Package user_functions :: Module structure
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Module structure

source code

The structure user function definitions.

Variables [hide private]
  uf_info = Uf_info()
  uf_tables = Uf_tables()
  paragraph_multi_struct = 'Support for multiple structures is p...
  paragraph_atom_id = 'The atom ID string, which uses the same n...
  paragraph_displace_id = 'The displacement ID string, which is ...
  uf_class = uf_info.add_class('structure')
  table = uf_tables.add_table(label= "table: diff tensor PDB sca...
  uf = uf_info.add_uf('structure.write_pdb')
  __package__ = 'user_functions'

Imports: eye, sep, WIZARD_IMAGE_PATH, pipe_names, pipe_control, Uf_info, Uf_tables, Desc_container, WILDCARD_STRUCT_GAUSSIAN_ALL, WILDCARD_STRUCT_PDB_ALL, WILDCARD_STRUCT_XYZ_ALL


Variables Details [hide private]

paragraph_multi_struct

Value:
'Support for multiple structures is provided by the data pipes, model \
numbers and molecule names arguments.  Each data pipe, model and molec\
ule combination will be treated as a separate structure.  As only atom\
ic coordinates with the same residue name and number and atom name wil\
l be assembled, structures with slightly different atomic structures c\
an be compared.  If the list of models is not supplied, then all model\
s of all data pipes will be used.  If the optional molecules list is s\
upplied, each molecule in the list will be considered as a separate st\
...

paragraph_atom_id

Value:
'The atom ID string, which uses the same notation as the spin ID, can \
be used to restrict the coordinates compared to a subset of molecules,\
 residues, or atoms.  For example to only use backbone heavy atoms in \
a protein, set the atom ID to \'@N,C,CA,O\', assuming those are the na\
mes of the atoms in the 3D structural file.'

paragraph_displace_id

Value:
'The displacement ID string, which is similar to the atom ID, gives fi\
ner control over which atoms are translated and rotated by the algorit\
hm.  When not set this allows, for example, to align structures based \
on a set of backbone heavy atoms and the backbone protons and side-cha\
ins are displaced by default.  Or if set to the same as the atom ID, i\
f a single domain is aligned, then just that domain will be displaced.\
'

table

Value:
uf_tables.add_table(label= "table: diff tensor PDB scaling", caption= \
"Diffusion tensor PDB representation sizes using the default scaling f\
or different diffusion tensors", caption_short= "Diffusion tensor PDB \
scaling.")