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Imported modules
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import chimera
from chimera import selection
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Functions
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add_model_closed_callback
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add_model_closed_callback ( model, callback )
Invoke a callback when a specified model is closed.
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atom_chains
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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.
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atom_position
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atom_position ( atom )
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attribute_strings
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attribute_strings ( dict )
Make string name1="value1" name2="value2" ... string for XML output.
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chimera_color
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chimera_color ( rgba )
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create_marker_sets
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create_marker_sets ( marker_set_tuples )
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distance
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distance ( xyz_1, xyz_2 )
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leftover_keys
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leftover_keys ( dict, keys )
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load_marker_set_xml
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load_marker_set_xml ( input )
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pick_marker
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pick_marker (
pointer_x,
pointer_y,
marker_sets,
)
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pick_marker_3d
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pick_marker_3d ( xyz, marker_sets )
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save_marker_sets
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save_marker_sets ( mslist, out )
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trace_chain
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trace_chain ( atom, bond )
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transfer_markers
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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.
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transform_coordinates
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transform_coordinates (
xyz,
from_xform,
to_xform,
)
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xml_escape
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xml_escape ( s )
Replace & by & " by " and < by < and > by > in a string.
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Classes
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Link | Link is implemented as a Chimera Bond.
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Marker | Marker is implemented as a Chimera Atom.
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Marker_Set | Set of Markers and Links between them.
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