HappyDoc Generated Documentation ./MultiScale

. / MultiScale 

Functions   
  molecule_copies 
molecule_copies (
        molecule,
        matrices,
        associate_molecule_with_identity_matrix=None,
        )
  show_multiscale_model_dialog 
show_multiscale_model_dialog ()
  fully_selected_pieces 
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 
subtract_lists ( list1,  list2 )
  containing_chain_pieces 
containing_chain_pieces ( surface_pieces,  residues=None )
  numbered_xforms 
numbered_xforms ( matrices )
  atomAndBondSurfacePieces 
atomAndBondSurfacePieces (
        self,
        atoms,
        bonds,
        )

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

  position_atoms 
position_atoms (
        atoms,
        xyz_array,
        xform,
        )

Set position of atoms.

  surfacePieceAtomsAndBonds 
surfacePieceAtomsAndBonds (
        self,
        plist,
        create,
        )

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

  identity_xform_index 
identity_xform_index (
        xforms,
        default_index=None,
        angle_tolerance=None,
        translation_tolerance=None,
        )
  find_pieces 
find_pieces (
        pieces,
        piece_type,
        already_checked=None,
        )
  multiscale_model_dialog 
multiscale_model_dialog ( create=None )
  multimer_chain_group 
multimer_chain_group (
        multimer_name,
        group_name,
        xforms,
        lan_molecules,
        chain_ids,
        chain_colors,
        surfacer,
        )
  make_chain_groups 
make_chain_groups (
        name_prefix,
        chain_names,
        mcopies,
        color=None,
        chain_colors=None,
        )
  modeled_molecules 
modeled_molecules ( pieces,  mtable=None )
  multimeric_molecule_pieces 
multimeric_molecule_pieces (
        molecule,
        surfacer,
        xforms,
        associate_molecule_with_identity_matrix=None,
        )
  float_variable_value 
float_variable_value ( v,  default=None )
  chain_pieces 
chain_pieces (
        lan_chains,
        chain_colors,
        xform,
        surfacer,
        )
  make_group 
make_group ( name,  plist )
  integer_variable_value 
integer_variable_value ( v,  default=None )
  make_lan_molecules 
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 
color_surfaces_to_match_atoms ()
  transformed_points 
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 
chimera_color ( rgba )
  find_fully_selected_pieces 
find_fully_selected_pieces ( p,  fstable )
  random_colors 
random_colors ( n,  seed=None )
  parent_pieces 
parent_pieces ( plist )
  make_chain_group 
make_chain_group (
        name,
        chain_names,
        mcopies,
        chain_colors,
        )
  show_biological_unit 
show_biological_unit ()
Classes   

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

Python files   

ChimeraExtension.py

accelerators.py

chaindata.py

nearby.py

session.py

surface.py

viper_file_reader.py


This document was automatically generated Wed Jul 9 15:49:04 2008 by HappyDoc version 3.1