HappyDoc Generated Documentation ./VolumePath/markerset.py

. / VolumePath / markerset.py 

Functions   
  distance 
distance ( xyz_1,  xyz_2 )
  pick_marker_3d 
pick_marker_3d ( xyz,  marker_sets )
  transform_coordinates 
transform_coordinates (
        xyz,
        from_xform,
        to_xform,
        )
  chimera_color 
chimera_color ( rgba )
  save_marker_sets 
save_marker_sets ( mslist,  out )
  atom_position 
atom_position ( atom )
  create_marker_sets 
create_marker_sets ( marker_set_tuples )
  load_marker_set_xml 
load_marker_set_xml ( input )
  leftover_keys 
leftover_keys ( dict,  keys )
  attribute_strings 
attribute_strings ( dict )

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

  pick_marker 
pick_marker (
        pointer_x,
        pointer_y,
        marker_sets,
        )
  select_markers 
select_markers ( markers,  only=None )
  transfer_markers 
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 
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 
xml_escape ( s )

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

  trace_chain 
trace_chain ( atom,  bond )
Classes   

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.


This document was automatically generated Wed Jul 9 15:49:17 2008 by HappyDoc version 3.1