molecule_copies (
        molecule,
        matrices,
        associate_molecule_with_identity_matrix=None,
        )

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_pieces,  residues=None )

numbered_xforms ( matrices )

atomAndBondSurfacePieces (
        self,
        atoms,
        bonds,
        )

Added as a method to SurfaceModel to allow Chimera Actions menu to work on selected multiscale surfaces.

position_atoms (
        atoms,
        xyz_array,
        xform,
        )

Set position of atoms.

surfacePieceAtomsAndBonds (
        self,
        plist,
        create,
        )

Added as a method to SurfaceModel to allow Chimera Actions menu to work on selected multiscale surfaces.

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

find_pieces (
        pieces,
        piece_type,
        already_checked=None,
        )

multiscale_model_dialog ( create=None )

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=None,
        )

modeled_molecules ( pieces,  mtable=None )

multimeric_molecule_pieces (
        molecule,
        surfacer,
        xforms,
        associate_molecule_with_identity_matrix=None,
        )

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=None,
        )

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 ()

transformed_points ( varray,  tf )

varray is an N by 3 array of xyz positions to be transformed using a 3 by 4 transform matrix.

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