molecule_copies (
        molecule,
        matrices,
        associate_molecule_with_identity_matrix=True,
        )

show_multiscale_model_dialog ()

fully_selected_pieces ( plist )

A fully selected piece is one that is selected or has at least one child and all children are fully selected.

subtract_lists ( list1,  list2 )

containing_chain_pieces ( surface_groups,  residues=[] )

numbered_xforms ( matrices )

position_atoms (
        atoms,
        xyz_array,
        xform,
        )

Set position of atoms.

identity_xform_index (
        xforms,
        default_index=None,
        angle_tolerance=0.001,
        translation_tolerance=0.001,
        )

get_atom_coordinates ( atoms,  coords )

find_pieces (
        pieces,
        piece_type,
        already_checked=None,
        )

multiscale_model_dialog ( create=False )

multimer_chain_group (
        multimer_name,
        group_name,
        xforms,
        lan_molecules,
        chain_ids,
        chain_colors,
        surfacer,
        )

make_chain_groups (
        name_prefix,
        chain_names,
        mcopies,
        color=None,
        chain_colors=[],
        )

modeled_molecules ( pieces,  mtable=None )

multimeric_molecule_pieces (
        molecule,
        surfacer,
        xforms,
        associate_molecule_with_identity_matrix=True,
        )

hide_molecule ( m )

transformed_vertices ( varray,  xform )

varray is an N by 3 array of xyz positions to be transformed using a Chimera xform.

float_variable_value ( v,  default=None )

chain_pieces (
        lan_chains,
        chain_colors,
        xform,
        surfacer,
        )

make_group ( name,  plist )

integer_variable_value ( v,  default=None )

make_lan_molecules (
        molecule,
        n,
        associate=0,
        )

The associate argument gives the index of the LAN_Molecule in the returned list which has the given molecule associated with it.

color_surfaces_to_match_atoms ()

chimera_color ( rgba )

find_fully_selected_pieces ( p,  fstable )

random_colors ( n,  seed=None )

parent_pieces ( plist )

make_chain_group (
        name,
        chain_names,
        mcopies,
        chain_colors,
        )

show_biological_unit ()

Model_Piece

Base class for pieces of multiscale model.

Stop_Dialog

Chain_Piece

LAN_Molecule

Load As Needed Molecule.

LAN_Chain

Group_Piece

MultiScale_Model_Dialog

Chain_Surfacer

ChimeraExtension.py

accelerators.py

chaindata.py

nearby.py

session.py

surface.py

viper_file_reader.py