Package csb :: Package bio :: Package io :: Module clans :: Class ClansFileWriter

Class ClansFileWriter

      object --+    
               |    
ClansFileBuilder --+
                   |
                  ClansFileWriter

Class for serializing a Clans instance to a file in CLANS format.

Nested Classes
Inherited from `ClansFileBuilder`: `__metaclass__`

Instance Methods

__init__(self, output)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

add_hsp_block(self, clans_instance)
Appends a <hsp>data</hsp> CLANS file block to the output.

source code

add_param_block(self, clans_instance)
Appends a <param>data</param> CLANS file block to the output.

source code

add_pos_block(self, clans_instance)
Appends a <pos>data</pos> CLANS file block to the output.

source code

add_rotmtx_block(self, clans_instance)
Appends a <rotmtx>data</rotmtx> CLANS file block to the output.

source code

add_seq_block(self, clans_instance)
Appends a <seq>data</seq> CLANS file block to the output.

source code

add_seqgroups_block(self, clans_instance)
Appends a <seqgroupsparam>data</seqgroups> CLANS file block to the output.

source code

add_sequences_line(self, clans_instance)
Appends the 'sequences=<#sequences>' line to the output.

source code

serialize(self, clans_instance)
Creates a CLANS file containing all data from clans_instance source code

Inherited from ClansFileBuilder: write, writeline

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

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties

Inherited from ClansFileBuilder: output

Inherited from object: __class__

Method Details

init(self, output)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

output (stream) - the output stream

Overrides: object.__init__

(inherited documentation)

add_hsp_block(self, clans_instance)

source code

Appends a <hsp>data</hsp> CLANS file block to the output. If the CLANS instance has hsp_att_mode=="att" we add a <att>data<att> block which has the same format.

Parameters: