本文整理汇总了Python中mdt.uniform_bins函数的典型用法代码示例。如果您正苦于以下问题：Python uniform_bins函数的具体用法？Python uniform_bins怎么用？Python uniform_bins使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了uniform_bins函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: test_disulfide
def test_disulfide(self):
"""Test handling of disulfide bonds"""
mlib = self.get_all_libraries()
bsep = mdt.features.AtomBondSeparation(mlib,
bins=mdt.uniform_bins(20, 0, 1.0))
bsep_ss = mdt.features.AtomBondSeparation(mlib,
bins=mdt.uniform_bins(20, 0, 1.0),
disulfide=True)
env = self.get_environ()
mdl = modeller.model(env)
mdl.build_sequence('CC')
# When SG-SG distance is small enough, an extra bond
# (separation feature = 1) should be detected, but only with
# disulfide=True
for (dist, num) in [(2.6, 11.0), (2.4, 12.0)]:
sg1 = mdl.residues[0].atoms['SG']
sg2 = mdl.residues[1].atoms['SG']
sg1.x = sg1.y = sg1.z = 0.
sg2.x = sg2.y = 0.
sg2.z = dist
a = modeller.alignment(env)
a.append_model(mdl, atom_files='test', align_codes='test')
m = mdt.Table(mlib, features=bsep)
m.add_alignment(a, residue_span_range=(-999,0,0,999))
self.assertEqual(m[1], 11.0)
m2 = mdt.Table(mlib, features=bsep_ss)
m2.add_alignment(a, residue_span_range=(-999,0,0,999))
self.assertEqual(m2[1], num)
开发者ID:salilab，项目名称:mdt，代码行数:28，代码来源:test_bondsep.py
示例2: test_feature_sidechain_biso
def test_feature_sidechain_biso(self):
"""Check average sidechain Biso feature"""
env = self.get_environ()
mlib = self.get_mdt_library()
self.assertRaises(ValueError, mdt.features.SidechainBiso, mlib, bins=mdt.uniform_bins(5, 0, 10), protein=3)
sidechain_biso = mdt.features.SidechainBiso(mlib, bins=mdt.uniform_bins(5, 0, 10))
mdl = modeller.model(env)
mdl.build_sequence("A")
aln = modeller.alignment(env)
aln.append_model(mdl, align_codes="test")
s = aln[0]
# Mainchain atom Biso should be ignored:
for mainchain in ("N:1", "C:1", "O:1", "OXT:1", "CA:1"):
s.atoms[mainchain].biso = 1000
for (biso, bin) in (
(22, 2),
(32, 3), # Map regular values to bins
(0, -1), # Zero Biso should be "undefined"
(1, 3),
): # Biso < 2 is multiplied by 4pi^2
s.atoms["CB:1"].biso = biso
m = mdt.Table(mlib, features=sidechain_biso)
m.add_alignment(aln)
self.assertEqual(m.shape, (6,))
self.assertEqual(m.sum(), 1)
self.assertEqual(m[bin], 1)
开发者ID:salilab，项目名称:mdt，代码行数:26，代码来源:test_feature.py
示例3: test_feature_resind_diff
def test_feature_resind_diff(self):
"""Test the residue index difference feature"""
env = self.get_environ()
mlib = self.get_mdt_library()
diff = mdt.features.ResidueIndexDifference(mlib, bins=mdt.uniform_bins(21, -10, 1))
absdiff = mdt.features.ResidueIndexDifference(mlib, absolute=True, bins=mdt.uniform_bins(21, -10, 1))
aln = modeller.alignment(env, file="test/data/alignment.ali", align_codes="5fd1")
m1 = mdt.Table(mlib, features=diff)
m2 = mdt.Table(mlib, features=absdiff)
self.assertEqual(m1.symmetric, False)
self.assertEqual(m2.symmetric, True)
