def testFindMultipleMatches(self):
"""
It must be possible to find more than one matching amino acid.
"""
aa1, aa2 = list(find('acid'))
self.assertEqual('Aspartic acid', aa1.name)
self.assertEqual('Glutamic acid', aa2.name)
def findOrDie(s):
"""
Look up an amino acid.
@param s: A C{str} amino acid specifier. This may be a full name,
a 3-letter abbreviation or a 1-letter abbreviation. Case is ignored.
@return: An C{AminoAcid} instance, if one can be found. Else exit.
"""
aa = find(s)
if aa:
return aa
else:
print("Unknown amino acid or codon: %s" % s, file=sys.stderr)
print("Valid arguments are: %s." % list(CODONS.keys()), file=sys.stderr)
sys.exit(1)
def findOrDie(s):
"""
Look up an amino acid.
@param s: A C{str} amino acid specifier. This may be a full name,
a 3-letter abbreviation or a 1-letter abbreviation. Case is ignored.
@return: An C{AminoAcid} instance, if one can be found. Else exit.
"""
aa = find(s)
if aa:
return aa
else:
print('Unknown amino acid or codon: %s' % s, file=sys.stderr)
print('Valid arguments are: %s.' % list(CODONS.keys()),
file=sys.stderr)
sys.exit(1)
def testFindByNameCaseIgnoredNameWithSpace(self):
"""
It must be possible to find an amino acid by its name when the name is
given in mixed case, including if the name has a space in it.
"""
aa = find('asparTIC aCId')
self.assertEqual('Aspartic acid', aa.name)
self.assertEqual('Asp', aa.abbrev3)
self.assertEqual('D', aa.abbrev1)
self.assertEqual(('GAC', 'GAT'), aa.codons)
self.assertEqual(HYDROPHILIC | SMALL | POLAR | NEGATIVE, aa.properties)
self.assertEqual(
{
'aliphaticity': -0.818181818182,
'aromaticity': -1.0,
'composition': 0.00363636363636,
'hydrogenation': -0.90243902439,
'hydropathy': -0.777777777778,
'hydroxythiolation': -0.348394768133,
'iep': -1.0,
'polar requirement': 1.0,
'polarity': 1.0,
'volume': -0.389221556886,
},
aa.propertyDetails)
self.assertEqual(
{
'aliphaticity': 1,
'aromaticity': 1,
'composition': 2,
'hydrogenation': 1,
'hydropathy': 1,
'hydroxythiolation': 2,
'iep': 1,
'polar requirement': 4,
'polarity': 4,
'volume': 3,
},
aa.propertyClusters)
def testFindByNameCaseIgnored(self):
"""
It must be possible to find an amino acid by its name when the name is
given in mixed case.
"""
aa = find('alaNIne')
self.assertEqual('Alanine', aa.name)
self.assertEqual('Ala', aa.abbrev3)
self.assertEqual('A', aa.abbrev1)
self.assertEqual(('GCA', 'GCC', 'GCG', 'GCT'), aa.codons)
self.assertEqual(HYDROPHOBIC | SMALL | TINY, aa.properties)
self.assertEqual(
{
'aliphaticity': 0.305785123967,
'aromaticity': -0.550128534704,
'composition': -1.0,
'hydrogenation': 0.8973042362,
'hydropathy': 0.4,
'hydroxythiolation': -0.265160523187,
'iep': -0.191489361702,
'polar requirement': -0.463414634146,
'polarity': -0.20987654321,
'volume': -0.664670658683,
},
aa.propertyDetails)
self.assertEqual(
{
'aliphaticity': 1,
'aromaticity': 1,
'composition': 1,
'hydrogenation': 1,
'hydropathy': 3,
'hydroxythiolation': 2,
'iep': 2,
'polar requirement': 2,
'polarity': 2,
'volume': 2,
},
aa.propertyClusters)
def testFindByNameCaseIgnoredNameWithSpace(self):
"""
It must be possible to find an amino acid by its name when the name is
given in mixed case, including if the name has a space in it.
