.venv_haddock/lib/python3.12/site-packages/Bio/ExPASy/Enzyme.py

# Copyright 1999 by Jeffrey Chang.  All rights reserved.
# Copyright 2009 by Michiel de Hoon.  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.

"""Parse the enzyme.dat file from Enzyme at ExPASy.

See https://www.expasy.org/enzyme/

Tested with the release of 03-Mar-2009.

Functions:
 - read       Reads a file containing one ENZYME entry
 - parse      Reads a file containing multiple ENZYME entries

Classes:
 - Record     Holds ENZYME data.

"""


def parse(handle):
    """Parse ENZYME records.

    This function is for parsing ENZYME files containing multiple
    records.

    Arguments:
     - handle   - handle to the file.

    """
    while True:
        record = __read(handle)
        if not record:
            break
        yield record


def read(handle):
    """Read one ENZYME record.

    This function is for parsing ENZYME files containing
    exactly one record.

    Arguments:
     - handle   - handle to the file.

    """
    record = __read(handle)
    # We should have reached the end of the record by now
    remainder = handle.read()
    if remainder:
        raise ValueError("More than one ENZYME record found")
    return record


class Record(dict):
    """Holds information from an ExPASy ENZYME record as a Python dictionary.

    Each record contains the following keys:

    - ID: EC number
    - DE: Recommended name
    - AN: Alternative names (if any)
    - CA: Catalytic activity
    - CF: Cofactors (if any)
    - PR: Pointers to any Prosite documentation entries that correspond to the
      enzyme
    - DR: Pointers to any Swiss-Prot protein sequence entries that correspond
      to the enzyme
    - CC: Comments

    """

    def __init__(self):
        """Initialize the class."""
        dict.__init__(self)
        self["ID"] = ""
        self["DE"] = ""
        self["AN"] = []
        self["CA"] = ""
        self["CF"] = ""
        self["CC"] = []  # one comment per line
        self["PR"] = []
        self["DR"] = []

    def __repr__(self):
        """Return the canonical string representation of the Record object."""
        if self["ID"]:
            if self["DE"]:
                return f"{self.__class__.__name__} ({self['ID']}, {self['DE']})"
            else:
                return f"{self.__class__.__name__} ({self['ID']})"
        else:
            return f"{self.__class__.__name__} ( )"

    def __str__(self):
        """Return a readable string representation of the Record object."""
        output = [
            "ID: " + self["ID"],
            "DE: " + self["DE"],
            "AN: " + repr(self["AN"]),
            "CA: '" + self["CA"] + "'",
            "CF: " + self["CF"],
            "CC: " + repr(self["CC"]),
            "PR: " + repr(self["PR"]),
            "DR: %d Records" % len(self["DR"]),
        ]
        return "\n".join(output)


# Everything below is private


def __read(handle):
    record = None
    for line in handle:
        key, value = line[:2], line[5:].rstrip()
        if key == "ID":
            record = Record()
            record["ID"] = value
        elif key == "DE":
            record["DE"] += value
        elif key == "AN":
            if record["AN"] and not record["AN"][-1].endswith("."):
                record["AN"][-1] += " " + value
            else:
                record["AN"].append(value)
        elif key == "CA":
            record["CA"] += value
        elif key == "DR":
            pair_data = value.rstrip(";").split(";")
            for pair in pair_data:
                t1, t2 = pair.split(",")
                row = [t1.strip(), t2.strip()]
                record["DR"].append(row)
        elif key == "CF":
            if record["CF"]:
                record["CF"] += " " + value
            else:
                record["CF"] = value
        elif key == "PR":
            assert value.startswith("PROSITE; ")
            value = value[9:].rstrip(";")
            record["PR"].append(value)
        elif key == "CC":
            if value.startswith("-!- "):
                record["CC"].append(value[4:])
            elif value.startswith("    ") and record["CC"]:
                record["CC"][-1] += value[3:]
            # copyright notice is silently skipped
        elif key == "//":
            if record:
                return record
            else:  # This was the copyright notice
                continue
    if record:
        raise ValueError("Unexpected end of stream")