ampal

• ampal package
  • Submodules
  • ampal.align module
    • MMCAlign
      • MMCAlign.check_move()
      • MMCAlign.float_f()
      • MMCAlign.start_optimisation()
    • align_backbones()
  • ampal.amino_acids module
    • add_amino_acid_to_json()
    • get_aa_code()
    • get_aa_info()
    • get_aa_letter()
  • ampal.ampal_warnings module
    • DependencyNotFoundWarning
    • MalformedPDBWarning
    • NoncanonicalWarning
    • NotParameterisedWarning
    • check_availability()
  • ampal.analyse_protein module
    • alpha_angles()
    • cc_to_local_params()
    • charge_series()
    • classify_angle_as_rotamer()
    • crick_angles()
    • flip_reference_axis_if_antiparallel()
    • make_primitive()
    • make_primitive_extrapolate_ends()
    • make_primitive_smoothed()
    • measure_sidechain_torsion_angles()
    • measure_torsion_angles()
    • partial_charge()
    • polymer_to_reference_axis_distances()
    • polypeptide_vector()
    • reference_axis_from_chains()
    • residues_per_turn()
    • sequence_charge()
    • sequence_isoelectric_point()
    • sequence_molar_extinction_280()
    • sequence_molecular_weight()
  • ampal.assembly module
    • AmpalContainer
      • AmpalContainer.id
      • AmpalContainer.append()
      • AmpalContainer.extend()
      • AmpalContainer.pdb
      • AmpalContainer.sort_by_tag()
    • Assembly
      • Assembly.append()
      • Assembly.backbone
      • Assembly.extend()
      • Assembly.fasta
      • Assembly.filter_mol_types()
      • Assembly.get_atoms()
      • Assembly.get_ligands()
      • Assembly.get_monomers()
      • Assembly.is_within()
      • Assembly.isoelectric_point
      • Assembly.make_pdb()
      • Assembly.molar_extinction_280
      • Assembly.molecular_weight
      • Assembly.pdb
      • Assembly.primitives
      • Assembly.relabel_all()
      • Assembly.relabel_atoms()
      • Assembly.relabel_monomers()
      • Assembly.relabel_polymers()
      • Assembly.sequences
      • Assembly.tag_ca_geometry()
      • Assembly.tag_torsion_angles()
  • ampal.base_ampal module
    • Atom
      • Atom.id
      • Atom.res_label
      • Atom.element
      • Atom.parent
      • Atom.tags
      • Atom.array
      • Atom.rotate()
      • Atom.translate()
      • Atom.unique_id
      • Atom.x
      • Atom.y
      • Atom.z
    • BaseAmpal
      • BaseAmpal.centre_of_mass
      • BaseAmpal.get_atoms()
      • BaseAmpal.is_within()
      • BaseAmpal.make_pdb()
      • BaseAmpal.pdb
      • BaseAmpal.rmsd()
      • BaseAmpal.rotate()
      • BaseAmpal.translate()
    • Monomer
      • Monomer.states
      • Monomer.id
      • Monomer.parent
      • Monomer.tags
      • Monomer.active_state
      • Monomer.atoms
      • Monomer.close_monomers()
      • Monomer.get_atoms()
      • Monomer.get_monomers()
      • Monomer.make_pdb()
    • Polymer
      • Polymer.id
      • Polymer.parent
      • Polymer.molecule_type
      • Polymer.ligands
      • Polymer.tags
      • Polymer.sl
      • Polymer.append()
      • Polymer.extend()
      • Polymer.get_atoms()
      • Polymer.get_monomers()
      • Polymer.get_reference_coords()
      • Polymer.make_pdb()
      • Polymer.relabel_all()
      • Polymer.relabel_atoms()
      • Polymer.relabel_monomers()
    • cap()
    • centre_of_atoms()
    • find_atoms_within_distance()
    • write_pdb()
