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

source code

         object --+    
                  |    
      TLSFileFormat --+
                      |
         object --+   |
                  |   |
PDB.RecordProcessor --+
                      |
                     TLSFileFormatPDB

Reads TLS descriptions from the REMARK records in PDB files. These records are only written by REFMAC5.

Instance Methods [hide private]
 
load_supported(self)
Returns True if file loading is supported, otherwise returns False.
source code
 
load(self, fil)
Returns a list containing one TLSGroupDesc object for each TLS group description found in the file.
source code
 
complete_T(self) source code
 
complete_L(self) source code
 
complete_S(self) source code
 
process_REMARK(self, rec)
Callback for the PDBFile parser for REMARK records.
source code

Inherited from TLSFileFormat: save, save_supported

Inherited from PDB.RecordProcessor: preprocess_default, process_ATOM, process_default, process_pdb_records

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  pdb_regex_dict = {'group': re.compile(r'\s*TLS GROUP :\s+(\d+)...
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

load_supported(self)

source code 

Returns True if file loading is supported, otherwise returns False.

Overrides: TLSFileFormat.load_supported
(inherited documentation)

load(self, fil)

source code 

Returns a list containing one TLSGroupDesc object for each TLS group description found in the file.

Overrides: TLSFileFormat.load
(inherited documentation)

process_REMARK(self, rec)

source code 

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 [hide private]

pdb_regex_dict

Value:
{'group': re.compile(r'\s*TLS GROUP :\s+(\d+)\s*$'),
 'l11_l22': re.compile(r'\s*L11:\s*(\S+)\s+L22:\s*(\S+)\s*$'),
 'l13_l23': re.compile(r'\s*L13:\s*(\S+)\s+L23:\s*(\S+)\s*$'),
 'l33_l12': re.compile(r'\s*L33:\s*(\S+)\s+L12:\s*(\S+)\s*$'),
 'origin': re.compile(r'\s*ORIGIN\s+FOR\s+THE\s+GROUP\s+\(A\):([\s-\.0\
-9]+)$'),
 'phenix_range': re.compile(r'\s*SELECTION:\s+CHAIN\s+(\w+)\s+AND\s+RE\
SID\s+(-?\w+):(-?\w+)\s*$'),
...