Index

A

a (ampal.interactions.CovalentBond property) (ampal.interactions.Interaction attribute) acceptor (ampal.interactions.HydrogenBond attribute) (ampal.interactions.NonCovalentInteraction attribute) (ampal.interactions.NonCovalentInteraction property) acceptor_monomer (ampal.interactions.HydrogenBond property) active_state (ampal.base_ampal.Monomer property) add_amino_acid_to_json() (in module ampal.amino_acids) align() (in module ampal.protein) align_backbones() (in module ampal.align) alpha (ampal.geometry.HelicalCurve property) alpha_and_pitch() (ampal.geometry.HelicalCurve class method) alpha_and_radius() (ampal.geometry.HelicalCurve class method) alpha_angles() (in module ampal.analyse_protein) ampal module ampal.align module ampal.amino_acids module ampal.ampal_warnings module ampal.analyse_protein module ampal.assembly module ampal.base_ampal module ampal.data module ampal.dssp module ampal.geometry module

ampal.interactions module ampal.ligands module ampal.nucleic_acid module ampal.pdb_parser module ampal.protein module ampal.pseudo_atoms module AmpalContainer (class in ampal.assembly) ang_a (ampal.interactions.HydrogenBond attribute) ang_d (ampal.interactions.HydrogenBond attribute) angle_and_axis() (ampal.geometry.Quaternion class method) angle_between_vectors() (in module ampal.geometry) append() (ampal.assembly.AmpalContainer method) (ampal.assembly.Assembly method) (ampal.base_ampal.Polymer method) apply_conjugation() (ampal.geometry.Quaternion method) apply_unit_quaternion() (in module ampal.geometry) arc_length() (ampal.geometry.Axis method) (ampal.geometry.HelicalCurve method) array (ampal.base_ampal.Atom property) as_array (ampal.geometry.Quaternion property) as_rotation() (ampal.geometry.Quaternion method) Assembly (class in ampal.assembly) Atom (class in ampal.base_ampal) atoms (ampal.base_ampal.Monomer property) (ampal.ligands.Ligand attribute) axis (ampal.geometry.HelicalCurve property) Axis (class in ampal.geometry)

B

b (ampal.interactions.CovalentBond property) (ampal.interactions.Interaction attribute) backbone (ampal.assembly.Assembly property) (ampal.protein.Polypeptide property) (ampal.protein.Residue property)

backbone_bond_angles (ampal.protein.Polypeptide property) backbone_bond_lengths (ampal.protein.Polypeptide property) BaseAmpal (class in ampal.base_ampal)

C

c_join() (ampal.protein.Polypeptide method) cap() (in module ampal.base_ampal) cartesian_to_cylindrical() (in module ampal.geometry) cartesian_to_spherical() (in module ampal.geometry) cc_to_local_params() (in module ampal.analyse_protein) centre_of_atoms() (in module ampal.base_ampal) centre_of_mass (ampal.base_ampal.BaseAmpal property) centre_of_mass() (in module ampal.geometry) centroid (ampal.protein.Residue property) change_state() (ampal.pdb_parser.PdbParser method) charge_series() (in module ampal.analyse_protein) check_availability() (in module ampal.ampal_warnings) check_for_non_canonical() (ampal.pdb_parser.PdbParser static method)

check_move() (ampal.align.MMCAlign static method) classify_angle_as_rotamer() (in module ampal.analyse_protein) close_monomers() (ampal.base_ampal.Monomer method) closest_distance() (in module ampal.geometry) closest_points_on_lines() (in module ampal.geometry) conjugate (ampal.geometry.Quaternion property) coordinates (ampal.pseudo_atoms.Primitive property) covalent_bonds() (in module ampal.interactions) CovalentBond (class in ampal.interactions) crick_angles() (in module ampal.analyse_protein) current_line (ampal.pdb_parser.PdbParser attribute) curvature() (ampal.geometry.HelicalCurve method) Curve (class in ampal.geometry) cylindrical_to_cartesian() (in module ampal.geometry)

D

DependencyNotFoundWarning dihedral() (in module ampal.geometry) direction_vector (ampal.geometry.Axis property) dist (ampal.interactions.HydrogenBond attribute) (ampal.interactions.Interaction attribute) (ampal.interactions.NonCovalentInteraction attribute) distance() (ampal.geometry.Quaternion method) (in module ampal.geometry)

distance_to_point() (ampal.geometry.Axis method) donor (ampal.interactions.HydrogenBond attribute) (ampal.interactions.NonCovalentInteraction attribute) (ampal.interactions.NonCovalentInteraction property) donor_monomer (ampal.interactions.HydrogenBond property) dssp_available() (in module ampal.dssp)

