neurosnap.algos namespace

Subpackages

• neurosnap.algos.evoef2_lib namespace
  • Submodules
    • neurosnap.algos.evoef2_lib.constants module
    • neurosnap.algos.evoef2_lib.weights module
      • get_weights()

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
    • AAppTable.aap
  • Atom
    • Atom.name
    • Atom.param
    • Atom.chain
    • Atom.pos
    • Atom.res
    • Atom.xyz
    • Atom.is_xyz_valid
    • Atom.is_in_hbond
    • Atom.__post_init__()
    • Atom.chain
    • Atom.charge
    • Atom.eef1_free_dg
    • Atom.eef1_lambda
    • Atom.eef1_volume
    • Atom.hb_b2
    • Atom.hb_d_or_b
    • Atom.hb_h_or_a
    • Atom.hybrid
    • Atom.is_bb
    • Atom.is_h
    • Atom.is_hbond_a
    • Atom.is_hbond_h
    • Atom.is_in_hbond
    • Atom.is_xyz_valid
    • Atom.name
    • Atom.param
    • Atom.polarity
    • Atom.pos
    • Atom.res
    • Atom.vdw_epsilon
    • Atom.vdw_radius
    • Atom.xyz
  • AtomParam
    • AtomParam.name
    • AtomParam.type
    • AtomParam.is_bb
    • AtomParam.polarity
    • AtomParam.epsilon
    • AtomParam.radius
    • AtomParam.charge
    • AtomParam.hb_h_or_a
    • AtomParam.hb_d_or_b
    • AtomParam.hb_b2
    • AtomParam.hybrid
    • AtomParam.eef1_free_dg
    • AtomParam.eef1_volume
    • AtomParam.eef1_lambda
    • AtomParam.charge
    • AtomParam.eef1_free_dg
    • AtomParam.eef1_lambda
    • AtomParam.eef1_volume
    • AtomParam.epsilon
    • AtomParam.hb_b2
    • AtomParam.hb_d_or_b
    • AtomParam.hb_h_or_a
    • AtomParam.hybrid
    • AtomParam.is_bb
    • AtomParam.is_hbond_a
    • AtomParam.is_hbond_h
    • AtomParam.name
    • AtomParam.polarity
    • AtomParam.radius
    • AtomParam.type
  • Bond
    • Bond.a
    • Bond.b
    • Bond.bond_type
  • Chain
    • Chain.is_protein
    • Chain.name
    • Chain.residues
  • CharmmIC
    • CharmmIC.atom_a
    • CharmmIC.atom_b
    • CharmmIC.atom_c
    • CharmmIC.atom_d
    • CharmmIC.ic_param
    • CharmmIC.torsion_proper
  • DunbrackBin
    • DunbrackBin.by_residue
  • DunbrackLibrary
    • DunbrackLibrary.bins
  • DunbrackRotamer
    • DunbrackRotamer.deviations
    • DunbrackRotamer.probability
    • DunbrackRotamer.torsions
  • RamaTable
    • RamaTable.rama
  • Residue
    • Residue.atoms
    • Residue.bonds
    • Residue.chain
    • Residue.get_atom()
    • Residue.is_nucleic
    • Residue.is_protein
    • Residue.n_cb_in_8a
    • Residue.na_torsions
    • Residue.name
    • Residue.patches
    • Residue.phipsi
    • Residue.pos
    • Residue.xtorsions
  • ResidueTopology
    • ResidueTopology.atoms
    • ResidueTopology.bonds
    • ResidueTopology.deletes
    • ResidueTopology.ics
    • ResidueTopology.name
  • Structure
    • Structure.all_residues()
    • Structure.chains
  • 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()