m1.add_alignment(aln, residue_span_range=(-999, -2, 2, 999))
m2.add_alignment(aln, residue_span_range=(-999, -2, 2, 999))
self.assertEqual(m1.sum(), 10920)
self.assertEqual(m2.sum(), 5460)
# span range should result in 0, +/- 1 bins being zero:
for m in (m1, m2):
self.assertEqual(m[9], 0.0)
self.assertEqual(m[10], 0.0)
self.assertEqual(m[11], 0.0)
# Non-absolute feature should have other bins symmetrically distributed:
for i in range(9):
self.assertEqual(m1[i], m[-2 - i])
# Absolute feature should have no negative values:
for i in range(9):
self.assertEqual(m2[i], 0.0)
开发者ID:salilab，项目名称:mdt，代码行数:26，代码来源:test_feature.py
示例4: test_feature_hbond
def test_feature_hbond(self):
"""Check hydrogen bond features"""
env = self.get_environ()
mlib = self.get_mdt_library()
mlib.hbond_classes.read("data/atmcls-hbda.lib")
donor = mdt.features.HydrogenBondDonor(mlib, mdt.uniform_bins(7, 1.0, 1.0))
accep = mdt.features.HydrogenBondAcceptor(mlib, mdt.uniform_bins(7, 1.0, 1.0))
totchg = mdt.features.HydrogenBondCharge(mlib, mdt.uniform_bins(9, 1.0, 1.0))
satisf = mdt.features.HydrogenBondSatisfaction(mlib, mdt.uniform_bins(100, 0.0, 10.0))
self.assertRaises(mdt.MDTError, mlib.hbond_classes.read, "data/atmcls-hbda.lib")
m = mdt.Table(mlib, features=donor)
m2 = mdt.Table(mlib, features=accep)
m3 = mdt.Table(mlib, features=satisf)
m4 = mdt.Table(mlib, features=totchg)
aln = modeller.alignment(env, file="test/data/alignment.ali")
m.add_alignment(aln)
m2.add_alignment(aln)
m3.add_alignment(aln)
m4.add_alignment(aln)
self.assertInTolerance(m[0], 295.0, 0.0005)
self.assertInTolerance(m[1], 139.0, 0.0005)
self.assertEqual(m[-1], 349.0)
self.assertInTolerance(m2[0], 236.0, 0.0005)
self.assertInTolerance(m2[1], 223.0, 0.0005)
self.assertEqual(m2[-1], 168.0)
self.assertInTolerance(m3[0], 1.0, 0.0005)
self.assertInTolerance(m3[1], 0.0, 0.0005)
self.assertEqual(m3[-1], 0.0)
self.assertInTolerance(m4[0], 78.0, 0.0005)
self.assertInTolerance(m4[1], 24.0, 0.0005)
self.assertEqual(m4[-1], 739.0)
# Exercise writing of hbond information to HDF5 files:
for t in (m, m2, m3, m4):
t.write_hdf5("test.hdf5")
os.unlink("test.hdf5")
开发者ID:salilab，项目名称:mdt，代码行数:35，代码来源:test_feature.py
示例5: test_feature_triplet_type
def test_feature_triplet_type(self):
"""Check triplet type features"""
env = self.get_environ()
mlib = self.get_mdt_library()
mlib.tuple_classes.read("data/trpcls.lib")
tuple_type = mdt.features.TupleType(mlib)
tuple_type2 = mdt.features.TupleType(mlib, pos2=True)
tuple_dist = mdt.features.TupleDistance(mlib, bins=mdt.uniform_bins(9, 2.0, 0.2))
tuple_angle1 = mdt.features.TupleAngle1(mlib, bins=mdt.uniform_bins(6, 0, 30.0))
tuple_dihed1 = mdt.features.TupleDihedral1(mlib, bins=mdt.uniform_bins(6, -180, 60.0))
tuple_dihed2 = mdt.features.TupleDihedral2(mlib, bins=mdt.uniform_bins(6, -180, 60.0))
tuple_dihed3 = mdt.features.TupleDihedral3(mlib, bins=mdt.uniform_bins(6, -180, 60.0))
