26a5ab042e
- use autosummary (with custom module template) - updated module docs for all modules so that they are included with sphinx autodocs
69 lines
2.1 KiB
Python
69 lines
2.1 KiB
Python
"""
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Hybrid36 PDB-like file format
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=============================
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`hybrid36`_ is an alternative PDB format that can encode larger atom
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numbers. This module provides the :func:`decode` functon to parse the
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atom numbers in hybrid36 "PDB" files.
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.. _hybrid36: http://cci.lbl.gov/hybrid_36/
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"""
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import string
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_HYBRID36_UPPER_CHARS = set(string.ascii_uppercase)
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_HYBRID36_LOWER_CHARS = set(string.ascii_lowercase)
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_HYBRID36_DIGITS = set(string.digits)
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_HYBRID36_UPPER_SET = _HYBRID36_UPPER_CHARS | _HYBRID36_DIGITS
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_HYBRID36_LOWER_SET = _HYBRID36_LOWER_CHARS | _HYBRID36_DIGITS
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def decode(input_string):
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"""Convert an input string of a number in hybrid-36 format to an integer.
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Args:
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input_string: input string
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Returns:
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integer
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"""
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value_error_message = "invalid literal for hybrid-36 conversion: '{0:s}'"
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original_input_string = input_string
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input_string = input_string.strip()
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# Manually handle negative sign.
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if input_string.startswith("-"):
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sign = -1
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input_string = input_string[1:]
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else:
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sign = 1
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if len(input_string) == 0:
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raise ValueError(value_error_message.format(input_string))
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# See http://cci.lbl.gov/hybrid_36/ for documentation on the format.
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num_chars = len(input_string)
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first_char = input_string[0]
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if first_char in _HYBRID36_DIGITS:
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return sign * int(input_string)
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elif first_char in _HYBRID36_UPPER_CHARS:
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reference = - (10 * 36 ** (num_chars - 1) - 10 ** num_chars)
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_hybrid36_set = _HYBRID36_UPPER_SET
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elif first_char in _HYBRID36_LOWER_CHARS:
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reference = (16 * 36 ** (num_chars - 1) + 10 ** num_chars)
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_hybrid36_set = _HYBRID36_LOWER_SET
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else:
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raise ValueError(value_error_message.format(original_input_string))
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# Check the validity of the input string: ASCII characters should be
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# either all uppercase or all lowercase.
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for char in input_string[1:]:
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if char not in _hybrid36_set:
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raise ValueError(value_error_message.format(original_input_string))
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# Convert with the int function.
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return sign * (int(input_string, 36) + reference)
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