E

element (ampal.base_ampal.Atom attribute) (ampal.pseudo_atoms.PseudoAtom attribute) end() (ampal.pdb_parser.PdbParser method) extend() (ampal.assembly.AmpalContainer method) (ampal.assembly.Assembly method) (ampal.base_ampal.Polymer method)

extract_all_ss_dssp() (in module ampal.dssp) extract_angle_and_axis() (ampal.geometry.Quaternion method)

F

fasta (ampal.assembly.Assembly property) (ampal.protein.Polypeptide property) filter_mol_types() (ampal.assembly.Assembly method) find_atoms_within_distance() (in module ampal.base_ampal) find_covalent_bonds() (in module ampal.interactions) find_foot() (in module ampal.geometry) find_foot_on_plane() (in module ampal.geometry)

find_limits() (in module ampal.geometry) find_ss_regions() (in module ampal.dssp) find_transformations() (in module ampal.geometry) flat_list_to_dummy_chain() (in module ampal.protein) flat_list_to_polymer() (in module ampal.protein) flip_reference_axis_if_antiparallel() (in module ampal.analyse_protein) float_f() (ampal.align.MMCAlign static method) from_coordinates() (ampal.pseudo_atoms.Primitive class method)

G

gen_sectors() (in module ampal.geometry) gen_states() (ampal.pdb_parser.PdbParser method) generate_bond_subgraphs_from_break() (in module ampal.interactions) generate_covalent_bond_graph() (in module ampal.interactions) get_aa_code() (in module ampal.amino_acids) get_aa_info() (in module ampal.amino_acids) get_aa_letter() (in module ampal.amino_acids) get_atoms() (ampal.assembly.Assembly method) (ampal.base_ampal.BaseAmpal method) (ampal.base_ampal.Monomer method) (ampal.base_ampal.Polymer method)

get_coords() (ampal.geometry.Axis method) (ampal.geometry.HelicalCurve method) get_ligands() (ampal.assembly.Assembly method) get_monomers() (ampal.assembly.Assembly method) (ampal.base_ampal.Monomer method) (ampal.base_ampal.Polymer method) get_reference_coords() (ampal.base_ampal.Polymer method) get_slice_from_res_id() (ampal.protein.Polypeptide method) get_ss_regions() (in module ampal.dssp)

H

HelicalCurve (class in ampal.geometry)

HydrogenBond (class in ampal.interactions)

I

id (ampal.assembly.AmpalContainer attribute) (ampal.base_ampal.Atom attribute) (ampal.base_ampal.Monomer attribute) (ampal.base_ampal.Polymer attribute) (ampal.ligands.Ligand attribute) (ampal.nucleic_acid.Nucleotide attribute) (ampal.nucleic_acid.Polynucleotide attribute) (ampal.pdb_parser.PdbParser attribute) (ampal.protein.Polypeptide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoAtom attribute) (ampal.pseudo_atoms.PseudoGroup attribute) (ampal.pseudo_atoms.PseudoMonomer attribute) ignore_end (ampal.pdb_parser.PdbParser attribute) insertion_code (ampal.ligands.Ligand attribute) (ampal.nucleic_acid.Nucleotide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoMonomer attribute)

Interaction (class in ampal.interactions) intersection_start_and_end() (in module ampal.geometry) is_acute() (in module ampal.geometry) is_hetero (ampal.ligands.Ligand attribute) (ampal.nucleic_acid.Nucleotide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoMonomer attribute) is_within() (ampal.assembly.Assembly method) (ampal.base_ampal.BaseAmpal method) isoelectric_point (ampal.assembly.Assembly property) (ampal.protein.Polypeptide property)

L

length (ampal.geometry.Axis property) Ligand (class in ampal.ligands) LigandGroup (class in ampal.ligands) ligands (ampal.base_ampal.Polymer attribute) (ampal.nucleic_acid.Polynucleotide attribute) (ampal.protein.Polypeptide attribute) (ampal.pseudo_atoms.PseudoGroup attribute)

load_pdb() (in module ampal.pdb_parser)