self.assertRaises(mdt.MDTError, mlib.tuple_classes.read, "data/trpcls.lib")
m1 = mdt.Table(mlib, features=tuple_type)
m2 = mdt.Table(mlib, features=tuple_type2)
m3 = mdt.Table(mlib, features=tuple_dist)
m4 = mdt.Table(mlib, features=tuple_angle1)
m5 = mdt.Table(mlib, features=tuple_dihed1)
m6 = mdt.Table(mlib, features=tuple_dihed2)
m7 = mdt.Table(mlib, features=tuple_dihed3)
aln = modeller.alignment(env, file="test/data/tiny.ali")
for m in (m1, m2, m3, m4, m5, m6, m7):
m.add_alignment(aln, residue_span_range=(-9999, 0, 0, 9999))
self.assertInTolerance(m1[0], 1.0, 0.0005)
self.assertInTolerance(m1[1], 0.0, 0.0005)
self.assertInTolerance(m1[2], 1.0, 0.0005)
self.assertEqual(m1.shape, (236,))
self.assertEqual(m1[-1], 0.0)
self.assertInTolerance(m2[0], 60.0, 0.0005)
self.assertInTolerance(m2[1], 0.0, 0.0005)
self.assertInTolerance(m2[2], 60.0, 0.0005)
self.assertEqual(m2.shape, (236,))
self.assertEqual(m2[-1], 0.0)
self.assertInTolerance(m3[0], 0.0, 0.0005)
self.assertInTolerance(m3[1], 82.0, 0.0005)
self.assertInTolerance(m3[2], 226.0, 0.0005)
self.assertEqual(m3.shape, (10,))
self.assertInTolerance(m3[-1], 3018.0, 0.0005)
self.assertInTolerance(m4[0], 479.0, 0.0005)
self.assertInTolerance(m4[1], 806.0, 0.0005)
self.assertInTolerance(m4[2], 471.0, 0.0005)
self.assertEqual(m4.shape, (7,))
self.assertEqual(m4[-1], 0.0)
self.assertInTolerance(m5[0], 556.0, 0.0005)
self.assertInTolerance(m5[1], 642.0, 0.0005)
self.assertInTolerance(m5[2], 470.0, 6.0005)
self.assertEqual(m5.shape, (7,))
self.assertInTolerance(m5[-1], 180.0, 0.0005)
self.assertInTolerance(m6[0], 661.0, 0.0005)
self.assertInTolerance(m6[1], 520.0, 0.0005)
self.assertInTolerance(m6[2], 545.0, 6.0005)
self.assertEqual(m6.shape, (7,))
self.assertInTolerance(m6[-1], 112.0, 0.0005)
self.assertInTolerance(m7[0], 661.0, 0.0005)
self.assertInTolerance(m7[1], 520.0, 0.0005)
self.assertInTolerance(m7[2], 545.0, 6.0005)
self.assertEqual(m7.shape, (7,))
self.assertInTolerance(m7[-1], 112.0, 0.0005)
开发者ID:salilab，项目名称:mdt，代码行数:58，代码来源:test_feature.py
示例6: test_feature_combination
def test_feature_combination(self):
"""Check that invalid feature combinations are rejected"""
mlib = self.get_mdt_library()
atmdist = mdt.features.AtomDistance(mlib,
bins=mdt.uniform_bins(60, 0, 0.5))
resdist = mdt.features.ResidueDistance(mlib, protein=1,
bins=mdt.uniform_bins(7, 0, 2.0))
self.assertRaises(ValueError, self.get_test_mdt, mlib,
features=(resdist,atmdist))
开发者ID:salilab，项目名称:mdt，代码行数:9，代码来源:test_mdt.py
示例7: test_bond_span_range
def test_bond_span_range(self):
"""Test bond_span_range argument"""
env = self.get_environ()
mdl = model(env)
mdl.build_sequence('A')
aln = alignment(env)
aln.append_model(mdl, align_codes='test')
mlib = self.get_mdt_library()
mlib.bond_classes.read('data/bndgrp.lib')
dist = mdt.features.AtomDistance(mlib,
bins=mdt.uniform_bins(60, 0, 0.5))
