Module structure

The structure user function definitions.

Variables

FD_OPEN = 1

FD_SAVE = 2

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, dep_check, 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

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.")