Neurosnap SDK package

Subpackages

• neurosnap.algos namespace
  • Subpackages
    • neurosnap.algos.evoef2_lib namespace
      • Submodules
  • Submodules
    • neurosnap.algos.alphafold module
      • score_af2m_binding()
    • neurosnap.algos.amber_relax module
      • Requirements
      • Key functions
      • Notes & caveats
      • minimize()
    • neurosnap.algos.clusterprot module
      • ClusterProt()
      • animate_results()
      • create_figure_plotly()
    • neurosnap.algos.ec_interface module
      • Key features
      • compute_ec()
      • parse_chain_pairs()
      • write_single_chain_pdb()
    • neurosnap.algos.evoef2 module
      • AAppTable
      • Atom
      • AtomParam
      • Bond
      • Chain
      • CharmmIC
      • DunbrackBin
      • DunbrackLibrary
      • DunbrackRotamer
      • RamaTable
      • Residue
      • ResidueTopology
      • Structure
      • 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
      • calc_d0()
      • calc_d0_array()
      • calculate_ipSAE()
      • contiguous_ranges()
      • extract_interchain_metrics()
      • init_pairdict_array()
      • init_pairdict_scalar()
      • init_pairdict_set()
      • ptm_func()
    • neurosnap.algos.kluster module
      • check_alignment_tool()
      • cluster_projection()
      • compute_distance_matrix()
      • reduce_dimensions()
      • run_alignment()
      • visualize_projection()
      • visualize_projection_interactive()
    • neurosnap.algos.lddt module
      • calc_lddt()
    • neurosnap.algos.pdockq module
      • calculate_pDockQ()
• neurosnap.chemistry package
  • align_molecule_to_reference()
  • calculate_distance_matrix()
  • calculate_rmsd()
  • canonicalize_smiles()
  • find_LCS()
  • generate()
  • get_mol_center()
  • largest_fragment()
  • minimize()
  • move_ligand_to_center()
  • neutralize_molecule()
  • remove_salts()
  • sdf_to_smiles()
  • smiles_to_sdf()
  • standardize_molecule()
  • translate_molecule()
  • validate_smiles()
  • Submodules
    • neurosnap.chemistry.conformers module
      • find_LCS()
      • generate()
      • minimize()
    • neurosnap.chemistry.geometry module
      • align_molecule_to_reference()
      • calculate_distance_matrix()
      • calculate_rmsd()
      • get_mol_center()
      • move_ligand_to_center()
      • translate_molecule()
    • neurosnap.chemistry.smiles module
      • canonicalize_smiles()
      • largest_fragment()
      • neutralize_molecule()
      • remove_salts()
      • sdf_to_smiles()
      • smiles_to_sdf()
      • standardize_molecule()
      • validate_smiles()
• neurosnap.constants package
  • AARecord
    • AARecord.abr
    • AARecord.code
    • AARecord.is_standard
    • AARecord.name
    • AARecord.standard_equiv_abr
  • Submodules
    • neurosnap.constants.api module
    • neurosnap.constants.chemistry module
    • neurosnap.constants.sequence module
      • AARecord
    • neurosnap.constants.structure module
• neurosnap.database package
  • CCD
    • CCD.code
    • CCD.name
    • CCD.smiles
    • CCD.code
    • CCD.name
    • CCD.smiles
    • CCD.smiles_canonical()
    • CCD.to_mol()
  • fetch_accessions()
  • fetch_uniprot()
  • foldseek_search()
  • get_ccd()
  • get_ccd_entries()
  • run_blast()
  • Submodules
    • neurosnap.database.blast module
      • run_blast()
    • neurosnap.database.ccd module
      • CCD
      • get_ccd()
      • get_ccd_entries()
    • neurosnap.database.foldseek module
      • foldseek_search()
    • neurosnap.database.uniprot module
      • fetch_accessions()
      • fetch_uniprot()
• neurosnap.io namespace
  • Submodules
    • neurosnap.io.mmcif module
      • parse_mmcif()
      • save_cif()
    • neurosnap.io.pdb module
      • parse_pdb()
      • save_pdb()
    • neurosnap.io.sdf module
      • parse_sdf()
      • save_sdf()
• neurosnap.sequence package
  • Submodules
    • neurosnap.sequence.align module
      • align_mafft()
      • alignment_coverage()
      • consensus_sequence()
      • pad_seqs()
      • read_msa()
      • run_mmseqs2()
      • run_mmseqs2_modes()
      • run_phmmer()
      • run_phmmer_mafft()
      • seqid()
      • write_msa()
    • neurosnap.sequence.nucleotide module
      • get_reverse_complement()
      • split_interleaved_fastq()
    • neurosnap.sequence.protein module
      • getAA()
      • isoelectric_point()
      • molecular_weight()