# Only 4 direct chemical bonds (N-CA, CA-CB, CA-C, C-O) in ALA; note
# that bond library does not include OXT so C-OXT interaction is
# excluded
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, bond_span_range=(1,1),
residue_span_range=(0,0,0,0))
self.assertEqual(m.sample_size, 4.0)
# Only 2 dihedrals (N-CA-C-O, O-C-CA-CB)
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, bond_span_range=(3,3),
residue_span_range=(0,0,0,0))
self.assertEqual(m.sample_size, 2.0)
# 4 bonds, 4 angles and 2 dihedrals: 10 in total
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, bond_span_range=(1,3),
residue_span_range=(0,0,0,0))
self.assertEqual(m.sample_size, 10.0)
# Check for bonds between residues (just the N-C bond here)
mdl = model(env)
mdl.build_sequence('AA')
aln = alignment(env)
aln.append_model(mdl, align_codes='test')
# Force a non-symmetric scan (to check handling of bond separation
# regardless of which order atom indices are in)
diff = mdt.features.ResidueIndexDifference(mlib,
bins=mdt.uniform_bins(21, -10, 1))
m = mdt.Table(mlib, features=(dist,diff))
m.add_alignment(aln, bond_span_range=(0,1),
residue_span_range=(-10,-1,1,10))
self.assertEqual(m.sample_size, 2.0)
# Bonds never span chains
mdl = model(env)
mdl.build_sequence('A/A')
aln = alignment(env)
aln.append_model(mdl, align_codes='test')
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, bond_span_range=(0,99999),
residue_span_range=(-10,-1,1,10))
self.assertEqual(m.sample_size, 0.0)
开发者ID:salilab，项目名称:mdt，代码行数:56，代码来源:test_mdt.py
示例8: test_feature_alpha_content
def test_feature_alpha_content(self):
"""Check alpha content feature"""
env = self.get_environ()
mlib = self.get_mdt_library()
self.assertRaises(ValueError, mdt.features.AlphaContent, mlib, bins=mdt.uniform_bins(10, 0, 0.1), protein=3)
alpha = mdt.features.AlphaContent(mlib, bins=mdt.uniform_bins(10, 0, 0.1))
for (alnfile, bin) in (("tiny.ali", 0), ("alignment.ali", 5)):
m = mdt.Table(mlib, features=alpha)
a = modeller.alignment(env, file=os.path.join("test", "data", alnfile))
m.add_alignment(a)
self.assertEqual(m.shape, (11,))
self.assertEqual(m.sum(), 1)
self.assertEqual(m[bin], 1)
开发者ID:salilab，项目名称:mdt，代码行数:13，代码来源:test_feature.py
示例9: test_write_2dsplinelib
def test_write_2dsplinelib(self):
"""Test the write_2dsplinelib function"""
mlib = self.get_mdt_library()
restype = mdt.features.ResidueType(mlib)
phi = mdt.features.PhiDihedral(mlib,
bins=mdt.uniform_bins(18, -180.0, 40.0))
psi = mdt.features.PsiDihedral(mlib,
bins=mdt.uniform_bins(18, -180.0, 40.0))
m = self.get_test_mdt(mlib, [restype, phi, psi])
mdt.write_2dsplinelib(open('test.out', 'w'), m)
# Make sure that valid Python code was produced
code = compile(open('test.out').read(), 'test.out', 'exec')
os.unlink('test.out')
开发者ID:salilab，项目名称:mdt，代码行数:15，代码来源:test_bondlib.py
示例10: test_abstract
def test_abstract(self):
"""Should not be able to instantiate abstract features"""
env = self.get_environ()
mlib = self.get_mdt_library()
bins = mdt.uniform_bins(10, 0, 1.0)