  • ampal.data module
  • ampal.dssp module
    • dssp_available()
    • extract_all_ss_dssp()
    • find_ss_regions()
    • get_ss_regions()
    • run_dssp()
    • tag_dssp_data()
  • ampal.geometry module
    • Axis
      • Axis.arc_length()
      • Axis.direction_vector
      • Axis.distance_to_point()
      • Axis.get_coords()
      • Axis.length
      • Axis.midpoint
      • Axis.point()
      • Axis.t_from_arc_length()
      • Axis.unit_binormal
      • Axis.unit_normal
      • Axis.unit_tangent
    • Curve
      • Curve.point()
    • HelicalCurve
      • HelicalCurve.alpha
      • HelicalCurve.alpha_and_pitch()
      • HelicalCurve.alpha_and_radius()
      • HelicalCurve.arc_length()
      • HelicalCurve.axis
      • HelicalCurve.curvature()
      • HelicalCurve.get_coords()
      • HelicalCurve.pitch
      • HelicalCurve.pitch_and_radius()
      • HelicalCurve.point()
      • HelicalCurve.radius
      • HelicalCurve.t_from_arc_length()
      • HelicalCurve.torsion()
      • HelicalCurve.unit_binormal()
      • HelicalCurve.unit_normal()
      • HelicalCurve.unit_tangent()
      • HelicalCurve.x()
      • HelicalCurve.y()
      • HelicalCurve.z()
    • Quaternion
      • Quaternion.angle_and_axis()
      • Quaternion.apply_conjugation()
      • Quaternion.as_array
      • Quaternion.as_rotation()
      • Quaternion.conjugate
      • Quaternion.distance()
      • Quaternion.extract_angle_and_axis()
      • Quaternion.norm
      • Quaternion.real_and_vector()
      • Quaternion.rotate_vector()
      • Quaternion.vector
    • angle_between_vectors()
    • apply_unit_quaternion()
    • cartesian_to_cylindrical()
    • cartesian_to_spherical()
    • centre_of_mass()
    • closest_distance()
    • closest_points_on_lines()
    • cylindrical_to_cartesian()
    • dihedral()
    • distance()
    • find_foot()
    • find_foot_on_plane()
    • find_limits()
    • find_transformations()
    • gen_sectors()
    • intersection_start_and_end()
    • is_acute()
    • minimal_distance_between_lines()
    • points_on_a_circle()
    • radius_of_circumcircle()
    • rmsd()
    • rotation_matrix()
    • spherical_to_cartesian()
    • unit_vector()
  • ampal.interactions module
    • CovalentBond
      • CovalentBond.a
      • CovalentBond.b
    • HydrogenBond
      • HydrogenBond.donor
      • HydrogenBond.acceptor
      • HydrogenBond.dist
      • HydrogenBond.ang_a
      • HydrogenBond.ang_d
      • HydrogenBond.acceptor_monomer
      • HydrogenBond.donor_monomer
    • Interaction
      • Interaction.a
      • Interaction.b
      • Interaction.dist
    • NonCovalentInteraction
      • NonCovalentInteraction.donor
      • NonCovalentInteraction.acceptor
      • NonCovalentInteraction.dist
      • NonCovalentInteraction.acceptor
      • NonCovalentInteraction.donor
    • covalent_bonds()
    • find_covalent_bonds()
    • generate_bond_subgraphs_from_break()
    • generate_covalent_bond_graph()
  • ampal.ligands module
    • Ligand
      • Ligand.atoms
      • Ligand.mol_code
      • Ligand.insertion_code
      • Ligand.is_hetero
      • Ligand.id
      • Ligand.parent
      • Ligand.tags
    • Ligand.self.states
    • LigandGroup
  • ampal.nucleic_acid module
    • Nucleotide
      • Nucleotide.mol_code
      • Nucleotide.insertion_code
      • Nucleotide.is_hetero
      • Nucleotide.states
