_ATOMS">BACKBONE_ATOMS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.BASE_AMINO_ACIDS">BASE_AMINO_ACIDS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.BASE_ATOMS">BASE_ATOMS (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.parse_biogrid.BIOGRID_df">BIOGRID_df() (in module graphein.ppi.parse_biogrid)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.config.BioGridConfig">BioGridConfig (class in graphein.ppi.config)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.embeddings.biovec_sequence_embedding">biovec_sequence_embedding() (in module graphein.protein.features.sequence.embeddings)</a>, <a href="modules/graphein.protein.html#id0">[1]</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.edges.bonds.bond_is_aromatic">bond_is_aromatic() (in module graphein.molecule.features.edges.bonds)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.edges.bonds.bond_is_conjugated">bond_is_conjugated() (in module graphein.molecule.features.edges.bonds)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.edges.bonds.bond_is_in_ring">bond_is_in_ring() (in module graphein.molecule.features.edges.bonds)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.edges.bonds.bond_is_in_ring_size">bond_is_in_ring_size() (in module graphein.molecule.features.edges.bonds)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.BOND_LENGTHS">BOND_LENGTHS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.BOND_ORDERS">BOND_ORDERS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.edges.bonds.bond_stereo">bond_stereo() (in module graphein.molecule.features.edges.bonds)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.BOND_TYPES">BOND_TYPES (in module graphein.protein.resi_atoms)</a>
</li>
</ul></td>
</tr></table>
</section>
<section id="C" class="genindex-section">
<h2>C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.calculate_centroid_positions">calculate_centroid_positions() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.rna.html#graphein.rna.constants.CANONICAL_BASE_PAIRINGS">CANONICAL_BASE_PAIRINGS (in module graphein.rna.constants)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.CARBOHYDRATE_CODE_NAME_MAPPING">CARBOHYDRATE_CODE_NAME_MAPPING (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.CARBOHYDRATE_CODES">CARBOHYDRATE_CODES (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.CARBOHYDRATE_NAMES">CARBOHYDRATE_NAMES (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.CATION_PI_RESIS">CATION_PI_RESIS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.CATION_RESIS">CATION_RESIS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.rna.html#graphein.rna.edges.check_base_pairing_type">check_base_pairing_type() (in module graphein.rna.edges)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.meshes.check_for_pymol_installation">check_for_pymol_installation() (in module graphein.protein.meshes)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.nodes.atom_type.chiral_tag">chiral_tag() (in module graphein.molecule.features.nodes.atom_type)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.CHIRAL_TYPE">CHIRAL_TYPE (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.CHIRAL_TYPE_TO_CHANNEL">CHIRAL_TYPE_TO_CHANNEL (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.COFACTOR_CODE_NAME_MAPPING">COFACTOR_CODE_NAME_MAPPING (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.COFACTOR_CODES">COFACTOR_CODES (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.COFACTOR_NAMES">COFACTOR_NAMES (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.visualisation.colour_edges">colour_edges() (in module graphein.protein.visualisation)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.visualisation.colour_nodes">colour_nodes() (in module graphein.protein.visualisation)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.testing.utils.compare_approximate">compare_approximate() (in module graphein.testing.utils)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.testing.utils.compare_exact">compare_exact() (in module graphein.testing.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_charge">composition_charge() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_descriptor">composition_descriptor() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_hydrophobicity">composition_hydrophobicity() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_normalized_vdwv">composition_normalized_vdwv() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_polarity">composition_polarity() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_polarizability">composition_polarizability() (in module graphein.protein.features.sequence.propy)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_secondary_str">composition_secondary_str() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.composition_solvent_accessibility">composition_solvent_accessibility() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.compute_chain_graph">compute_chain_graph() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.edges.distance.compute_distmat">compute_distmat() (in module graphein.molecule.edges.distance)</a>
