Package schrodinger :: Package application :: Package jaguar :: Module autots_bonding :: Class ReactiqStructureReader
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Class ReactiqStructureReader

                           object --+        
                                    |        
structure._ReaderWriterContextManager --+    
                                        |    
                structure.StructureReader --+
                                            |
                                           ReactiqStructureReader

Local version of StructureReader which redefines bonding when reading

Instance Methods [hide private]
 
__init__(self, *args, **kwargs)
The format is determined from the file extension if no format is specified.
 
__iter__(self)
 
next(self)

Inherited from structure.StructureReader: clearReadErrors, close, getReadErrors

Inherited from structure.StructureReader (private): _set_iterator

Inherited from structure._ReaderWriterContextManager: __enter__, __exit__

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

Static Methods [hide private]

Inherited from structure.StructureReader: fromString

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, *args, **kwargs)
(Constructor)

 

The format is determined from the file extension if no format is specified.

Parameters:
  • filename - The filename to read.
  • index - The index of the first structure to read.
  • error_handler - The handle of the mmerr object to use for error logging. Defaults to schrodinger.infra.mm.error_handler.
  • format - The format of the file, either 'pdb', 'sd', 'mol2', 'maestro' or 'maestro_text' (determined from file extension by default).
  • ignore_errors - If True, bad structures will be skipped instead of raising an exception. Currently only used by the SD reader.
  • input_string - Use of this argument is pending deprecation. Please use the StructureReader.fromString static method instead. If this is specified then the structure will be read from this string and the filename will be ignored. The format must be specified. Currently this is only supported for Maestro and SD format.
Overrides: object.__init__
(inherited documentation)

__iter__(self)

 
Overrides: structure.StructureReader.__iter__

next(self)

 
Overrides: structure.StructureReader.next