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from __future__ import with_statement
import sys
import unittest2
import tempfile
import shutil
import os
import support
try:
import rdkit
has_rdkit = True
skip_rdkit = False
except ImportError:
has_rdkit = False
skip_rdkit = True
if not support.can_skip("rdkit"):
skip_rdkit = False
import rdkit
if has_rdkit:
from chemfp.commandline import rdkit2fps
runner = support.Runner(rdkit2fps.main)
else:
runner = None
MACCS_SMI = support.fullpath("maccs.smi")
class TestMACCS(unittest2.TestCase):
def test_bitorder(self):
result = runner.run_fps("--maccs166", 7, MACCS_SMI)
# The fingerprints are constructed to test the first few bytes.
self.assertEquals(result[0][:6], support.set_bit(2))
self.assertEquals(result[1][:6], support.set_bit(3))
self.assertEquals(result[2][:6], support.set_bit(4))
self.assertEquals(result[3][:6], support.set_bit(5))
self.assertEquals(result[4][:6], support.set_bit(9))
self.assertEquals(result[5][:6], support.set_bit(10))
self.assertEquals(result[6][:6], support.set_bit(16))
def test_type(self):
for line in runner.run("--maccs166", MACCS_SMI):
if line.startswith("#type="):
self.assertEquals(line, "#type=RDKit-MACCS166/1")
return
self.assertEquals("could not find", "#type line")
TestMACCS = unittest2.skipIf(skip_rdkit, "RDKit not installed")(TestMACCS)
_fp1 = "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"
assert len(_fp1) == 2048 // 4
def get_field_and_first(cmdline, field):
result = runner.run(cmdline)
field_value = None
first = None
for line in result:
if line.startswith(field):
field_value = line
if not line.startswith("#"):
first = line
break
return (field_value, first)
class TestRDKFingerprints(unittest2.TestCase):
def assertIn(self, substr, str):
self.assertEquals(substr in str, True, str)
def test_default(self):
result = runner.run_fps("", 19)
self.assertEquals(result[0], _fp1 + "\t9425004")
self.assertNotEquals(result[1].split()[0], _fp1)
# All must have the same length (since the fp lengths and ids lengths are the same
self.assertEquals(len(set(map(len, result))), 1, set(map(len, result)))
def test_as_rdk(self):
result = runner.run_fps("--RDK", 19)
self.assertEquals(result[0], _fp1 + "\t9425004")
self.assertNotEquals(result[1].split()[0], _fp1)
# All must have the same length (since the fp lengths and ids lengths are the same
self.assertEquals(len(set(map(len, result))), 1, set(map(len, result)))
def test_num_bits_default(self):
result = runner.run_fps("--fpSize 2048", 19)
self.assertEquals(result[0], _fp1 + "\t9425004")
self.assertNotEquals(result[1].split()[0], _fp1)
def test_num_bits_64(self):
field, first = get_field_and_first("--fpSize 16", "#num_bits=")
self.assertEquals(field, "#num_bits=16")
self.assertEquals(first, "ffff\t9425004")
def test_num_bits_1(self):
field, first = get_field_and_first("--fpSize 1", "#num_bits=")
self.assertEquals(field, "#num_bits=1")
self.assertEquals(first, "01\t9425004")
def test_num_bits_2(self):
field, first = get_field_and_first("--fpSize 2", "#num_bits=")
self.assertEquals(field, "#num_bits=2")
self.assertEquals(first, "03\t9425004")
def test_num_bits_too_small(self):
result = runner.run_exit("--fpSize 0")
self.assertIn("--fpSize must be positive", result)
def test_bits_per_hash_default(self):
field, first = get_field_and_first("--nBitsPerHash 4", "#type=")
self.assertEquals(field,