<ul>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.compute_distmat">(in module graphein.protein.edges.distance)</a>
</li>
</ul></li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.compute_edges">compute_edges() (in module graphein.protein.graphs)</a>
<ul>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.compute_edges">(in module graphein.utils.utils)</a>
</li>
</ul></li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.embeddings.compute_esm_embedding">compute_esm_embedding() (in module graphein.protein.features.sequence.embeddings)</a>, <a href="modules/graphein.protein.html#id3">[1]</a>
</li>
<li><a href="modules/graphein.grn.html#graphein.grn.graphs.compute_grn_graph">compute_grn_graph() (in module graphein.grn.graphs)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.graphs.compute_ppi_graph">compute_ppi_graph() (in module graphein.ppi.graphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.compute_propy_feature">compute_propy_feature() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.utils.compute_rgroup_dataframe">compute_rgroup_dataframe() (in module graphein.protein.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.compute_secondary_structure_graph">compute_secondary_structure_graph() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.compute_weighted_graph_from_multigraph">compute_weighted_graph_from_multigraph() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.config_parser.config_constructor">config_constructor() (in module graphein.utils.config_parser)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.meshes.configure_pymol_session">configure_pymol_session() (in module graphein.protein.meshes)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.graphs.construct_graph">construct_graph() (in module graphein.molecule.graphs)</a>
<ul>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.construct_graph">(in module graphein.protein.graphs)</a>
</li>
</ul></li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.construct_graphs_mp">construct_graphs_mp() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.rna.html#graphein.rna.graphs.construct_rna_graph">construct_rna_graph() (in module graphein.rna.graphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.utils.convert_graph_dict_feat_to_series">convert_graph_dict_feat_to_series() (in module graphein.protein.features.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.convert_structure_to_centroids">convert_structure_to_centroids() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.meshes.convert_verts_and_face_to_mesh">convert_verts_and_face_to_mesh() (in module graphein.protein.meshes)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.COVALENT_RADII">COVALENT_RADII (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.meshes.create_mesh">create_mesh() (in module graphein.protein.meshes)</a>
</li>
</ul></td>
</tr></table>
</section>
<section id="D" class="genindex-section">
<h2>D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.DEFAULT_BOND_STATE">DEFAULT_BOND_STATE (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.nodes.atom_type.degree">degree() (in module graphein.molecule.features.nodes.atom_type)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.deprotonate_structure">deprotonate_structure() (in module graphein.protein.graphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.dipeptide_composition">dipeptide_composition() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_charge">distribution_charge() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_descriptor">distribution_descriptor() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_hydrophobicity">distribution_hydrophobicity() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_normalized_vdwv">distribution_normalized_vdwv() (in module graphein.protein.features.sequence.propy)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_polarity">distribution_polarity() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_polarizability">distribution_polarizability() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_secondary_str">distribution_secondary_str() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.propy.distribution_solvent_accessibility">distribution_solvent_accessibility() (in module graphein.protein.features.sequence.propy)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.DISULFIDE_ATOMS">DISULFIDE_ATOMS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.DISULFIDE_RESIS">DISULFIDE_RESIS (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.utils.download_alphafold_structure">download_alphafold_structure() (in module graphein.protein.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.utils.download_pdb">download_pdb() (in module graphein.protein.utils)</a>
</li>
</ul></td>
</tr></table>
</section>
<section id="E" class="genindex-section">
