Neurosnap SDK package

Subpackages

• neurosnap.algos namespace
  • Subpackages
    • neurosnap.algos.evoef2_lib namespace
      • Submodules
  • Submodules
    • neurosnap.algos.LDDT module
      • calc_lddt()
    • 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.pdockq module
      • calculate_pDockQ()

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.chemicals module
  • fetch_ccd()
  • get_ccds()
  • get_mol_center()
  • move_ligand_to_center()
  • sdf_to_smiles()
  • smiles_to_sdf()
  • validate_smiles()
• neurosnap.conformers module
  • find_LCS()
  • generate()
  • minimize()
• neurosnap.constants module
  • AARecord
    • AARecord.abr
    • AARecord.code
    • AARecord.is_standard
    • AARecord.name
    • AARecord.standard_equiv_abr
• neurosnap.log module
  • CustomLogger
    • CustomLogger.format()
    • CustomLogger.log_format_basic
    • CustomLogger.log_format_detailed
  • c
    • c.b
    • c.br
    • c.c
    • c.g
    • c.grey
    • c.o
    • c.p
    • c.r
    • c.y
• neurosnap.msa 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.nucleotide module
  • get_reverse_complement()
  • split_interleaved_fastq()
• neurosnap.protein module
  • Protein
    • Protein.__call__()
    • Protein.__sub__()
    • Protein.align()
    • Protein.calculate_center_of_mass()
    • Protein.calculate_distance_matrix()
    • Protein.calculate_hydrogen_bonds()
    • Protein.calculate_interface_hydrogen_bonding_residues()
    • Protein.calculate_protein_volume()
    • Protein.calculate_rmsd()
    • Protein.calculate_rog()
    • Protein.calculate_surface_area()
    • Protein.center()
    • Protein.chains()
    • Protein.distances_from_com()
    • Protein.find_disulfide_bonds()
    • Protein.find_hydrophobic_residues()
    • Protein.find_interface_contacts()
    • Protein.find_interface_residues()
    • Protein.find_missing_residues()
    • Protein.find_non_interface_hydrophobic_patches()
    • Protein.find_salt_bridges()
    • Protein.generate_df()
    • Protein.get_aas()
    • Protein.get_backbone()
    • Protein.models()
    • Protein.remove()
    • Protein.remove_non_biopolymers()
    • Protein.remove_nucleotides()
    • Protein.remove_waters()
    • Protein.renumber()
    • Protein.save()
    • Protein.select_residues()
    • Protein.to_sdf()
  • calculate_bsa()
  • extract_non_biopolymers()
  • fetch_accessions()
  • fetch_uniprot()
  • find_contacts()
  • foldseek_search()
  • getAA()
  • isoelectric_point()
  • molecular_weight()
  • net_charge()
  • run_blast()
  • sanitize_aa_seq()
• neurosnap.rendering module
  • animate_frames()
  • render_protein_pseudo3D()
  • render_pseudo3D()