"#type=RDKit-Fingerprint/1 minPath=1 maxPath=7 fpSize=2048 nBitsPerHash=4 useHs=1")
self.assertEquals(first.split()[0], _fp1)
def test_bits_per_hash(self):
field, first = get_field_and_first("--nBitsPerHash 1", "#type")
self.assertEquals(field,
"#type=RDKit-Fingerprint/1 minPath=1 maxPath=7 fpSize=2048 nBitsPerHash=1 useHs=1")
self.assertNotEquals(first.split()[0], _fp1)
def test_bits_per_hash_too_small(self):
result = runner.run_exit("--nBitsPerHash 0")
self.assertIn("--nBitsPerHash must be a positive value", result)
def test_min_path_default(self):
field, first = get_field_and_first("--minPath 1", "#type")
self.assertEquals(field,
"#type=RDKit-Fingerprint/1 minPath=1 maxPath=7 fpSize=2048 nBitsPerHash=4 useHs=1")
self.assertEquals(first.split()[0], _fp1)
def test_min_path_2(self):
field, first = get_field_and_first("--minPath 2", "#type")
self.assertEquals(field,
"#type=RDKit-Fingerprint/1 minPath=2 maxPath=7 fpSize=2048 nBitsPerHash=4 useHs=1")
self.assertNotEquals(first.split()[0], _fp1)
def test_min_path_too_small(self):
result = runner.run_exit("--minPath 0")
self.assertIn("--minPath must be a positive value", result)
def test_min_path_too_large(self):
result = runner.run_exit("--minPath 5 --maxPath 4")
self.assertIn("--minPath must not be greater than --maxPath", result)
def test_max_path_default(self):
field, first = get_field_and_first("--maxPath 7", "#type")
self.assertEquals(field,
"#type=RDKit-Fingerprint/1 minPath=1 maxPath=7 fpSize=2048 nBitsPerHash=4 useHs=1")
self.assertEquals(first.split()[0], _fp1)
def test_max_path_6(self):
field, first = get_field_and_first("--maxPath 6", "#type")
self.assertEquals(field,
"#type=RDKit-Fingerprint/1 minPath=1 maxPath=6 fpSize=2048 nBitsPerHash=4 useHs=1")
self.assertNotEquals(first.split()[0], _fp1)
# def test_ignore_Hs(self):
# I don't have a good test case for this... XXX
TestRDKFingerprints = unittest2.skipIf(skip_rdkit, "RDKit not installed")(TestRDKFingerprints)
class TestIO(unittest2.TestCase, support.TestIdAndErrors):
_runner = runner
def test_input_format(self):
def without_source_header(cmdline, source):
return [line for line in runner.run(cmdline, source)
if not line.startswith("#source=") and
not line.startswith("#date=")]
result1 = without_source_header("", support.PUBCHEM_SDF)
result2 = without_source_header("", support.PUBCHEM_SDF_GZ)
self.assertEquals(result1, result2)
result3 = without_source_header("--in sdf.gz", support.PUBCHEM_SDF_GZ)
self.assertEquals(result1, result3)
result4 = without_source_header("--in sdf", support.PUBCHEM_ANOTHER_EXT)
self.assertEquals(result1, result4)
def test_output(self):
dirname = tempfile.mkdtemp(prefix="test_rdkit2fps")
output_filename = os.path.join(dirname, "blah.fps")
assert len(output_filename.split()) == 1
try:
result = runner.run("-o " + output_filename)
assert len(result) == 0
with open(output_filename) as f:
result = f.readlines()
finally:
shutil.rmtree(dirname)
self.assertEquals(result[0], "#FPS1\n")
while result and result[0].startswith("#"):
del result[0]
self.assertEquals(len(result), 19)
self.assertEquals(result[0], _fp1 + "\t9425004\n")
def test_bad_format(self):
result = runner.run_exit("--in spam")
self.assertIn("Unsupported format specifier: 'spam'", result)
TestIO = unittest2.skipIf(skip_rdkit, "RDKit not installed")(TestIO)
if __name__ == "__main__":
unittest2.main()
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