Index

A

add() (scoria.Quaternion.Quaternion method) add_atom() (scoria.AtomsAndBonds.AtomsAndBonds method) (scoria.Molecule.Molecule method) add_bond() (scoria.AtomsAndBonds.AtomsAndBonds method) (scoria.Molecule.Molecule method)

assign_elements_from_atom_names() (scoria.Information.Information method) (scoria.Molecule.Molecule method) assign_masses() (scoria.Information.Information method) (scoria.Molecule.Molecule method) AtomsAndBonds (class in scoria.AtomsAndBonds)

B

belongs_to_dna() (scoria.Information.Information method) (scoria.Molecule.Molecule method) belongs_to_protein() (scoria.Information.Information method) (scoria.Molecule.Molecule method)

belongs_to_rna() (scoria.Information.Information method) (scoria.Molecule.Molecule method)

C

coordinate_undo() (scoria.Manipulation.Manipulation method) (scoria.Molecule.Molecule method) copy() (scoria.Molecule.Molecule method) (scoria.Quaternion.Quaternion method)

create_bonds_by_distance() (scoria.AtomsAndBonds.AtomsAndBonds method) (scoria.Molecule.Molecule method)

D

define_molecule_chain_residue_spherical_boundaries() (scoria.Information.Information method) (scoria.Molecule.Molecule method) delete_atom() (scoria.AtomsAndBonds.AtomsAndBonds method) (scoria.Molecule.Molecule method)

delete_bond() (scoria.AtomsAndBonds.AtomsAndBonds method) (scoria.Molecule.Molecule method) delete_trajectory_frame() (scoria.Information.Information method) (scoria.Molecule.Molecule method)

F

FileIO (class in scoria.FileIO)

foo()

G

Geometry (class in scoria.Geometry) get_angle_between_three_points() (scoria.Geometry.Geometry method) (scoria.Molecule.Molecule method) get_atom_information() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_bonds() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_bounding_box() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_bounding_sphere() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_center_of_mass() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_constants() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_coordinates() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_coordinates_undo_point() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_default_trajectory_frame() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_dihedral_angle() (scoria.Geometry.Geometry method) (scoria.Molecule.Molecule method) get_distance_to_another_molecule() (scoria.Molecule.Molecule method) (scoria.OtherMolecules.OtherMolecules method) get_filename() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_geometric_center() (scoria.Information.Information method) (scoria.Molecule.Molecule method)

get_hierarchy() (scoria.Information.Information method) (scoria.Molecule.Molecule method) get_index_of_first_bond_partner_of_element() (scoria.AtomsAndBonds.AtomsAndBonds method) (scoria.Molecule.Molecule method) get_molecule_from_selection() (scoria.Molecule.Molecule method) (scoria.Selections.Selections method) get_number_of_bond_partners_of_element() (scoria.AtomsAndBonds.AtomsAndBonds method) (scoria.Molecule.Molecule method) get_other_molecule_aligned_to_this() (scoria.Molecule.Molecule method) (scoria.OtherMolecules.OtherMolecules method) get_planarity_deviation() (scoria.Geometry.Geometry method) (scoria.Molecule.Molecule method) get_remarks() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) get_rmsd_equivalent_atoms_specified() (pymolecule.Molecule.Molecule method) (pymolecule.OtherMolecules.OtherMolecules method) get_rmsd_heuristic() (pymolecule.Molecule.Molecule method) (pymolecule.OtherMolecules.OtherMolecules method) get_rmsd_order_dependent() (pymolecule.Molecule.Molecule method) (pymolecule.OtherMolecules.OtherMolecules method) get_total_mass() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) get_total_number_of_atoms() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) get_total_number_of_heavy_atoms() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) get_trajectory() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) get_trajectory_frame_count() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method)

I

Information (class in pymolecule.Information) insert_trajectory_frame() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) invert() (pymolecule.Quaternion.Quaternion method)

invert_selection() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) is_planar() (pymolecule.Geometry.Geometry method) (pymolecule.Molecule.Molecule method)

L

load_from_mat() (pymolecule.Quaternion.Quaternion method) load_MDAnalysis_into() (pymolecule.FileIO.FileIO method) load_pdb_into() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_pdb_into_using_file_object() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_pdb_trajectory_into() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_pdb_trajectory_into_using_file_object() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method)

load_pdbqt_into() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_pdbqt_into_using_file_object() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_pdbqt_trajectory_into() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_pdbqt_trajectory_into_using_file_object() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_pym_into() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) load_via_MDAnalysis() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method)

M

Manipulation (class in pymolecule.Manipulation) merge_with_another_molecule() (pymolecule.Molecule.Molecule method) (pymolecule.OtherMolecules.OtherMolecules method) minus() (pymolecule.Quaternion.Quaternion method)

Molecule (class in pymolecule.Molecule) multiply() (pymolecule.Quaternion.Quaternion method)

N

normalize() (pymolecule.Quaternion.Quaternion method)

numpy_structured_array_remove_field() (pymolecule.Molecule.Molecule method)

O

OtherMolecules (class in pymolecule.OtherMolecules)

P

pymolecule.AtomsAndBonds (module) pymolecule.FileIO (module) pymolecule.Geometry (module) pymolecule.Information (module) pymolecule.Manipulation (module)

pymolecule.Molecule (module) pymolecule.OtherMolecules (module) pymolecule.Quaternion (module) pymolecule.Selections (module)

Q

Quaternion (class in pymolecule.Quaternion)

R

rep_as_44_matrix() (pymolecule.Quaternion.Quaternion method) resseq_reindex() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) rotate_molecule_around_a_line_between_atoms() (pymolecule.Manipulation.Manipulation method) (pymolecule.Molecule.Molecule method)

rotate_molecule_around_a_line_between_points() (pymolecule.Manipulation.Manipulation method) (pymolecule.Molecule.Molecule method) rotate_molecule_around_pivot_atom() (pymolecule.Manipulation.Manipulation method) (pymolecule.Molecule.Molecule method) rotate_molecule_around_pivot_point() (pymolecule.Manipulation.Manipulation method) (pymolecule.Molecule.Molecule method)

S

save_pdb() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) save_pym() (pymolecule.FileIO.FileIO method) (pymolecule.Molecule.Molecule method) scale() (pymolecule.Quaternion.Quaternion method) select_all() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_all_atoms_bound_to_selection() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_atoms() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_atoms_from_same_molecule() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_atoms_in_bounding_box() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_atoms_in_same_residue() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_atoms_near_other_selection() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_branch() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) select_close_atoms_from_different_molecules() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) Selections (class in pymolecule.Selections) selections_of_chains() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) selections_of_constituent_molecules() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method)

selections_of_residues() (pymolecule.Molecule.Molecule method) (pymolecule.Selections.Selections method) serial_reindex() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_atom_information() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_atom_location() (pymolecule.Manipulation.Manipulation method) (pymolecule.Molecule.Molecule method) set_bonds() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_coordinate_undo_point() (pymolecule.Manipulation.Manipulation method) set_coordinates() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_coordinates_undo_point() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_default_trajectory_frame() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_filename() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_hierarchy() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_remarks() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) set_trajectory() (pymolecule.Information.Information method) (pymolecule.Molecule.Molecule method) steric_clash_with_another_molecule() (pymolecule.Molecule.Molecule method) (pymolecule.OtherMolecules.OtherMolecules method)

T

to_matrix() (pymolecule.Quaternion.Quaternion method)

translate_molecule() (pymolecule.Manipulation.Manipulation method) (pymolecule.Molecule.Molecule method)