class AtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID', model=1, chain='A', component_id='C',
component_number=50, name="C1'", symmetry='6_555',
x=-1, y=0, z=0)
def test_has_item_access(self):
self.assertEqual(-1, self.atom.x)
def test_computes_a_unit_id(self):
val = self.atom.unit_id()
ans = "1GID|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def test_computes_its_component_id(self):
val = self.atom.component_unit_id()
ans = "1GID|1|A|C|50||||6_555"
self.assertEqual(val, ans)
def test_can_get_coordinates(self):
val = self.atom.coordinates()
ans = np.array([-1, 0, 0])
np.testing.assert_array_equal(val, ans)
def test_can_get_distance_between_atoms(self):
val = self.atom.distance(Atom(x=1, y=0, z=0))
self.assertEqual(2.0, val)
class AtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID',
model=1,
chain='A',
component_id='C',
component_number=50,
name="C1'",
symmetry='6_555',
x=-1,
y=0,
z=0)
def test_has_item_access(self):
self.assertEqual(-1, self.atom.x)
def test_computes_a_unit_id(self):
val = self.atom.unit_id()
ans = "1GID|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def test_computes_its_component_id(self):
val = self.atom.component_unit_id()
ans = "1GID|1|A|C|50||||6_555"
self.assertEqual(val, ans)
def test_can_get_coordinates(self):
val = self.atom.coordinates()
ans = np.array([-1, 0, 0])
np.testing.assert_array_equal(val, ans)
def test_can_get_distance_between_atoms(self):
val = self.atom.distance(Atom(x=1, y=0, z=0))
self.assertEqual(2.0, val)
class AtomTransformationTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID',
model=1,
chain='A',
component_id='C',
component_number=50,
name="C1'",
symmetry='6_555',
x=-1,
y=0,
z=2,
type='Bob',
polymeric=True)
trans = np.array([[1.0, 0.0, 0.0, 0.0], [0.0, -1.0, 0.0, 97.240],
[0.0, 0.0, -1.0, 0.0], [0.0, 0.0, 0.0, 1.0]])
self.trans = self.atom.transform(trans)
def test_transform_moves_coordiantes(self):
val = [self.trans.x, self.trans.y, self.trans.z]
ans = [-1.0, 97.240, -2.0]
self.assertEquals(ans, val)
def test_transform_preserves_unit_id(self):
val = self.trans.unit_id()
ans = self.atom.unit_id()
self.assertEquals(ans, val)
def test_perserves_the_type(self):
self.assertEquals('Bob', self.trans.type)
def test_perserves_the_polymeric(self):
self.assertEquals(True, self.trans.polymeric)
def setUp(self):
atoms = [
Atom(name='N9', x=3.0, y=3.0, z=3.0),
Atom(name='C4', x=2.0, y=2.0, z=2.0),
Atom(name='N3', x=1.0, y=1.0, z=1.0),
]
self.residue = Component(atoms, sequence='A')
class AtomTransformationTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID', model=1, chain='A', component_id='C',
component_number=50, name="C1'", symmetry='6_555',
x=-1, y=0, z=2, type='Bob', polymeric=True)
trans = np.array([[1.0, 0.0, 0.0, 0.0],
[0.0, -1.0, 0.0, 97.240],
[0.0, 0.0, -1.0, 0.0],
[0.0, 0.0, 0.0, 1.0]])
self.trans = self.atom.transform(trans)
def test_transform_moves_coordiantes(self):
val = [self.trans.x, self.trans.y, self.trans.z]
ans = [-1.0, 97.240, -2.0]
self.assertEquals(ans, val)
def test_transform_preserves_unit_id(self):
val = self.trans.unit_id()
ans = self.atom.unit_id()
self.assertEquals(ans, val)
def test_perserves_the_type(self):
self.assertEquals('Bob', self.trans.type)
def test_perserves_the_polymeric(self):
self.assertEquals(True, self.trans.polymeric)
def setUp(self):
self.atoms = [
Atom(name='N9', x=3.0, y=3.0, z=3.0),
Atom(name='C4', x=2.0, y=2.0, z=2.0),
Atom(name='N3', x=1.0, y=1.0, z=1.0),
Atom(name='C3', x=0.0, y=0.0, z=0.0),
]
self.component = Component(self.atoms)
def setUp(self):
self.atoms = [
Atom(type='C', name='a1', component_number=3, x=1.0, y=0.0, z=0.0),
Atom(type='C', name='a2', component_number=2, x=2.0, y=0.0, z=0.0),
Atom(type='N', name='b1', component_number=1, x=3.0, y=0.0, z=0.0),
Atom(type='N', name='c2', component_number=0, x=0.0, y=1.0, z=0.0)
]
self.proxy = AtomProxy(self.atoms)
def setUp(self):
atoms = [
Atom(name='N9', x=3.0, y=3.0, z=3.0),
Atom(name='C4', x=2.0, y=2.0, z=2.0),
Atom(name='N3', x=1.0, y=1.0, z=1.0),
]
self.residue = Component(atoms, type='rna', pdb='1GID', model=1,
chain='A', sequence='C', number=50,
symmetry='6_555')
def setUp(self):
self.atom = Atom(pdb='4OQ8',
model=1,
chain='A',
component_id='SER',
component_number=27,
name='CA',
alt_id='A',
symmetry='PP')
def setUp(self):
self.atom = Atom(pdb='1GID',
model=1,
chain='A',
component_id='C',
component_number=50,
name="C1'",
symmetry='6_555',
x=-1,
y=0,
z=0)
class AlternativeAtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='4OQ8', model=1, chain='A', component_id='SER',
component_number=27, name='CA', alt_id='A',
symmetry='PP')
def test_has_a_unit_id(self):
self.assertEquals('4OQ8|1|A|SER|27|CA|A||PP', self.atom.unit_id())
def test_has_a_component_id(self):
self.assertEquals('4OQ8|1|A|SER|27||A||PP',
self.atom.component_unit_id())
def setUp(self):
self.atoms = [
Atom(type='C', name='a1', polymeric='A', component_number=3,
x=0.0, y=0.0, z=0.0),
Atom(type='C', name='a2', polymeric='B', component_number=2,
x=0.0, y=0.0, z=0.0),
Atom(type='N', name='b1', polymeric='C', component_number=1,
x=0.0, y=0.0, z=0.0),
Atom(type='N', name='c2', polymeric='C', component_number=0,
x=0.0, y=0.0, z=0.0)
]
self.component = Component(self.atoms, type='rna', pdb='1GID', model=1,
chain='A', sequence='C', number=50,
symmetry='6_555')
def setUp(self):
self.atoms = [
Atom(type='C', name='a1', component_number=3,
x=1.0, y=0.0, z=0.0, pdb='1S72', model=1, chain='A',
component_id='C'),
Atom(type='C', name='a2', component_number=2,
x=2.0, y=0.0, z=0.0, pdb='1S72', model=1, chain='A',
component_id='C'),
Atom(type='N', name='b1', component_number=1,
x=3.0, y=0.0, z=0.0, pdb='1S72', model=1, chain='A',
component_id='C'),
Atom(type='N', name='c2', component_number=0,
x=0.0, y=1.0, z=0.0, pdb='1S72', model=1, chain='A',
component_id='C')
]
def setUp(self):
self.atoms = [
Atom(type='C', name='a1', polymeric='A',
x=0.0, y=0.0, z=0.0),
Atom(type='C', name='a2', polymeric='B',
x=0.0, y=0.0, z=0.0),
Atom(type='N', name='b1', polymeric='C',
x=0.0, y=0.0, z=0.0),
Atom(type='N', name='c2', polymeric='C',
x=0.0, y=0.0, z=0.0)
]
self.component = Component(self.atoms, type='rna', pdb='1GID', model=1,
chain='A', sequence='C',
symmetry='6_555')
self.sub = self.component.select(name=['a1', 'a2'])
def setUp(self):
self.atom = Atom(pdb='1GID',
model=1,
chain='A',
component_id='C',
component_number=50,
name="C1'",
symmetry='6_555',
x=-1,
y=0,
z=2,
type='Bob',
polymeric=True)
trans = np.array([[1.0, 0.0, 0.0, 0.0], [0.0, -1.0, 0.0, 97.240],
[0.0, 0.0, -1.0, 0.0], [0.0, 0.0, 0.0, 1.0]])
self.trans = self.atom.transform(trans)
def __atom__(self, pdb, atom, symmetry):
x, y, z = self.__apply_symmetry__(atom, symmetry)
index = atom['label_seq_id']
if index != '.':
index = int(index)
else:
index = None
symmetry_name = self.__symmetry_name__(symmetry)
ins_code = atom['pdbx_PDB_ins_code']
if ins_code == '?':
ins_code = None
alt_id = atom['label_alt_id']
if alt_id == '.':
alt_id = None
return Atom(pdb=pdb,
model=int(atom['pdbx_PDB_model_num']),
chain=atom['auth_asym_id'],
component_id=atom['label_comp_id'],
component_number=int(atom['auth_seq_id']),
component_index=index,
insertion_code=ins_code,
alt_id=alt_id,
x=x, y=y, z=z,
group=atom['group_PDB'],
type=atom['type_symbol'],
name=atom['label_atom_id'],
symmetry=symmetry_name,
polymeric=self.is_polymeric_atom(atom))
def test_can_build_problematic_id(self):
atom = Atom(pdb='3V27',
model=1,
chain='A',
component_id='G',
component_number=94,
component_index=1,
insertion_code='A',
x=None, y=None, z=None,
group='ATOM',
type='OP1',
name='P',
symmetry='1_555',
polymeric=False)
