/usr/share/pyshared/chemfp/bitops.py is in python-chemfp 1.1p1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 | from __future__ import absolute_import
import os
import sys
import _chemfp
from _chemfp import (hex_isvalid, hex_popcount, hex_intersect_popcount,
hex_tanimoto, hex_contains)
from _chemfp import (byte_popcount, byte_intersect_popcount,
byte_tanimoto, byte_contains,
byte_intersect, byte_union, byte_difference)
__all__ = ["byte_popcount", "byte_intersect_popcount",
"byte_tanimoto", "byte_contains",
"hex_isvalid", "hex_popcount", "hex_intersect_popcount",
"hex_tanimoto", "hex_contains",
"get_methods", "get_alignments",
"get_alignment_methods", "set_alignment_method", "select_fastest_method"]
def get_methods():
return [_chemfp.get_method_name(i) for i in range(_chemfp.get_num_methods())]
def get_alignments():
return [_chemfp.get_alignment_name(i) for i in range(_chemfp.get_num_alignments())]
def get_alignment_methods():
settings = {}
for alignment in range(_chemfp.get_num_alignments()):
method = _chemfp.get_alignment_method(alignment)
settings[_chemfp.get_alignment_name(alignment)] = _chemfp.get_method_name(method)
return settings
def get_alignment_method(alignment):
try:
alignment_i = get_alignments().index(alignment)
except ValueError:
raise ValueError("Unknown alignment %r" % (alignment,))
return _chemfp.get_method_name(_chemfp.get_alignment_method(alignment_i))
def set_alignment_method(alignment, method):
try:
alignment_i = get_alignments().index(alignment)
except ValueError:
raise ValueError("Unknown alignment %r" % (alignment,))
try:
method_i = get_methods().index(method)
except ValueError:
raise ValueError("Unknown method %r" % (method,))
_chemfp.set_alignment_method(alignment_i, method_i)
def select_fastest_method(repeat=10000):
if repeat > 100000:
raise ValueError("repeat size is meaninglessly large")
if repeat < 1:
raise ValueError("repeat size must be 1 or larger (values under 1000 are likely useless)")
for alignment_i, name in enumerate(get_alignments()):
_chemfp.select_fastest_method(alignment_i, repeat)
def get_options():
return [_chemfp.get_option_name(i) for i in range(_chemfp.get_num_options())]
def get_option(option):
_chemfp.get_option(option)
def set_option(option, value):
_chemfp.set_option(option, value)
def print_report(out=sys.stdout):
from . import SOFTWARE
print >>out, "== Configuration report for", SOFTWARE, "=="
print >>out, "Available methods:", " ".join(get_methods())
print >>out, "Alignment methods:"
for alignment in get_alignments():
method = get_alignment_method(alignment)
print >>out, " %s: %s" % (alignment, method)
print >>out, "Option settings:"
for option in get_options():
print >>out, " %s: %s" % (option, _chemfp.get_option(option))
def use_environment_variables(environ=None):
if environ is None:
environ = os.environ
known = set()
for alignment in get_alignments():
name = "CHEMFP-" + alignment.upper()
known.add(name)
try:
value = environ[name]
except KeyError:
pass
else:
try:
set_alignment_method(alignment, value)
except ValueError, err:
print >>sys.stderr, "WARNING: Unable to use $%s = %r: %s" % (
(name, value, err))
for option in get_options():
name = "CHEMFP-" + option.upper()
known.add(name)
try:
value = environ[name]
except KeyError:
pass
else:
try:
set_option(option, int(value))
except ValueError, err:
print >>sys.stderr, "WARNING: Unable to use $%s = %r: %s" % (
(name, value, err))
known.add("CHEMFP-REPORT")
report = environ.get("CHEMFP-REPORT", "0") == "1"
if report:
set_option("report-popcount", 1)
set_option("report-intersect", 1)
known.add("CHEMFP-PRINT-CONFIG")
if (environ.get("CHEMFP-PRINT-CONFIG", "0") == "1" or report):
print_report(sys.stderr)
for k in environ:
if not k.startswith("CHEMFP-"):
continue
if k not in known:
print >>sys.stderr, "WARNING: Unknown chemfp environment variable %r" % (k,)
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