M

make_ampal() (ampal.pdb_parser.PdbParser method) make_pdb() (ampal.assembly.Assembly method) (ampal.base_ampal.BaseAmpal method) (ampal.base_ampal.Monomer method) (ampal.base_ampal.Polymer method) make_primitive() (in module ampal.analyse_protein) make_primitive_extrapolate_ends() (in module ampal.analyse_protein) make_primitive_smoothed() (in module ampal.analyse_protein) MalformedPDBWarning measure_sidechain_torsion_angles() (in module ampal.analyse_protein) measure_torsion_angles() (in module ampal.analyse_protein) midpoint (ampal.geometry.Axis property) minimal_distance_between_lines() (in module ampal.geometry) MMCAlign (class in ampal.align) module ampal ampal.align ampal.amino_acids ampal.ampal_warnings ampal.analyse_protein ampal.assembly ampal.base_ampal ampal.data ampal.dssp ampal.geometry ampal.interactions ampal.ligands ampal.nucleic_acid ampal.pdb_parser ampal.protein ampal.pseudo_atoms

mol_code (ampal.ligands.Ligand attribute) (ampal.nucleic_acid.Nucleotide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoMonomer attribute) molar_extinction_280 (ampal.assembly.Assembly property) (ampal.protein.Polypeptide property) molecular_weight (ampal.assembly.Assembly property) (ampal.protein.Polypeptide property) molecule_type (ampal.base_ampal.Polymer attribute) (ampal.nucleic_acid.Polynucleotide attribute) (ampal.protein.Polypeptide attribute) (ampal.pseudo_atoms.PseudoGroup attribute) Monomer (class in ampal.base_ampal)

N

n_join() (ampal.protein.Polypeptide method) new_labels (ampal.pdb_parser.PdbParser attribute) NoncanonicalWarning

NonCovalentInteraction (class in ampal.interactions) norm (ampal.geometry.Quaternion property) NotParameterisedWarning Nucleotide (class in ampal.nucleic_acid)

P

parent (ampal.base_ampal.Atom attribute) (ampal.base_ampal.Monomer attribute) (ampal.base_ampal.Polymer attribute) (ampal.ligands.Ligand attribute) (ampal.nucleic_acid.Nucleotide attribute) (ampal.nucleic_acid.Polynucleotide attribute) (ampal.protein.Polypeptide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoAtom attribute) (ampal.pseudo_atoms.PseudoGroup attribute) (ampal.pseudo_atoms.PseudoMonomer attribute) parse_pdb_file() (ampal.pdb_parser.PdbParser method) partial_charge() (in module ampal.analyse_protein) pdb (ampal.assembly.AmpalContainer property) (ampal.assembly.Assembly property) (ampal.base_ampal.BaseAmpal property) (ampal.pseudo_atoms.PseudoMonomer property) pdb_lines (ampal.pdb_parser.PdbParser attribute) pdb_parse_tree (ampal.pdb_parser.PdbParser attribute) PdbParser (class in ampal.pdb_parser) pitch (ampal.geometry.HelicalCurve property)

pitch_and_radius() (ampal.geometry.HelicalCurve class method) point() (ampal.geometry.Axis method) (ampal.geometry.Curve method) (ampal.geometry.HelicalCurve method) points_on_a_circle() (in module ampal.geometry) Polymer (class in ampal.base_ampal) polymer_to_reference_axis_distances() (in module ampal.analyse_protein) Polynucleotide (class in ampal.nucleic_acid) Polypeptide (class in ampal.protein) polypeptide_vector() (in module ampal.analyse_protein) primitive (ampal.protein.Polypeptide property) Primitive (class in ampal.pseudo_atoms) primitives (ampal.assembly.Assembly property) proc_atom() (ampal.pdb_parser.PdbParser method) proc_chain() (ampal.pdb_parser.PdbParser method) proc_functions (ampal.pdb_parser.PdbParser attribute) proc_line_coordinate() (ampal.pdb_parser.PdbParser method) proc_monomer() (ampal.pdb_parser.PdbParser method) proc_state() (ampal.pdb_parser.PdbParser method) PseudoAtom (class in ampal.pseudo_atoms) PseudoGroup (class in ampal.pseudo_atoms) PseudoMonomer (class in ampal.pseudo_atoms)

Q

Quaternion (class in ampal.geometry)