      • net_charge()
      • sanitize_aa_seq()
• neurosnap.structure package
  • Atom
    • Atom.annotations
    • Atom.atom_name
    • Atom.chain_id
    • Atom.coord
    • Atom.element
    • Atom.hetero
    • Atom.ins_code
    • Atom.res_id
    • Atom.res_name
    • Atom.x
    • Atom.y
    • Atom.z
  • Chain
    • Chain.chain_id
    • Chain.__getitem__()
    • Chain.__iter__()
    • Chain.chain_id
    • Chain.missing_residue_ids()
    • Chain.residues()
    • Chain.sequence()
  • Residue
    • Residue.chain_id
    • Residue.res_id
    • Residue.ins_code
    • Residue.res_name
    • Residue.hetero
    • Residue.__eq__()
    • Residue.__hash__()
    • Residue.atom_indices()
    • Residue.atoms()
    • Residue.chain_id
    • Residue.hetero
    • Residue.ins_code
    • Residue.key()
    • Residue.res_id
    • Residue.res_name
  • Structure
    • Structure.__getitem__()
    • Structure.__init__()
    • Structure.__iter__()
    • Structure.__len__()
    • Structure.__repr__()
    • Structure.add_annotation()
    • Structure.calculate_center_of_mass()
    • Structure.calculate_geometric_center()
    • Structure.calculate_rog()
    • Structure.center_at()
    • Structure.chain_ids()
    • Structure.chains()
    • Structure.distances_from()
    • Structure.remove_annotation()
    • Structure.renumber()
    • Structure.to_dataframe()
    • Structure.translate()
  • StructureEnsemble
    • StructureEnsemble.__getitem__()
    • StructureEnsemble.__init__()
    • StructureEnsemble.__iter__()
    • StructureEnsemble.__len__()
    • StructureEnsemble.__repr__()
    • StructureEnsemble.append()
    • StructureEnsemble.first()
    • StructureEnsemble.models()
    • StructureEnsemble.remove_model()
    • StructureEnsemble.renumber()
    • StructureEnsemble.to_dataframe()
    • StructureEnsemble.to_stack()
  • StructureStack
    • StructureStack.__getitem__()
    • StructureStack.__init__()
    • StructureStack.__iter__()
    • StructureStack.__len__()
    • StructureStack.__repr__()
    • StructureStack.append()
    • StructureStack.atom_count
    • StructureStack.first()
    • StructureStack.from_ensemble()
    • StructureStack.models()
    • StructureStack.remove_model()
    • StructureStack.renumber()
    • StructureStack.to_dataframe()
    • StructureStack.to_ensemble()
  • align()
  • 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()
  • remove_atoms()
  • remove_chains()
  • remove_non_biopolymers()
  • remove_nucleotides()
  • remove_waters()
  • render_pseudo3D()
  • render_structure_pseudo3D()
  • select_residues()
  • Submodules
    • neurosnap.structure.analysis module
      • ca_distance_matrix()
      • calculate_distance_matrix()
      • calculate_protein_volume()
      • calculate_surface_area()
      • extract_non_biopolymers()
      • get_backbone()
    • neurosnap.structure.compare module
      • align()
      • calculate_rmsd()
    • neurosnap.structure.filters module
      • fix_nucleic_termini()
      • remove_atoms()
      • remove_chains()
      • remove_non_biopolymers()
      • remove_nucleotides()
      • remove_residues()
      • remove_waters()
    • neurosnap.structure.interactions module
      • calculate_hydrogen_bonds()
      • calculate_interface_hydrogen_bonding_residues()
      • find_disulfide_bonds()
      • find_hydrophobic_residues()
      • find_salt_bridges()
    • neurosnap.structure.interface module
      • calculate_bsa()
      • find_contacts()
      • find_interface_contacts()
      • find_interface_residues()
      • find_non_interface_hydrophobic_patches()
    • neurosnap.structure.rendering module
      • animate_frames()
      • render_pseudo3D()
      • render_structure_pseudo3D()
    • neurosnap.structure.selectors module
      • select_residues()
    • neurosnap.structure.structure module
      • Atom
      • Chain
      • Residue
      • Structure
      • StructureEnsemble
      • StructureStack

Submodules

• neurosnap.api module
  • NeurosnapAPI
    • NeurosnapAPI.BASE_URL
    • NeurosnapAPI.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
  • CustomLogger
    • CustomLogger.format()
    • CustomLogger.log_format_basic
    • CustomLogger.log_format_detailed
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    • c.br
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    • c.grey
    • c.o
    • c.p
    • c.r
    • c.y