"""
aa = find('asparTIC aCId')
self.assertEqual('Aspartic acid', aa.name)
self.assertEqual('Asp', aa.abbrev3)
self.assertEqual('D', aa.abbrev1)
self.assertEqual(('GAC', 'GAT'), aa.codons)
self.assertEqual(HYDROPHILIC | SMALL | POLAR | NEGATIVE, aa.properties)
self.assertEqual(
{
'aliphaticity': -0.818181818182,
'aromaticity': -1.0,
'composition': 0.00363636363636,
'hydrogenation': -0.90243902439,
'hydropathy': -0.777777777778,
'hydroxythiolation': -0.348394768133,
'iep': -1.0,
'polar requirement': 1.0,
'polarity': 1.0,
'volume': -0.389221556886,
},
aa.propertyDetails)
self.assertEqual(
{
'aliphaticity': 1,
'aromaticity': 1,
'composition': 2,
'hydrogenation': 1,
'hydropathy': 1,
'hydroxythiolation': 2,
'iep': 1,
'polar requirement': 4,
'polarity': 4,
'volume': 3,
},
aa.propertyClusters)
def testFindByNameCaseIgnored(self):
"""
It must be possible to find an amino acid by its name when the name is
given in mixed case.
"""
aa = find('alaNIne')
self.assertEqual('Alanine', aa.name)
self.assertEqual('Ala', aa.abbrev3)
self.assertEqual('A', aa.abbrev1)
self.assertEqual(('GCA', 'GCC', 'GCG', 'GCT'), aa.codons)
self.assertEqual(HYDROPHOBIC | SMALL | TINY, aa.properties)
self.assertEqual(
{
'aliphaticity': 0.305785123967,
'aromaticity': -0.550128534704,
'composition': -1.0,
'hydrogenation': 0.8973042362,
'hydropathy': 0.4,
'hydroxythiolation': -0.265160523187,
'iep': -0.191489361702,
'polar requirement': -0.463414634146,
'polarity': -0.20987654321,
'volume': -0.664670658683,
},
aa.propertyDetails)
self.assertEqual(
{
'aliphaticity': 1,
'aromaticity': 1,
'composition': 1,
'hydrogenation': 1,
'hydropathy': 3,
'hydroxythiolation': 2,
'iep': 2,
'polar requirement': 2,
'polarity': 2,
'volume': 2,
},
aa.propertyClusters)
def testFindUnknown(self):
"""
find must return C{None} when called with an unrecognized value.
"""
self.assertEqual(None, find('silly'))
def testFindUnknown(self):
"""
find must return C{None} when called with an unrecognized value.
"""
self.assertEqual(None, find('silly'))
#!/usr/bin/env python
from __future__ import print_function
import sys
from dark.aa import find
from dark.aa import CODONS
from dark.aa import AA_LETTERS, ALL_PROPERTIES, PROPERTY_NAMES
args = AA_LETTERS if len(sys.argv) == 1 else sys.argv[1:]
error = False
for arg in args:
aas = list(find(arg))
if aas:
for aa in aas:
print(aa.name)
print(' 3-letter abbreviation: %s' % aa.abbrev3)
print(' 1-letter abbreviation: %s' % aa.abbrev1)
print(' Codons: %s' % ', '.join(sorted(aa.codons)))
properties = []
print(' Properties:', end=' ')
for prop in ALL_PROPERTIES:
if aa.properties & prop:
properties.append(PROPERTY_NAMES[prop])
print(', '.join(properties))
print(' Property details:')
def testFindByPartialNameMixedCase(self):
"""
It must be possible to find an amino acid by a mixed-case partial name.
"""
aa = list(find('NiNe'))[0]
self.assertEqual('Alanine', aa.name)
def testFindUnknown(self):
"""
find must return an empty generator when called with an unrecognized
value.
"""
self.assertEqual([], list(find('silly')))
