Neurosnap SDK package#
Subpackages#
- neurosnap.algos namespace
- Subpackages
- Submodules
- neurosnap.algos.alphafold module
- neurosnap.algos.amber_relax module
- neurosnap.algos.clusterprot module
- neurosnap.algos.ec_interface module
- neurosnap.algos.evoef2 module
AAppTableAtomAtomParamBondChainCharmmICDunbrackBinDunbrackLibraryDunbrackRotamerMutationRamaTableResidueResidueTopologyStructurebuild_mutant()build_mutants()calculate_binding()calculate_interface_energy()calculate_stability()load_aapropensity()load_atom_params()load_dunbrack()load_ramachandran()load_topology()rebuild_missing_atoms()
- neurosnap.algos.ipsae module
- neurosnap.algos.kluster module
- neurosnap.algos.lddt module
- neurosnap.algos.pdb2pqr module
- neurosnap.algos.pdockq module
- neurosnap.chemistry package
CharacterizationReportChemicalGraphChemicalGraph.adjacency()ChemicalGraph.average_path_length()ChemicalGraph.connected_components()ChemicalGraph.count_edges()ChemicalGraph.count_nodes()ChemicalGraph.degrees()ChemicalGraph.edges_of_type()ChemicalGraph.from_dict()ChemicalGraph.label()ChemicalGraph.n_edgesChemicalGraph.n_nodesChemicalGraph.neighborhood()ChemicalGraph.neighbors()ChemicalGraph.node_id_of_compound()ChemicalGraph.node_id_of_smiles()ChemicalGraph.nodes_of_type()ChemicalGraph.pagerank()ChemicalGraph.shortest_path()ChemicalGraph.to_dict()ChemicalGraph.weighted_adjacency()
ChemicalLandscapeChemicalLandscape.build_all()ChemicalLandscape.build_fragments()ChemicalLandscape.build_scaffolds()ChemicalLandscape.build_similarity_graph()ChemicalLandscape.characterize()ChemicalLandscape.common_cores()ChemicalLandscape.compound_idsChemicalLandscape.decompose()ChemicalLandscape.enumerate()ChemicalLandscape.export_graphml()ChemicalLandscape.export_json()ChemicalLandscape.failuresChemicalLandscape.fingerprintsChemicalLandscape.from_store()ChemicalLandscape.graphChemicalLandscape.island_of()ChemicalLandscape.load()ChemicalLandscape.neighbors()ChemicalLandscape.node_of()ChemicalLandscape.path_between()ChemicalLandscape.plot()ChemicalLandscape.reassemble()ChemicalLandscape.reportChemicalLandscape.rgroups_at()ChemicalLandscape.save()ChemicalLandscape.smilesChemicalLandscape.swap_rgroup()
EdgeTypeFingerprintConfigFragmentConfigFragmentMethodLandscapeConfigLandscapeConfig.chunk_sizeLandscapeConfig.delimiterLandscapeConfig.fingerprintsLandscapeConfig.fragmentsLandscapeConfig.from_dict()LandscapeConfig.id_columnLandscapeConfig.limitLandscapeConfig.scaffoldsLandscapeConfig.similarityLandscapeConfig.smiles_columnLandscapeConfig.to_dict()LandscapeConfig.workers
NodeTypeRGroupDecompositionResultReverseFragmentRecordScaffoldConfigSimilarityConfigalign_molecule_to_reference()attach_rgroup()calculate_distance_matrix()calculate_rmsd()canonicalize_smiles()decompose_molecules()enumerate_core()find_LCS()generate()get_mol_center()largest_fragment()minimize()move_ligand_to_center()neutralize_molecule()reassemble_fragments()remove_salts()reversible_fragment_record()sdf_to_smiles()smiles_to_sdf()standardize_molecule()translate_molecule()validate_smiles()- Submodules
- neurosnap.chemistry.conformers module
- neurosnap.chemistry.geometry module
- neurosnap.chemistry.landscape module
CharacterizationReportChemicalGraphChemicalLandscapeDiversityMetricsEdgeTypeFingerprintBlockFingerprintConfigFragmentConfigFragmentMethodFragmentResultGraphBuilderIslandResultLandscapeConfigNetworkMetricsNodeTypeRGroupDecompositionResultReverseFragmentRecordScaffoldConfigScaffoldNetworkResultSimilarityConfigapply_reversible_cut()attach_rgroup()build_similarity_edges()characterize()decompose_molecules()detect_islands()diversity_metrics()enumerate_core()export_graphml()export_json()fragment_cut_bonds()fragment_library()fragment_molecule()frontier_scaffolds()load_landscape()louvain_local_moving()minhash_signatures()morgan_packed()murcko_smiles()network_metrics()popcount_rows()popcount_words()reassemble_fragments()reversible_fragment_record()save_landscape()scaffold_network()shannon_entropy()shared_fragment_edges()stream_chunks()
- neurosnap.chemistry.smiles module
- neurosnap.constants package
- neurosnap.database package
- neurosnap.io namespace
- neurosnap.sequence package
- neurosnap.structure package
AtomAtomReferenceBondTypeChainCoordinationCenterRecordCoordinationCenterRecord.atom_nameCoordinationCenterRecord.center_idCoordinationCenterRecord.chainCoordinationCenterRecord.coordination_numberCoordinationCenterRecord.donor_atom_indicesCoordinationCenterRecord.donor_elementsCoordinationCenterRecord.elementCoordinationCenterRecord.entityCoordinationCenterRecord.evidenceCoordinationCenterRecord.geometryCoordinationCenterRecord.geometry_deviation_degCoordinationCenterRecord.ins_codeCoordinationCenterRecord.metal_atom_indexCoordinationCenterRecord.model_idCoordinationCenterRecord.res_idCoordinationCenterRecord.res_nameCoordinationCenterRecord.rule_setCoordinationCenterRecord.rule_version