      • Nucleotide.id
      • Nucleotide.reference_atom
      • Nucleotide.parent
      • Nucleotide.tags
    • Polynucleotide
      • Polynucleotide.id
      • Polynucleotide.parent
      • Polynucleotide.molecule_type
      • Polynucleotide.ligands
      • Polynucleotide.tags
      • Polynucleotide.sl
      • Polynucleotide.sequence
  • ampal.pdb_parser module
    • PdbParser
      • PdbParser.proc_functions
      • PdbParser.id
      • PdbParser.pdb_lines
      • PdbParser.new_labels
      • PdbParser.state
      • PdbParser.pdb_parse_tree
      • PdbParser.current_line
      • PdbParser.ignore_end
      • PdbParser.change_state()
      • PdbParser.check_for_non_canonical()
      • PdbParser.end()
      • PdbParser.gen_states()
      • PdbParser.make_ampal()
      • PdbParser.parse_pdb_file()
      • PdbParser.proc_atom()
      • PdbParser.proc_chain()
      • PdbParser.proc_line_coordinate()
      • PdbParser.proc_monomer()
      • PdbParser.proc_state()
    • load_pdb()
  • ampal.protein module
    • Polypeptide
      • Polypeptide.id
      • Polypeptide.parent
      • Polypeptide.molecule_type
      • Polypeptide.ligands
      • Polypeptide.tags
      • Polypeptide.sl
      • Polypeptide.backbone
      • Polypeptide.backbone_bond_angles
      • Polypeptide.backbone_bond_lengths
      • Polypeptide.c_join()
      • Polypeptide.fasta
      • Polypeptide.get_slice_from_res_id()
      • Polypeptide.isoelectric_point
      • Polypeptide.molar_extinction_280
      • Polypeptide.molecular_weight
      • Polypeptide.n_join()
      • Polypeptide.primitive
      • Polypeptide.radii_of_curvature()
      • Polypeptide.rise_per_residue()
      • Polypeptide.sequence
      • Polypeptide.tag_ca_geometry()
      • Polypeptide.tag_sidechain_dihedrals()
      • Polypeptide.tag_torsion_angles()
      • Polypeptide.valid_backbone_bond_angles()
      • Polypeptide.valid_backbone_bond_lengths()
    • Residue
      • Residue.mol_code
      • Residue.insertion_code
      • Residue.is_hetero
      • Residue.states
      • Residue.id
      • Residue.reference_atom
      • Residue.parent
      • Residue.tags
      • Residue.backbone
      • Residue.centroid
      • Residue.side_chain
      • Residue.unique_id
    • align()
    • flat_list_to_dummy_chain()
    • flat_list_to_polymer()
  • ampal.pseudo_atoms module
    • Primitive
      • Primitive.mol_code
      • Primitive.insertion_code
      • Primitive.is_hetero
      • Primitive.states
      • Primitive.id
      • Primitive.reference_atom
      • Primitive.parent
      • Primitive.tags
      • Primitive.coordinates
      • Primitive.from_coordinates()
      • Primitive.radii_of_curvature()
      • Primitive.rise_per_residue()
    • PseudoAtom
      • PseudoAtom.id
      • PseudoAtom.res_label
      • PseudoAtom.element
      • PseudoAtom.parent
      • PseudoAtom.tags
    • PseudoGroup
      • PseudoGroup.id
      • PseudoGroup.parent
      • PseudoGroup.molecule_type
      • PseudoGroup.ligands
      • PseudoGroup.tags
      • PseudoGroup.sl
    • PseudoMonomer
      • PseudoMonomer.mol_code
      • PseudoMonomer.insertion_code
      • PseudoMonomer.is_hetero
      • PseudoMonomer.states
      • PseudoMonomer.id
      • PseudoMonomer.reference_atom
      • PseudoMonomer.parent
      • PseudoMonomer.tags
      • PseudoMonomer.pdb
  • Module contents