Package mmLib :: Module TLS :: Class TLSFileFormatPDB
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Type TLSFileFormatPDB

     object --+    
              |    
RecordProcessor --+
                  |
     object --+   |
              |   |
  TLSFileFormat --+
                  |
                 TLSFileFormatPDB


Reads TLS descriptions from the REMARK records in PDB files. These records are only written by REFMAC5.
Method Summary
  complete_L(self)
  complete_S(self)
  complete_T(self)
  load(self, fil)
Returns a list containing one TLSGroupDesc object for each TLS group description found in the file.
  load_supported(self)
Returns True if file loading is supported, otherwise returns False.
  process_REMARK(self, rec)
Callback for the PDBFile parser for REMARK records.
    Inherited from TLSFileFormat
  save(self, fil, tls_desc_list)
Writes the list of TLSGroupDesc object to the given file.
  save_supported(self)
Return True if file saving is supported, otherwise returns False.
    Inherited from RecordProcessor
  preprocess_default(self, rec)
  process_ATOM(self, rec)
  process_default(self, rec)
  process_pdb_records(self, pdb_rec_iter, filter_func)
Iterates the PDB records in self, and searches for handling methods in the processor object for reading the objects.
    Inherited from object
  __init__(...)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
  __delattr__(...)
x.__delattr__('name') <==> del x.name
  __getattribute__(...)
x.__getattribute__('name') <==> x.name
  __hash__(x)
x.__hash__() <==> hash(x)
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T
  __reduce__(...)
helper for pickle
  __reduce_ex__(...)
helper for pickle
  __repr__(x)
x.__repr__() <==> repr(x)
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value
  __str__(x)
x.__str__() <==> str(x)

Class Variable Summary
dict pdb_regex_dict = {'origin': <_sre.SRE_Pattern object at ...

Method Details

load(self, fil)

Returns a list containing one TLSGroupDesc object for each TLS group description found in the file.
Overrides:
mmLib.TLS.TLSFileFormat.load (inherited documentation)

load_supported(self)

Returns True if file loading is supported, otherwise returns False.
Overrides:
mmLib.TLS.TLSFileFormat.load_supported (inherited documentation)

process_REMARK(self, rec)

Callback for the PDBFile parser for REMARK records. If the REMARK records contain TLS group information, then it is extracted and added to the TLSGroups list.

Class Variable Details

pdb_regex_dict

Type:
dict
Value:
{'group': <_sre.SRE_Pattern object at 0xb7941620>,
 'l11_l22': <_sre.SRE_Pattern object at 0xb7979210>,
 'l13_l23': <_sre.SRE_Pattern object at 0xb7979400>,
 'l33_l12': <_sre.SRE_Pattern object at 0xb7979308>,
 'origin': <_sre.SRE_Pattern object at 0x91d5768>,
 'range': <_sre.SRE_Pattern object at 0x9148360>,
 's11_s12_s13': <_sre.SRE_Pattern object at 0x905faf8>,
 's21_s22_s23': <_sre.SRE_Pattern object at 0x910a268>,
...                                                                    

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