InteractionEntityInteractionRecordInteractionRecord.angle_degInteractionRecord.atom_index1InteractionRecord.atom_index2InteractionRecord.atom_name1InteractionRecord.atom_name2InteractionRecord.chain1InteractionRecord.chain2InteractionRecord.detailsInteractionRecord.distance_aInteractionRecord.element1InteractionRecord.element2InteractionRecord.entity1InteractionRecord.entity2InteractionRecord.evidenceInteractionRecord.ins_code1InteractionRecord.ins_code2InteractionRecord.interaction_idInteractionRecord.interaction_typeInteractionRecord.model_idInteractionRecord.res_id1InteractionRecord.res_id2InteractionRecord.res_name1InteractionRecord.res_name2InteractionRecord.role1InteractionRecord.role2InteractionRecord.rule_setInteractionRecord.rule_versionInteractionRecord.sourceInteractionRecord.vdw_gap_a
InteractionReportInteractionTypePLDDTReportResidueStructureStructure.__getitem__()Structure.__init__()Structure.__iter__()Structure.__len__()Structure.__repr__()Structure.add_annotation()Structure.add_atom()Structure.add_atoms()Structure.add_bond()Structure.add_bonds()Structure.add_interaction()Structure.add_interactions()Structure.annotation_namesStructure.calculate_center_of_mass()Structure.calculate_geometric_center()Structure.calculate_rog()Structure.center_at()Structure.chain_ids()Structure.chains()Structure.detect_coordination_centers()Structure.detect_interactions()Structure.distances_from()Structure.empty_like()Structure.entitiesStructure.get_raw_contacts()Structure.num_atomsStructure.remove_annotation()Structure.renumber()Structure.save_cif()Structure.save_pdb()Structure.select()Structure.to_dataframe()Structure.translate()Structure.validate_entities()
StructureEnsembleStructureEnsemble.__getitem__()StructureEnsemble.__init__()StructureEnsemble.__iter__()StructureEnsemble.__len__()StructureEnsemble.__repr__()StructureEnsemble.append()StructureEnsemble.first()StructureEnsemble.models()StructureEnsemble.remove_model()StructureEnsemble.renumber()StructureEnsemble.save_cif()StructureEnsemble.save_pdb()StructureEnsemble.select()StructureEnsemble.to_dataframe()StructureEnsemble.to_stack()
StructureStackStructureStack.__getitem__()StructureStack.__init__()StructureStack.__iter__()StructureStack.__len__()StructureStack.__repr__()StructureStack.append()StructureStack.atom_countStructureStack.first()StructureStack.from_ensemble()StructureStack.models()StructureStack.remove_model()StructureStack.renumber()StructureStack.save_cif()StructureStack.save_pdb()StructureStack.select()StructureStack.to_dataframe()StructureStack.to_ensemble()
add_hydrogens_with_pdb2pqr()add_terminal_capping_groups()align()analyze_interactions()animate_frames()ca_distance_matrix()calculate_bsa()calculate_distance_matrix()calculate_hydrogen_bonds()calculate_interface_hydrogen_bonding_residues()calculate_protein_volume()calculate_rmsd()calculate_surface_area()extract_non_biopolymers()find_contacts()find_disulfide_bonds()find_hydrophobic_residues()find_interface_contacts()find_interface_residues()find_non_interface_hydrophobic_patches()find_salt_bridges()fix_nucleic_termini()get_backbone()has_hydrogens()optimize_hydrogens_with_pdb2pqr()remove_altlocs_and_duplicate_atoms()remove_atoms()remove_chains()remove_non_biopolymers()remove_nucleotides()remove_waters()render_pseudo3D()render_structure_pseudo3D()select_residues()strip_hydrogens()summarize_plddt()- Submodules
- neurosnap.structure.analysis module
- neurosnap.structure.compare module
- neurosnap.structure.confidence module
- neurosnap.structure.filters module
- neurosnap.structure.interaction_report module
- neurosnap.structure.interaction_rules module
- neurosnap.structure.interactions module
- neurosnap.structure.interface module
- neurosnap.structure.prepare module
- neurosnap.structure.rendering module
- neurosnap.structure.selectors module
- neurosnap.structure.structure module
Submodules#
- neurosnap.api module
NeurosnapAPINeurosnapAPI.BASE_URLNeurosnapAPI.delete_job_share()NeurosnapAPI.get_job_data()NeurosnapAPI.get_job_file()NeurosnapAPI.get_job_status()NeurosnapAPI.get_jobs()NeurosnapAPI.get_pipeline()NeurosnapAPI.get_services()NeurosnapAPI.get_team_info()NeurosnapAPI.get_team_jobs()NeurosnapAPI.set_job_note()NeurosnapAPI.set_job_share()NeurosnapAPI.submit_job()NeurosnapAPI.wait_job_status()
- neurosnap.log module