for feat in [
mdt.features.Protein,
mdt.features.ProteinPair,
mdt.features.Residue,
mdt.features.ResiduePair,
mdt.features.AlignedResidue,
mdt.features.AlignedResiduePair,
mdt.features.Atom,
mdt.features.AtomPair,
mdt.features.Tuple,
mdt.features.TuplePair,
mdt.features.ChemicalBond,
]:
self.assertRaises(TypeError, feat, mlib, bins)
for feat in [
mdt.features.ResidueFixedBins,
mdt.features.AtomFixedBins,
mdt.features.TupleFixedBins,
mdt.features.ChemicalBondFixedBins,
]:
self.assertRaises(TypeError, feat, mlib)
开发者ID:salilab，项目名称:mdt，代码行数:26，代码来源:test_feature.py
示例11: test_integrate
def test_integrate(self):
"""Make sure MDT integration works"""
env = self.get_environ()
mlib = self.get_mdt_library()
restyp0 = mdt.features.ResidueType(mlib, protein=0)
restyp1 = mdt.features.ResidueType(mlib, protein=1)
chi1 = mdt.features.Chi1Dihedral(mlib,
mdt.uniform_bins(36, -180, 10))
m1 = mdt.Table(mlib, features=restyp0)
m2 = mdt.Table(mlib, features=restyp1)
mboth = mdt.Table(mlib, features=(restyp0,restyp1))
seq1 = "AFVVTDNCIK"
seq2 = "DCVEVCPVDC"
aln = alignment(env)
aln.append_sequence(seq1)
aln.append_sequence(seq2)
for m in (m1, m2, mboth):
m.add_alignment(aln)
# Number of features must be correct:
for features in ((), (restyp0,restyp1), (restyp0,restyp1,chi1)):
self.assertRaises(ValueError, mboth.integrate, features=features)
# Features must exist in input MDT:
self.assertRaises(ValueError, mboth.integrate, features=chi1)
m1int = mboth.integrate(features=restyp0)
self.assertMDTsEqual(m1, m1int)
m2int = mboth.integrate(features=restyp1)
self.assertMDTsEqual(m2, m2int)
开发者ID:salilab，项目名称:mdt，代码行数:28，代码来源:test_mdt.py
示例12: test_tuple_pair_bond_span_range
def test_tuple_pair_bond_span_range(self):
"""Test bond_span_range with tuple pair scan"""
env = self.get_environ()
mdl = model(env)
mdl.build_sequence('A')
aln = alignment(env)
aln.append_model(mdl, align_codes='test')
mlib = self.get_mdt_library()
mlib.bond_classes.read('data/bndgrp.lib')
mlib.tuple_classes.read('data/trpcls.lib')
typ = mdt.features.TupleType(mlib)
typ2 = mdt.features.TupleType(mlib, pos2=True)
dist = mdt.features.TupleDistance(mlib,
bins=mdt.uniform_bins(9, 2.0, 0.2))
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, residue_span_range=(0,0,0,0))
self.assertEqual(m.sample_size, 10.0)
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, bond_span_range=(1,1),
residue_span_range=(0,0,0,0))
# Bond span should restrict interactions to 6
# (C:CA:CB-CA:C:O, CA:C:O-N:CA:C, CA:C:O-N:CA:CB, and the reverse)
self.assertEqual(m.sample_size, 6.0)
开发者ID:salilab，项目名称:mdt，代码行数:25，代码来源:test_mdt.py
示例13: test_chain_span_range
def test_chain_span_range(self):
"""Test chain_span_range argument"""
env = self.get_environ()
mdl = model(env)
mdl.build_sequence('G/G')
aln = alignment(env)
aln.append_model(mdl, align_codes='test')
mlib = self.get_mdt_library()
mlib.tuple_classes.read('data/dblcls.lib')