R

radii_of_curvature() (ampal.protein.Polypeptide method) (ampal.pseudo_atoms.Primitive method) radius (ampal.geometry.HelicalCurve property) radius_of_circumcircle() (in module ampal.geometry) real_and_vector() (ampal.geometry.Quaternion class method) reference_atom (ampal.nucleic_acid.Nucleotide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoMonomer attribute) reference_axis_from_chains() (in module ampal.analyse_protein) relabel_all() (ampal.assembly.Assembly method) (ampal.base_ampal.Polymer method) relabel_atoms() (ampal.assembly.Assembly method) (ampal.base_ampal.Polymer method) relabel_monomers() (ampal.assembly.Assembly method) (ampal.base_ampal.Polymer method)

relabel_polymers() (ampal.assembly.Assembly method) res_label (ampal.base_ampal.Atom attribute) (ampal.pseudo_atoms.PseudoAtom attribute) Residue (class in ampal.protein) residues_per_turn() (in module ampal.analyse_protein) rise_per_residue() (ampal.protein.Polypeptide method) (ampal.pseudo_atoms.Primitive method) rmsd() (ampal.base_ampal.BaseAmpal method) (in module ampal.geometry) rotate() (ampal.base_ampal.Atom method) (ampal.base_ampal.BaseAmpal method) rotate_vector() (ampal.geometry.Quaternion method) rotation_matrix() (in module ampal.geometry) run_dssp() (in module ampal.dssp)

S

sequence (ampal.nucleic_acid.Polynucleotide property) (ampal.protein.Polypeptide property) sequence_charge() (in module ampal.analyse_protein) sequence_isoelectric_point() (in module ampal.analyse_protein) sequence_molar_extinction_280() (in module ampal.analyse_protein) sequence_molecular_weight() (in module ampal.analyse_protein) sequences (ampal.assembly.Assembly property) side_chain (ampal.protein.Residue property) sl (ampal.base_ampal.Polymer attribute) (ampal.nucleic_acid.Polynucleotide attribute) (ampal.protein.Polypeptide attribute) (ampal.pseudo_atoms.PseudoGroup attribute)

sort_by_tag() (ampal.assembly.AmpalContainer method) spherical_to_cartesian() (in module ampal.geometry) start_optimisation() (ampal.align.MMCAlign method) state (ampal.pdb_parser.PdbParser attribute) states (ampal.base_ampal.Monomer attribute) (ampal.ligands.Ligand.self attribute) (ampal.nucleic_acid.Nucleotide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoMonomer attribute)

T

t_from_arc_length() (ampal.geometry.Axis method) (ampal.geometry.HelicalCurve method) tag_ca_geometry() (ampal.assembly.Assembly method) (ampal.protein.Polypeptide method) tag_dssp_data() (in module ampal.dssp) tag_sidechain_dihedrals() (ampal.protein.Polypeptide method) tag_torsion_angles() (ampal.assembly.Assembly method) (ampal.protein.Polypeptide method) tags (ampal.base_ampal.Atom attribute) (ampal.base_ampal.Monomer attribute) (ampal.base_ampal.Polymer attribute) (ampal.ligands.Ligand attribute) (ampal.nucleic_acid.Nucleotide attribute) (ampal.nucleic_acid.Polynucleotide attribute) (ampal.protein.Polypeptide attribute) (ampal.protein.Residue attribute) (ampal.pseudo_atoms.Primitive attribute) (ampal.pseudo_atoms.PseudoAtom attribute) (ampal.pseudo_atoms.PseudoGroup attribute) (ampal.pseudo_atoms.PseudoMonomer attribute)

torsion() (ampal.geometry.HelicalCurve method) translate() (ampal.base_ampal.Atom method) (ampal.base_ampal.BaseAmpal method)

U

unique_id (ampal.base_ampal.Atom property) (ampal.protein.Residue property) unit_binormal (ampal.geometry.Axis property) unit_binormal() (ampal.geometry.HelicalCurve method)

unit_normal (ampal.geometry.Axis property) unit_normal() (ampal.geometry.HelicalCurve method) unit_tangent (ampal.geometry.Axis property) unit_tangent() (ampal.geometry.HelicalCurve method) unit_vector() (in module ampal.geometry)

V

valid_backbone_bond_angles() (ampal.protein.Polypeptide method)

valid_backbone_bond_lengths() (ampal.protein.Polypeptide method) vector (ampal.geometry.Quaternion property)

W

write_pdb() (in module ampal.base_ampal)

X

x (ampal.base_ampal.Atom property)

x() (ampal.geometry.HelicalCurve method)

Y

y (ampal.base_ampal.Atom property)

y() (ampal.geometry.HelicalCurve method)

Z

z (ampal.base_ampal.Atom property)

z() (ampal.geometry.HelicalCurve method)