<h2>E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.utils.html#graphein.testing.utils.edge_data_equal">edge_data_equal() (in module graphein.testing.utils)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.testing.utils.edges_equal">edges_equal() (in module graphein.testing.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.embeddings.esm_residue_embedding">esm_residue_embedding() (in module graphein.protein.features.sequence.embeddings)</a>, <a href="modules/graphein.protein.html#id4">[1]</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.sequence.embeddings.esm_sequence_embedding">esm_sequence_embedding() (in module graphein.protein.features.sequence.embeddings)</a>, <a href="modules/graphein.protein.html#id5">[1]</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.amino_acid.expasy_protein_scale">expasy_protein_scale() (in module graphein.protein.features.nodes.amino_acid)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.nodes.atom_type.explicit_valence">explicit_valence() (in module graphein.molecule.features.nodes.atom_type)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.atoms.EXTENDED_ATOMS">EXTENDED_ATOMS (in module graphein.molecule.atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_k_hop_subgraph">extract_k_hop_subgraph() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph">extract_subgraph() (in module graphein.protein.subgraphs)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_by_bond_type">extract_subgraph_by_bond_type() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_by_sequence_position">extract_subgraph_by_sequence_position() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_from_atom_types">extract_subgraph_from_atom_types() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_from_chains">extract_subgraph_from_chains() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_from_node_list">extract_subgraph_from_node_list() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_from_point">extract_subgraph_from_point() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_from_residue_types">extract_subgraph_from_residue_types() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_subgraph_from_secondary_structure">extract_subgraph_from_secondary_structure() (in module graphein.protein.subgraphs)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.subgraphs.extract_surface_subgraph">extract_surface_subgraph() (in module graphein.protein.subgraphs)</a>
</li>
</ul></td>
</tr></table>
</section>
<section id="F" class="genindex-section">
<h2>F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.protein.html#graphein.protein.features.nodes.aaindex.fetch_AAIndex">fetch_AAIndex() (in module graphein.protein.features.nodes.aaindex)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.parse_biogrid.filter_BIOGRID">filter_BIOGRID() (in module graphein.ppi.parse_biogrid)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.utils.filter_dataframe">filter_dataframe() (in module graphein.protein.utils)</a>
<ul>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.filter_dataframe">(in module graphein.utils.utils)</a>
</li>
</ul></li>
<li><a href="modules/graphein.protein.html#graphein.protein.graphs.filter_hetatms">filter_hetatms() (in module graphein.protein.graphs)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.grn.html#graphein.grn.parse_regnetwork.filter_RegNetwork">filter_RegNetwork() (in module graphein.grn.parse_regnetwork)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.parse_stringdb.filter_STRING">filter_STRING() (in module graphein.ppi.parse_stringdb)</a>
</li>
<li><a href="modules/graphein.grn.html#graphein.grn.parse_trrust.filter_TRRUST">filter_TRRUST() (in module graphein.grn.parse_trrust)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.features.nodes.atom_type.formal_charge">formal_charge() (in module graphein.molecule.features.nodes.atom_type)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.format_adjacency">format_adjacency() (in module graphein.utils.utils)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.config_parser.function_constructor">function_constructor() (in module graphein.utils.config_parser)</a>
</li>
</ul></td>
</tr></table>
</section>
<section id="G" class="genindex-section">
<h2>G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.generate_adjacency_tensor">generate_adjacency_tensor() (in module graphein.utils.utils)</a>
</li>
<li><a href="modules/graphein.utils.html#graphein.utils.utils.generate_feature_dataframe">generate_feature_dataframe() (in module graphein.utils.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.intramolecular.get_contacts_df">get_contacts_df() (in module graphein.protein.edges.intramolecular)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.visualisation.get_edge_trace">get_edge_trace() (in module graphein.ppi.visualisation)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.get_edges_by_bond_type">get_edges_by_bond_type() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.edges.distance.get_interacting_atoms">get_interacting_atoms() (in module graphein.molecule.edges.distance)</a>
<ul>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.get_interacting_atoms">(in module graphein.protein.edges.distance)</a>
</li>
</ul></li>