tuple_dist = mdt.features.TupleDistance(mlib,
bins=mdt.uniform_bins(49, 2.0, 0.2))
# All chain differences should be out of range, so this MDT should
# end up empty:
m = mdt.Table(mlib, features=tuple_dist)
m.add_alignment(aln, chain_span_range=(-999, -999, 999, 999),
residue_span_range=(-999, 0, 0, 999))
self.assertEqual(m.sum(), 0.0)
# Default chain separation should allow intra-chain interactions, so
# should yield more (56) than only allowing inter-chain
# interactions (32)
m = mdt.Table(mlib, features=tuple_dist)
m.add_alignment(aln, residue_span_range=(-999, 0, 0, 999))
self.assertEqual(m.sum(), 56.0)
m = mdt.Table(mlib, features=tuple_dist)
m.add_alignment(aln, chain_span_range=(-999, -1, 1, 999),
residue_span_range=(-999, 0, 0, 999))
self.assertEqual(m.sum(), 32.0)
开发者ID:salilab，项目名称:mdt，代码行数:27，代码来源:test_mdt.py
示例14: test_add
def test_add(self):
"""Check adding MDTs"""
mlib = self.get_mdt_library()
bins = mdt.uniform_bins(3, -1.0, 1.5)
xray0 = mdt.features.XRayResolution(mlib, bins, protein=0)
xray1 = mdt.features.XRayResolution(mlib, bins, protein=1)
m1 = mdt.Table(mlib, features=xray0)
for (n, val) in enumerate((1,2,3,4)):
m1[n] = val
m2 = mdt.Table(mlib, features=xray0)
for (n, val) in enumerate((10,20,30,40)):
m2[n] = val
m3 = m1 + m2
m1 += m2
self.assertMDTsEqual(m1, m3)
for (n, val) in enumerate((11,22,33,44)):
self.assertEqual(m3[n], val)
# Cannot add if numbers of features are different
badmdt = mdt.Table(mlib, features=(xray0, xray1))
self.assertRaises(ValueError, m1.__add__, badmdt)
# Cannot add if feature types are different
badmdt = mdt.Table(mlib, features=xray1)
self.assertRaises(ValueError, m1.__add__, badmdt)
# Cannot add if starts are different
badmdt = m2.reshape(features=xray0, offset=1, shape=0)
self.assertRaises(ValueError, m1.__add__, badmdt)
# Cannot add if nbins are different
badmdt = m2.reshape(features=xray0, offset=0, shape=-1)
self.assertRaises(ValueError, m1.__add__, badmdt)
开发者ID:salilab，项目名称:mdt，代码行数:32，代码来源:test_mdt.py
示例15: test_bond_span_range_disulfide
def test_bond_span_range_disulfide(self):
"""Test bond_span_range argument with disulfides"""
env = self.get_environ()
mdl = model(env)
mdl.read('1HEL.pdb')
aln = alignment(env)
aln.append_model(mdl, align_codes='test')
mlib = self.get_mdt_library()
mlib.bond_classes.read('data/bndgrp.lib')
dist = mdt.features.AtomDistance(mlib,
bins=mdt.uniform_bins(60, 0, 0.5))
# Four disulfide bond in this structure
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, bond_span_range=(1,1),
residue_span_range=(-9999,0,0,9999))
m2 = mdt.Table(mlib, features=dist)
m2.add_alignment(aln, bond_span_range=(1,1),
residue_span_range=(-9999,0,0,9999), disulfide=True)
self.assertEqual(m2.sample_size-m.sample_size, 4.0)
m = mdt.Table(mlib, features=dist)
m.add_alignment(aln, bond_span_range=(3,3),
residue_span_range=(-9999,0,0,9999))
m2 = mdt.Table(mlib, features=dist)
m2.add_alignment(aln, bond_span_range=(3,3),
