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

source code

object --+
         |
        ClansEntry

Class holding the data of one CLANS sequence entry.

Instance Methods
 
__init__(self, name=None, seq='', coords=None, parent=None)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
__repr__(self)
repr(x)		 source code
 
add_hsp(self, other, value)
Creates an HSP from self to other with the given value.		 source code
str
get_id(self)
Returns the id of the current entry.		 source code
 
initialize_coordinates(self)
Sets the coordinates to random numbers in [-1, 1]		 source code
str
output_string_hsp(self)
Creates the CLANS <hsp> block format representation of the entry.		 source code
str
output_string_pos(self)
Create the CLANS <pos> block format representation of the entry.		 source code
str
output_string_seq(self)
Creates the CLANS <seq> block format representation of the entry.		 source code
 
remove_hsp(self, other)
Removes the HSP between self and other; if none exists, does nothing.		 source code

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

Properties
string coords
entry coordinates in 3D space
list groups
ClansSeqgroups that contain the entry
dict hsp
connections between this and another ClansEntry
string name
name of the entry
Clans parent
Clans instance that parents this ClansEntry
string seq
protein sequence of the entry

Inherited from object: __class__

Method Details

__init__(self, name=None, seq='', coords=None, parent=None)
(Constructor)

source code 

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

Parameters:
  • name (str) - the entry name
  • seq (str) - the entry's amino acid sequence
  • coords (iterable with 3 items) - coordinates in 3D space
  • parent (Clans instance) - parent of this entry
Overrides: object.__init__
(inherited documentation)

__repr__(self)
(Representation operator)

source code 

repr(x)

Overrides: object.__repr__
(inherited documentation)

add_hsp(self, other, value)

source code 

Creates an HSP from self to other with the given value.

Parameters:
  • other (ClansEntry instance) - the other entry
  • value (float) - the value of the HSP

get_id(self)

source code 

Returns the id of the current entry.

Note: the first call to this method triggers Clans._update_index, which will make it appear slower than successive calls.

Returns: str
the entrys' id is returned unless it has no parent in which case -1 is returned

output_string_hsp(self)

source code 

Creates the CLANS <hsp> block format representation of the entry.

Returns: str
entrys' representation in CLANS <hsp> block format

output_string_pos(self)

source code 

Create the CLANS <pos> block format representation of the entry.

Returns: str
entrys' representation in CLANS <pos> block format

output_string_seq(self)

source code 

Creates the CLANS <seq> block format representation of the entry.

Returns: str
entrys' representation in CLANS <seq> block format

remove_hsp(self, other)

source code 

Removes the HSP between self and other; if none exists, does nothing.

Parameters:

Property Details

coords

entry coordinates in 3D space

raises ValueError if value is not an iterable with 3 items

Get Method:
unreachable.coords(self) - entry coordinates in 3D space
Set Method:
unreachable.coords(self, value)
Type:
string

groups

ClansSeqgroups that contain the entry

Get Method:
unreachable.groups(self) - ClansSeqgroups that contain the entry
Type:
list

hsp

connections between this and another ClansEntry

Get Method:
unreachable.hsp(self) - connections between this and another ClansEntry
Type:
dict

name

name of the entry

raises ValueError if value is not a string

Get Method:
unreachable.name(self) - name of the entry
Set Method:
unreachable.name(self, value)
Type:
string

parent

Clans instance that parents this ClansEntry

Get Method:
unreachable.parent(self) - Clans instance that parents this ClansEntry
Type:
Clans

seq

protein sequence of the entry

raises ValueError if value is not a string

Get Method:
unreachable.seq(self) - protein sequence of the entry
Set Method:
unreachable.seq(self, value)
Type:
string

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