val = atom.component_unit_id()
ans = '3V27|1|A|G|94|||A'
self.assertEquals(ans, val)
class AlternativeAtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='4OQ8',
model=1,
chain='A',
component_id='SER',
component_number=27,
name='CA',
alt_id='A',
symmetry='PP')
def test_has_a_unit_id(self):
self.assertEquals('4OQ8|1|A|SER|27|CA|A||PP', self.atom.unit_id())
def test_has_a_component_id(self):
self.assertEquals('4OQ8|1|A|SER|27||A||PP',
self.atom.component_unit_id())
def setUp(self):
self.atom = Atom(pdb='1GID', model=1, chain='A', component_id='C',
component_number=50, name="C1'", symmetry='6_555',
x=-1, y=0, z=2, type='Bob', polymeric=True)
trans = np.array([[1.0, 0.0, 0.0, 0.0],
[0.0, -1.0, 0.0, 97.240],
[0.0, 0.0, -1.0, 0.0],
[0.0, 0.0, 0.0, 1.0]])
self.trans = self.atom.transform(trans)
def standard_component(self, seq):
atoms = []
for name, coord in defs.RNAbasecoordinates[seq].items():
x, y, z = coord
atoms.append(Atom(x=x, y=y, z=z, name=name))
component = Component(atoms, sequence=seq)
component.infer_hydrogens()
assert_array_almost_equal(component.centers['base'], [0, 0, 0])
return component
def test_can_build_problematic_id(self):
atom = Atom(pdb='3V27',
model=1,
chain='A',
component_id='G',
component_number=94,
component_index=1,
insertion_code='A',
x=None,
y=None,
z=None,
group='ATOM',
type='OP1',
name='P',
symmetry='1_555',
polymeric=False)
val = atom.component_unit_id()
ans = '3V27|1|A|G|94|||A'
self.assertEquals(ans, val)
def setUp(self):
self.component1 = Component([
Atom(name='N9', x=3.0, y=3.0, z=3.0),
Atom(name='C4', x=2.0, y=2.0, z=2.0),
Atom(name='N3', x=1.0, y=1.0, z=1.0),
Atom(name='C3', x=0.0, y=0.0, z=0.0),
])
self.component2 = Component([
Atom(name='N1', x=0.0, y=-1.0, z=0.0),
Atom(name='N3', x=-10.0, y=0.0, z=-1.0),
Atom(name='C2', x=-2.0, y=0.0, z=-3.0)
])
def test_can_find_new_atom_positions(self):
self.atoms.append(Atom(name='s', x=3.0, y=2.0, z=1.0))
val = self.proxy['s']
ans = np.array([3.0, 2.0, 1.0])
np.testing.assert_almost_equal(ans, val)
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 20 12:50:43 2013
@author: zirbel
"""
from fr3d.data import Atom
from fr3d.data import Component
from fr3d.geometry.discrepancy import discrepancy
nt77_9 = Component([
Atom(type='N', name='N9', x=43.063866, y=60.593299, z=122.948693),
Atom(type='C', name='C4', x=42.888197, y=59.952482, z=121.742655),
Atom(type='N', name='N3', x=41.743000, y=59.665137, z=121.107361),
Atom(type='N', name='N1', x=43.174443, y=58.683103, z=119.409845),
Atom(type='C', name='C6', x=44.294465, y=58.989433, z=120.078177),
Atom(type='N', name='N6', x=45.492460, y=58.648576, z=119.551113),
Atom(type='C', name='C8', x=44.415702, y=60.651476, z=123.176564),
Atom(type='C', name='C5', x=44.188911, y=59.660647, z=121.315765),
Atom(type='C', name='C2', x=41.988409, y=59.033005, z=119.954772),
Atom(type='N', name='N7', x=45.139547, y=60.098841, z=122.214056),
Atom(type='H', name='H2', x=41.115198, y=58.758914, z=119.368203),
Atom(type='H', name='H8', x=44.822196, y=61.111613, z=124.067401),
Atom(type='H', name='H9', x=42.326540, y=60.946934, z=123.540317),
Atom(type='1', name='1H6', x=45.517242, y=58.171343, z=118.666736),
Atom(type='2', name='2H6', x=46.340025, y=58.872608, z=120.042414),
Atom(type='C', name='C1*', x=41.945000, y=61.063000, z=123.795000),
Atom(type='C', name='C2*', x=41.342000, y=59.980000, z=124.691000),
Atom(type='O', name='O2*', x=40.486000, y=59.109000, z=123.980000),
Atom(type='C', name='C3*', x=40.625000, y=60.844000, z=125.716000),
def setUp(self):
self.nt1 = Component(atoms=[
Atom(x=0, y=0, z=1, name='C1'),
Atom(x=0, y=0, z=0, name='C2'),
Atom(x=1, y=0, z=1, name='N'),
], sequence='A', model=1, chain='A', number=1, polymeric=True)
self.nt2 = Component(atoms=[
Atom(x=5, y=5, z=5, name='C1'),
Atom(x=5, y=5, z=5, name='C2'),