residue_span_range=(-9999,0,0,9999), disulfide=True)
self.assertEqual(m2.sample_size-m.sample_size, 12.0)
开发者ID:salilab，项目名称:mdt，代码行数:29，代码来源:test_mdt.py
示例16: test_feature_residue_distance_difference
def test_feature_residue_distance_difference(self):
"""Check residue-residue distance difference feature"""
env = self.get_environ()
mlib = self.get_mdt_library()
ddist = mdt.features.ResidueDistanceDifference(mlib, bins=mdt.uniform_bins(20, -10, 1))
aln = modeller.alignment(env, file="test/data/struc-struc.ali")
m = mdt.Table(mlib, features=ddist)
m.add_alignment(aln)
self.assertEqual(m[9], 20)
self.assertEqual(m[10], 20)
self.assertEqual(sum([b for b in m]), 40)
self.assertEqual(m[-1], 0)
# Undefined (-999) coordinates in either structure should put
# features in the undefined bin
oldx = aln[0].residues[0].atoms["CA"].x
aln[0].residues[0].atoms["CA"].x = -999
m = mdt.Table(mlib, features=ddist)
m.add_alignment(aln)
self.assertEqual(m[-1], 16)
aln[0].residues[0].atoms["CA"].x = oldx
aln[1].residues[0].atoms["CA"].x = -999
m = mdt.Table(mlib, features=ddist)
m.add_alignment(aln)
self.assertEqual(m[-1], 16)
开发者ID:salilab，项目名称:mdt，代码行数:26，代码来源:test_feature.py
示例17: test_symmetric
def test_symmetric(self):
"""Test symmetric/asymmetric residue pair features"""
env = self.get_environ()
mlib = self.get_mdt_library()
bins = mdt.uniform_bins(10, 0, 1.0)
dist = mdt.features.ResidueDistance(mlib, bins)
avresacc = mdt.features.AverageResidueAccessibility(mlib, bins)
avndif = mdt.features.AverageNeighborhoodDifference(mlib, bins)
diff = mdt.features.ResidueIndexDifference(mlib, bins)
ddist = mdt.features.ResidueDistanceDifference(mlib, bins)
avgapdist = mdt.features.AverageGapDistance(mlib, bins)
sym_features = (avndif, avresacc, avgapdist)
asym_features = (dist, ddist, diff)
for a in sym_features:
m = mdt.Table(mlib, features=a)
self.assertEqual(m.symmetric, True)
for a in asym_features:
m = mdt.Table(mlib, features=a)
self.assertEqual(m.symmetric, False)
# Combinations are only symmetric if all features are symmetric:
for (a, b, symm) in (
(sym_features[0], sym_features[1], True),
(asym_features[0], asym_features[1], False),
(sym_features[0], asym_features[0], False),
):
m = mdt.Table(mlib, features=(a, b))
self.assertEqual(m.symmetric, symm)
开发者ID:salilab，项目名称:mdt，代码行数:27，代码来源:test_feature.py
示例18: test_feature_dihedral_type
def test_feature_dihedral_type(self):
"""Check dihedral type features"""
env = self.get_environ()
mlib = self.get_mdt_library()
mlib.dihedral_classes.read("data/impgrp.lib")
dihedtype = mdt.features.DihedralType(mlib)
dihedral = mdt.features.Dihedral(mlib, bins=mdt.uniform_bins(288, -180, 1.25))
self.assertRaises(mdt.MDTError, mlib.dihedral_classes.read, "data/impgrp.lib")
m = mdt.Table(mlib, features=dihedtype)
m2 = mdt.Table(mlib, features=dihedral)
aln = modeller.alignment(env, file="test/data/alignment.ali")
m.add_alignment(aln)
