CloneSet43


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[Sequence Length]
89201.000compound_stmt
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
18953
Bio/ExPASy/Prosite.py
28998
Bio/Prosite/__init__.py
Clone Instance
1
Line Count
89
Source Line
53
Source File
Bio/ExPASy/Prosite.py

class Record: 
     """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.

    """ 

     def __init__(self): 
          self.name = "" 
          self.type = "" 
          self.accession = "" 
          self.created = "" 
          self.data_update = "" 
          self.info_update = "" 
          self.pdoc = "" 

          self.description = "" 
          self.pattern = "" 
          self.matrix = [ ] 
          self.rules = [ ] 
          self.prorules = [ ] 
          self.postprocessing = [ ] 

          self.nr_sp_release = "" 
          self.nr_sp_seqs = "" 
          self.nr_total = (None,None) 
          self.nr_positive = (None,None) 
          self.nr_unknown = (None,None) 
          self.nr_false_pos = (None,None) 
          self.nr_false_neg = None 
          self.nr_partial = None 

          self.cc_taxo_range = "" 
          self.cc_max_repeat = "" 
          self.cc_site = [ ] 
          self.cc_skip_flag = "" 

          self.dr_positive = [ ] 
          self.dr_false_neg = [ ] 
          self.dr_false_pos = [ ] 
          self.dr_potential = [ ] 
          self.dr_unknown = [ ] 

          self.pdb_structs = [ ] 


  # Everything below are private functions
     


Clone Instance
2
Line Count
89
Source Line
98
Source File
Bio/Prosite/__init__.py

class Record: 
     """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.

    """ 

     def __init__(self): 
          self.name = "" 
          self.type = "" 
          self.accession = "" 
          self.created = "" 
          self.data_update = "" 
          self.info_update = "" 
          self.pdoc = "" 

          self.description = "" 
          self.pattern = "" 
          self.matrix = [ ] 
          self.rules = [ ] 
          self.prorules = [ ] 
          self.postprocessing = [ ] 

          self.nr_sp_release = "" 
          self.nr_sp_seqs = "" 
          self.nr_total = (None,None) 
          self.nr_positive = (None,None) 
          self.nr_unknown = (None,None) 
          self.nr_false_pos = (None,None) 
          self.nr_false_neg = None 
          self.nr_partial = None 

          self.cc_taxo_range = "" 
          self.cc_max_repeat = "" 
          self.cc_site = [ ] 
          self.cc_skip_flag = "" 

          self.dr_positive = [ ] 
          self.dr_false_neg = [ ] 
          self.dr_false_pos = [ ] 
          self.dr_potential = [ ] 
          self.dr_unknown = [ ] 

          self.pdb_structs = [ ] 
     


Clone AbstractionParameter Count: 0Parameter Bindings

class Record:
  """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.

    """ 

  def __init__(self):
  
    self.name = "" 
    self.type = "" 
    self.accession = "" 
    self.created = "" 
    self.data_update = "" 
    self.info_update = "" 
    self.pdoc = "" 
    self.description = "" 
    self.pattern = "" 
    self.matrix = [ ] 
    self.rules = [ ] 
    self.prorules = [ ] 
    self.postprocessing = [ ] 
    self.nr_sp_release = "" 
    self.nr_sp_seqs = "" 
    self.nr_total = (None,None) 
    self.nr_positive = (None,None) 
    self.nr_unknown = (None,None) 
    self.nr_false_pos = (None,None) 
    self.nr_false_neg = None 
    self.nr_partial = None 
    self.cc_taxo_range = "" 
    self.cc_max_repeat = "" 
    self.cc_site = [ ] 
    self.cc_skip_flag = "" 
    self.dr_positive = [ ] 
    self.dr_false_neg = [ ] 
    self.dr_false_pos = [ ] 
    self.dr_potential = [ ] 
    self.dr_unknown = [ ] 
    self.pdb_structs = [ ] 
    # Everything below are private functions
  
 

CloneAbstraction
Parameter Bindings
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Index
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Value
None