<li><a href="modules/graphein.utils.html#graphein.utils.config_parser.get_loader">get_loader() (in module graphein.utils.config_parser)</a>
</li>
<li><a href="modules/graphein.ppi.html#graphein.ppi.visualisation.get_node_trace">get_node_trace() (in module graphein.ppi.visualisation)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.meshes.get_obj_file">get_obj_file() (in module graphein.protein.meshes)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.utils.get_obsolete_mapping">get_obsolete_mapping() (in module graphein.protein.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.utils.get_protein_name_from_filename">get_protein_name_from_filename() (in module graphein.protein.utils)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.get_ring_atoms">get_ring_atoms() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.edges.distance.get_ring_centroids">get_ring_centroids() (in module graphein.protein.edges.distance)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.config.GetContactsConfig">GetContactsConfig (class in graphein.protein.config)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.resi_atoms.GRANTHAM_CHEMICAL_DISTANCE_MATRIX">GRANTHAM_CHEMICAL_DISTANCE_MATRIX (in module graphein.protein.resi_atoms)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.config.GranularityOpts">GranularityOpts (in module graphein.protein.config)</a>
</li>
<li><a href="modules/graphein.protein.html#graphein.protein.analysis.graph_summary">graph_summary() (in module graphein.protein.analysis)</a>
</li>
<li><a href="modules/graphein.molecule.html#graphein.molecule.config.GraphAtoms">GraphAtoms (in module graphein.molecule.config)</a>
<ul>
<li><a href="modules/graphein.protein.html#graphein.protein.config.GraphAtoms">(in module graphein.protein.config)</a>
</li>
</ul></li>
<li>
graphein.grn.config
<ul>
<li><a href="modules/graphein.grn.html#module-graphein.grn.config">module</a>
</li>
</ul></li>
<li>
graphein.grn.edges
<ul>
<li><a href="modules/graphein.grn.html#module-graphein.grn.edges">module</a>
</li>
</ul></li>
<li>
graphein.grn.features.node_features
<ul>
<li><a href="modules/graphein.grn.html#module-graphein.grn.features.node_features">module</a>
</li>
</ul></li>
<li>
graphein.grn.graphs
<ul>
<li><a href="modules/graphein.grn.html#module-graphein.grn.graphs">module</a>
</li>
</ul></li>
<li>
graphein.grn.parse_regnetwork
<ul>
<li><a href="modules/graphein.grn.html#module-graphein.grn.parse_regnetwork">module</a>
</li>
</ul></li>
<li>
graphein.grn.parse_trrust
<ul>
<li><a href="modules/graphein.grn.html#module-graphein.grn.parse_trrust">module</a>
</li>
</ul></li>
<li>
graphein.molecule.atoms
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.atoms">module</a>
</li>
</ul></li>
<li>
graphein.molecule.config
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.config">module</a>
</li>
</ul></li>
<li>
graphein.molecule.edges.atomic
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.edges.atomic">module</a>
</li>
</ul></li>
<li>
graphein.molecule.edges.distance
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.edges.distance">module</a>
</li>
</ul></li>
<li>
graphein.molecule.features.edges.bonds
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.features.edges.bonds">module</a>
</li>
</ul></li>
<li>
graphein.molecule.features.graph.molecule
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.features.graph.molecule">module</a>
</li>
</ul></li>
<li>
graphein.molecule.features.nodes.atom_type
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.features.nodes.atom_type">module</a>
</li>
</ul></li>
<li>
graphein.molecule.graphs
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.graphs">module</a>
</li>
</ul></li>
<li>
graphein.molecule.visualisation
<ul>
<li><a href="modules/graphein.molecule.html#module-graphein.molecule.visualisation">module</a>
</li>
</ul></li>
<li>
graphein.ppi.config
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.config">module</a>
</li>
</ul></li>
<li>
graphein.ppi.edges
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.edges">module</a>
</li>
</ul></li>
<li>
graphein.ppi.features.node_features
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.features.node_features">module</a>
</li>
</ul></li>
<li>
graphein.ppi.graph_metadata
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.graph_metadata">module</a>
</li>
</ul></li>
<li>
graphein.ppi.graphs
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.graphs">module</a>
</li>
</ul></li>
<li>
graphein.ppi.parse_biogrid
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.parse_biogrid">module</a>
</li>
</ul></li>
<li>
graphein.ppi.parse_stringdb
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.parse_stringdb">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
graphein.ppi.visualisation
<ul>
<li><a href="modules/graphein.ppi.html#module-graphein.ppi.visualisation">module</a>
</li>
</ul></li>
<li>
graphein.protein.analysis
<ul>
<li><a href="modules/graphein.protein.html#module-graphein.protein.analysis">module</a>
</li>
</ul></li>
<li>
graphein.protein.config
<ul>
<li><a href="modules/graphein.protein.html#module-graphein.protein.config">module</a>
</li>