m2.add_alignment(aln)
self.assertInTolerance(m[0], 7.0, 0.0005)
self.assertInTolerance(m[2], 9.0, 0.0005)
self.assertInTolerance(m[4], 11.0, 0.0005)
self.assertEqual(m.shape, (79,))
self.assertEqual(m[-1], 0.0)
self.assertInTolerance(m2[143], 60.0, 1.0005)
self.assertInTolerance(m2[144], 53.0, 1.0005)
self.assertInTolerance(m2[145], 24.0, 0.0005)
self.assertEqual(m2.shape, (289,))
self.assertEqual(m2[-1], 0.0)
# Exercise writing of dihedral class information to HDF5 files:
m.write_hdf5("test.hdf5")
os.unlink("test.hdf5")
开发者ID:salilab，项目名称:mdt，代码行数:26，代码来源:test_feature.py
示例19: test_external
def test_external(self):
"""Check bond separation feature between residues"""
mlib = self.get_all_libraries()
attyp1 = mdt.features.AtomType(mlib)
attyp2 = mdt.features.AtomType(mlib, pos2=True)
bsep = mdt.features.AtomBondSeparation(mlib,
bins=mdt.uniform_bins(20, 0, 1.0))
m = self.build_mdt_from_sequence(mlib, [attyp1, attyp2, bsep],
'ARN', residue_span_range=(-999,-1,1,999))
atom_types = {}
for n, b in enumerate(m.features[0].bins):
atom_types[b.symbol] = n
def assertBondSep(at1, at2, numbond, sep):
bins = [b for b in m[atom_types[at1]][atom_types[at2]]]
self.assertEqual(sum(bins), numbond)
self.assertEqual(bins[sep], numbond)
# Check known bond separations between adjacent residues
assertBondSep('AN', 'RN', numbond=1, sep=3)
assertBondSep('AC', 'RN', numbond=1, sep=1)
# Check known bond separations between non-adjacent residues
assertBondSep('AN', 'NN', numbond=1, sep=6)
assertBondSep('AN', 'NC', numbond=1, sep=8)
assertBondSep('ACB', 'NCG', numbond=1, sep=9)
开发者ID:salilab，项目名称:mdt，代码行数:26，代码来源:test_bondsep.py
示例20: test_feature_iresol
def test_feature_iresol(self):
"""Check resolution features"""
env = self.get_environ()
mlib = self.get_mdt_library()
bins = mdt.uniform_bins(3, -1.0, 1.5)
xray0 = mdt.features.XRayResolution(mlib, bins, protein=0)
xray0_nmr = mdt.features.XRayResolution(mlib, bins, protein=0, nmr=1.0)
xray1 = mdt.features.XRayResolution(mlib, bins, protein=1)
xray2 = mdt.features.XRayResolution(mlib, bins, protein=2)
# Check valid range for protein argument
for p in (-1, 3):
self.assertRaises(ValueError, mdt.features.XRayResolution, mlib, bins, protein=p)
m = self.get_test_mdt(mlib, features=xray0)
m2 = self.get_test_mdt(mlib, features=xray1)
self.assertEqual(m.shape, (4,))
self.assertEqual([b for b in m], [0.0, 1.0, 1.0, 0.0])
self.assertMDTDataEqual(m, m2)
for (code, feat, bin) in (
("bin0", xray0, 0),
("bin0", xray0_nmr, 1),
("bin1", xray0, 1),
("bin2", xray0, 2),
("undef1", xray0, 3),
("undef2", xray0, 3),
):
m = mdt.Table(mlib, features=feat)
aln = modeller.alignment(env, file="test/data/resol.ali", align_codes=code)
m.add_alignment(aln)
self.assertEqual(m[bin], 1.0)
开发者ID:salilab，项目名称:mdt，代码行数:30，代码来源:test_feature.py
注：本文中的mdt.uniform_bins函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
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