distance ( xyz_1,  xyz_2 )

pick_marker_3d ( xyz,  marker_sets )

transform_coordinates (
        xyz,
        from_xform,
        to_xform,
        )

chimera_color ( rgba )

save_marker_sets ( mslist,  out )

atom_position ( atom )

create_marker_sets ( marker_set_tuples )

load_marker_set_xml ( input )

leftover_keys ( dict,  keys )

attribute_strings ( dict )

Make string name1="value1" name2="value2" ... string for XML output.

pick_marker (
        pointer_x,
        pointer_y,
        marker_sets,
        )

transfer_markers ( mlist,  marker_set )

Does not transfer markers to new marker set if different marker sets would be linked. Returns None in that case. Otherwise returns the number of markers transfered.

atom_chains ( molecule )

Return a list of atom chains for a molecule. An atom chain is a sequence of atoms connected by bonds where all non-end-point atoms have exactly 2 bonds. A chain is represented by a 2-tuple, the first element being the ordered list of atoms, and the second being the ordered list of bonds. In a chain which is a cycle all atoms have 2 bonds and the first and last atom in the chain are the same. Non-cycles have end point atoms with more or less than 2 bonds.

xml_escape ( s )

Replace & by & " by " and < by < and > by > in a string.

trace_chain ( atom,  bond )

Marker

Marker is implemented as a Chimera Atom.

Link

Link is implemented as a Chimera Bond.

Marker_Set

Set of Markers and Links between them.