Back to index

python-biopython  1.60
Public Member Functions | Public Attributes
Bio.ExPASy.Prosite.Record Class Reference

List of all members.

Public Member Functions

def __init__

Public Attributes

 name
 type
 accession
 created
 data_update
 info_update
 pdoc
 description
 pattern
 matrix
 rules
 prorules
 postprocessing
 nr_sp_release
 nr_sp_seqs
 nr_total
 nr_positive
 nr_unknown
 nr_false_pos
 nr_false_neg
 nr_partial
 cc_taxo_range
 cc_max_repeat
 cc_site
 cc_skip_flag
 dr_positive
 dr_false_neg
 dr_false_pos
 dr_potential
 dr_unknown
 pdb_structs

Detailed Description

Holds information from a Prosite record.

Members:
name           ID of the record.  e.g. ADH_ZINC
type           Type of entry.  e.g. PATTERN, MATRIX, or RULE
accession      e.g. PS00387
created        Date the entry was created.  (MMM-YYYY)
data_update    Date the 'primary' data was last updated.
info_update    Date data other than 'primary' data was last updated.
pdoc           ID of the PROSITE DOCumentation.

description    Free-format description.
pattern        The PROSITE pattern.  See docs.
matrix         List of strings that describes a matrix entry.
rules          List of rule definitions (from RU lines).  (strings)
prorules       List of prorules (from PR lines). (strings)

NUMERICAL RESULTS
nr_sp_release  SwissProt release.
nr_sp_seqs     Number of seqs in that release of Swiss-Prot. (int)
nr_total       Number of hits in Swiss-Prot.  tuple of (hits, seqs)
nr_positive    True positives.  tuple of (hits, seqs)
nr_unknown     Could be positives.  tuple of (hits, seqs)
nr_false_pos   False positives.  tuple of (hits, seqs)
nr_false_neg   False negatives.  (int)
nr_partial     False negatives, because they are fragments. (int)

COMMENTS
cc_taxo_range  Taxonomic range.  See docs for format
cc_max_repeat  Maximum number of repetitions in a protein
cc_site        Interesting site.  list of tuples (pattern pos, desc.)
cc_skip_flag   Can this entry be ignored?
cc_matrix_type
cc_scaling_db
cc_author
cc_ft_key
cc_ft_desc
cc_version     version number (introduced in release 19.0)

DATA BANK REFERENCES - The following are all
                       lists of tuples (swiss-prot accession,
                                        swiss-prot name)
dr_positive
dr_false_neg
dr_false_pos
dr_potential   Potential hits, but fingerprint region not yet available.
dr_unknown     Could possibly belong

pdb_structs    List of PDB entries.

Definition at line 53 of file Prosite.py.


Constructor & Destructor Documentation

Definition at line 105 of file Prosite.py.

00105 
00106     def __init__(self):
00107         self.name = ''
00108         self.type = ''
00109         self.accession = ''
00110         self.created = ''
00111         self.data_update = ''
00112         self.info_update = ''
00113         self.pdoc = ''
00114     
00115         self.description = ''
00116         self.pattern = ''
00117         self.matrix = []
00118         self.rules = []
00119         self.prorules = []
00120         self.postprocessing = []
00121 
00122         self.nr_sp_release = ''
00123         self.nr_sp_seqs = ''
00124         self.nr_total = (None, None)
00125         self.nr_positive = (None, None)
00126         self.nr_unknown = (None, None)
00127         self.nr_false_pos = (None, None)
00128         self.nr_false_neg = None
00129         self.nr_partial = None
00130 
00131         self.cc_taxo_range = ''
00132         self.cc_max_repeat = ''
00133         self.cc_site = []
00134         self.cc_skip_flag = ''
00135 
00136         self.dr_positive = []
00137         self.dr_false_neg = []
00138         self.dr_false_pos = []
00139         self.dr_potential = []
00140         self.dr_unknown = []
00141 
00142         self.pdb_structs = []
00143 
00144 
00145 # Everything below are private functions

Here is the caller graph for this function:


Member Data Documentation

Definition at line 108 of file Prosite.py.

Definition at line 131 of file Prosite.py.

Definition at line 132 of file Prosite.py.

Definition at line 133 of file Prosite.py.

Definition at line 130 of file Prosite.py.

Definition at line 109 of file Prosite.py.

Definition at line 110 of file Prosite.py.

Definition at line 114 of file Prosite.py.

Definition at line 136 of file Prosite.py.

Definition at line 137 of file Prosite.py.

Definition at line 135 of file Prosite.py.

Definition at line 138 of file Prosite.py.

Definition at line 139 of file Prosite.py.

Definition at line 111 of file Prosite.py.

Definition at line 116 of file Prosite.py.

Definition at line 106 of file Prosite.py.

Definition at line 127 of file Prosite.py.

Definition at line 126 of file Prosite.py.

Definition at line 128 of file Prosite.py.

Definition at line 124 of file Prosite.py.

Definition at line 121 of file Prosite.py.

Definition at line 122 of file Prosite.py.

Definition at line 123 of file Prosite.py.

Definition at line 125 of file Prosite.py.

Definition at line 115 of file Prosite.py.

Definition at line 141 of file Prosite.py.

Definition at line 112 of file Prosite.py.

Definition at line 119 of file Prosite.py.

Definition at line 118 of file Prosite.py.

Definition at line 117 of file Prosite.py.

Definition at line 107 of file Prosite.py.


The documentation for this class was generated from the following file: