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# Copyright 1999 by Jeffrey Chang.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

This module provides code to work with the enzyme.dat file from
Enzyme (OBSOLETE as of Biopython version 1.50).

The functionality of Bio.Enzyme has moved to Bio.ExPASy.Enzyme;
please use that module instead of Bio.Enzyme. Most likely, Bio.Enzyme
will be deprecated in a future release of Biopython.

_Scanner     Scans Enzyme data.


from Bio import File
from Bio.ParserSupport import *

00024 class _Scanner:
    """Scans Enzyme data.

    Tested with:
    Release 33

00031     def feed(self, handle, consumer):
        """feed(self, handle, consumer)

        Feed in Enzyme data for scanning.  handle is a file-like object
        that contains keyword information.  consumer is a Consumer
        object that will receive events as the report is scanned.

        if isinstance(handle, File.UndoHandle):
            uhandle = handle
            uhandle = File.UndoHandle(handle)

        while not is_blank_line(uhandle.peekline()):   # Am I done yet?
            self._scan_record(uhandle, consumer)

    def _scan_record(self, uhandle, consumer):
        # The first record is just copyright information embedded in
        # comments.  Check to see if I'm at the first record.  If so,
        # then just scan the comments and the terminator.
        line = uhandle.peekline()
        if line[:2] == 'CC':
            self._scan_cc(uhandle, consumer)
            self._scan_terminator(uhandle, consumer)
            for fn in self._scan_fns:
                fn(self, uhandle, consumer)

    def _scan_line(self, line_type, uhandle, event_fn,
                   exactly_one=None, one_or_more=None, any_number=None,
        # Callers must set exactly one of exactly_one, one_or_more, or
        # any_number to a true value.  I do not explicitly check to
        # make sure this function is called correctly.
        # This does not guarantee any parameter safety, but I
        # like the readability.  The other strategy I tried was have
        # parameters min_lines, max_lines.
        if exactly_one or one_or_more:
            read_and_call(uhandle, event_fn, start=line_type)
        if one_or_more or any_number:
            while 1:
                if not attempt_read_and_call(uhandle, event_fn,
        if up_to_one:
            attempt_read_and_call(uhandle, event_fn, start=line_type)

    def _scan_id(self, uhandle, consumer):
        self._scan_line('ID', uhandle, consumer.identification, exactly_one=1)

    def _scan_de(self, uhandle, consumer):
        self._scan_line('DE', uhandle, consumer.description, one_or_more=1)
    def _scan_an(self, uhandle, consumer):
        self._scan_line('AN', uhandle, consumer.alternate_name, any_number=1)
    def _scan_ca(self, uhandle, consumer):
        self._scan_line('CA', uhandle, consumer.catalytic_activity,
    def _scan_cf(self, uhandle, consumer):
        self._scan_line('CF', uhandle, consumer.cofactor, any_number=1)

    def _scan_cc(self, uhandle, consumer):
        self._scan_line('CC', uhandle, consumer.comment, any_number=1)
    def _scan_di(self, uhandle, consumer):
        self._scan_line('DI', uhandle, consumer.disease, any_number=1)
    def _scan_pr(self, uhandle, consumer):
        self._scan_line('PR', uhandle, consumer.prosite_reference,
    def _scan_dr(self, uhandle, consumer):
        self._scan_line('DR', uhandle, consumer.databank_reference,

    def _scan_terminator(self, uhandle, consumer):
        self._scan_line('//', uhandle, consumer.terminator, exactly_one=1)
    _scan_fns = [
00127 class DataRecord:
    def __init__(self,tr_code='',sw_code=''):
        self.tr_code = tr_code
        self.sw_code = sw_code
    def __str__(self):
        return self.tr_code + ", " + self.sw_code
00135 class EnzymeRecord:
    def __init__(self):
        self.ID = ''
        self.DE = []
        self.AN = []
        self.CA = ''
        self.CF = []
        self.CC = []   # one comment per line
        self.DI = []
        self.PR = []
        self.DR = []
    def __repr__(self):
        if self.ID:
            if self.DE:
                return "%s (%s, %s)" % (self.__class__.__name__, 
                                        self.ID, self.DE[0])
                return "%s (%s)" % (self.__class__.__name__, 
            return "%s ( )" % (self.__class__.__name__)
    def __str__(self):
        output = "ID: " + self.ID
        output += " DE: " + repr(self.DE)
        output += " AN: " + repr(self.AN)
        output += " CA: '" + self.CA + "'"
        output += " CF: " + repr(self.CF)
        output += " CC: " + repr(self.CC)
        output += " DI: " + repr(self.DI)
        output += " PR: " + repr(self.PR)
        output += " DR: %d Records" % len(self.DR)
        return output
00171 class RecordParser(AbstractParser):
      def __init__(self):
            self._scanner = _Scanner()
            self._consumer = _RecordConsumer()

      def parse(self, handle):
            if isinstance(handle, File.UndoHandle):
                  uhandle = handle
                  uhandle = File.UndoHandle(handle)
                  self._scanner.feed(uhandle, self._consumer)
            return self._consumer.enzyme_record

00184 class Iterator:
      def __init__(self, handle, parser=None):
            self._uhandle = File.UndoHandle(handle)

      def next(self):
            self._parser = RecordParser()
            lines = []
            while 1:
                  line = self._uhandle.readline()
                  if not line: break
                  if line[:2] == '//':
            if not lines:
                  return None
            data = string.join(lines,'')
            if self._parser is not None:
                  return self._parser.parse(File.StringHandle(data))
            return data

        def __iter__(self):
                return iter(self.next, None)

00208 class _RecordConsumer(AbstractConsumer):
    def __init__(self):
        self.enzyme_record = EnzymeRecord()
    def identification(self, id_info):
        self.enzyme_record.ID = id_info.split()[1]
    def description(self,de_info):
    def alternate_name(self,an_info):
    def catalytic_activity(self, ca_info):
        self.enzyme_record.CA = string.join([self.enzyme_record.CA,ca_info[2:].strip()],'')
    def cofactor(self, cf_info):
    def comment(self, cc_info):
        cc = cc_info[2:].strip()
        if cc.startswith("-!-"):
            # The header is all CC, but doesn't start with -!-
            if self.enzyme_record.CC:
                pre_cc = self.enzyme_record.CC.pop()
                pre_cc = ""
            new_cc = pre_cc + " " + cc
    def disease(self, di_info):
    def prosite_reference(self,pr_info):

    def databank_reference(self,dr_info):
        good_data = dr_info[2:].strip()
        pair_data = good_data.split(';')
        for pair in pair_data:
            if not pair: continue
            data_record = DataRecord()
            t1, t2 = pair.split(',')
            data_record.tr_code, data_record.sw_code = \
                t1.strip(), t2.strip()

      def terminator(self,schwarzenegger):
            pass # Hasta la Vista, baby!

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