handle structures with 100,000 or more atoms

- the pdb format requires a 5-character field for the atom number; the
  hybrid-36 format allows up to a ridiculous number of atoms

propka/hybrid36.py

@@ -0,0 +1,52 @@
+import string
+
+_hybrid36_upper_chars = set(string.ascii_uppercase)
+_hybrid36_lower_chars = set(string.ascii_lowercase)
+_hybrid36_digits = set(string.digits)
+_hybrid36_upper_set = _hybrid36_upper_chars | _hybrid36_digits
+_hybrid36_lower_set = _hybrid36_lower_chars | _hybrid36_digits
+
+def decode(input_string):
+    """
+    Convert an input string of a number in hybrid-36 format to an integer.
+
+    """
+    value_error_message = "invalid literal for hybrid-36 conversion: '%s'"
+
+    original_input_string = input_string
+    input_string = input_string.strip()
+
+    # Manually handle negative sign.
+    if input_string.startswith("-"):
+        sign = -1
+        input_string = input_string[1:]
+    else:
+        sign = 1
+
+    if not len(input_string):
+        raise ValueError(value_error_message % input_string)
+
+    # See http://cci.lbl.gov/hybrid_36/ for documentation on the format.
+
+    num_chars = len(input_string)
+    first_char = input_string[0]
+
+    if first_char in _hybrid36_digits:
+        return sign * int(input_string)
+    elif first_char in _hybrid36_upper_chars:
+        reference = - (10 * 36 ** (num_chars - 1) - 10 ** num_chars)
+        _hybrid36_set = _hybrid36_upper_set
+    elif first_char in _hybrid36_lower_chars:
+        reference = (16 * 36 ** (num_chars - 1) + 10 ** num_chars)
+        _hybrid36_set = _hybrid36_lower_set
+    else:
+        raise ValueError(value_error_message % original_input_string)
+
+    # Check the validity of the input string: ASCII characters should be
+    # either all uppercase or all lowercase.
+    for c in input_string[1:]:
+        if c not in _hybrid36_set:
+            raise ValueError(value_error_message % original_input_string)
+
+    # Convert with the int function.
+    return sign * (int(input_string, 36) + reference)