Atom(x=5, y=5, z=5, name='N'),
], sequence='U', model=1, chain='A', number=2, polymeric=True)
self.nt3 = Component(atoms=[
Atom(x=-5, y=-5, z=-5, name='C1'),
Atom(x=-5, y=-5, z=-5, name='C2'),
Atom(x=-5, y=-5, z=-5, name='N'),
], sequence='C', model=1, chain='A', number=3, polymeric=True)
self.nt4 = Component(atoms=[
Atom(x=0, y=0, z=3, name='C1'),
Atom(x=0, y=0, z=3, name='C2'),
Atom(x=0, y=0, z=3, name='N'),
], sequence='U', model=1, chain='A', number=4, polymeric=True)
self.nt5 = Component(atoms=[
Atom(x=0, y=0, z=8, name='C1'),
Atom(x=0, y=0, z=8, name='C2'),
Atom(x=0, y=0, z=3, name='N'),
], sequence='G', model=1, chain='A', number=5, polymeric=True)
structure = Structure([self.nt1, self.nt2, self.nt3, self.nt4,
self.nt5], pdb='0000', model='1')
self.pairs = Pairs(structure)
def setUp(self):
self.atom = Atom(pdb='4OQ8', model=1, chain='A', component_id='SER',
component_number=27, name='CA', alt_id='A',
symmetry='PP')
def setUp(self):
some_atoms = [
Atom(insertion_code='?', component_id='G', name='P',
symmetry='1_555', component_number='118', chain='B', y=54.015,
x=47.242, model='1', z=51.393, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='OP1',
symmetry='1_555', component_number='118', chain='B', y=53.619,
x=45.943, model='1', z=50.812, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='OP2',
symmetry='1_555', component_number='118', chain='B', y=55.016,
x=48.096, model='1', z=50.668, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O5'",
symmetry='1_555', component_number='118', chain='B', y=54.52,
x=47.009, model='1', z=52.887, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C5'",
symmetry='1_555', component_number='118', chain='B', y=53.848,
x=46.12, model='1', z=53.764, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C4'",
symmetry='1_555', component_number='118', chain='B', y=54.529,
x=46.123, model='1', z=55.11, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O4'",
symmetry='1_555', component_number='118', chain='B', y=54.338,
x=47.426, model='1', z=55.73, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C3'",
symmetry='1_555', component_number='118', chain='B', y=56.037,
x=45.94, model='1', z=55.051, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O3'",
symmetry='1_555', component_number='118', chain='B', y=56.374,
x=44.553, model='1', z=54.993, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C2'",
symmetry='1_555', component_number='118', chain='B', y=56.495,
x=46.647, model='1', z=56.326, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O2'",
symmetry='1_555', component_number='118', chain='B', y=56.349,
x=45.878, model='1', z=57.494, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C1'",
symmetry='1_555', component_number='118', chain='B', y=55.528,
x=47.827, model='1', z=56.387, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N9',
symmetry='1_555', component_number='118', chain='B', y=56.026,
x=49.033, model='1', z=55.738, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C8',
symmetry='1_555', component_number='118', chain='B', y=55.785,
x=49.442, model='1', z=54.455, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N7',
symmetry='1_555', component_number='118', chain='B', y=56.371,
x=50.566, model='1', z=54.161, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C5',
symmetry='1_555', component_number='118', chain='B', y=57.031,
x=50.913, model='1', z=55.323, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C6',
symmetry='1_555', component_number='118', chain='B', y=57.827,
x=52.019, model='1', z=55.608, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='O6',
symmetry='1_555', component_number='118', chain='B', y=58.131,
x=52.969, model='1', z=54.873, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N1',
symmetry='1_555', component_number='118', chain='B', y=58.301,
x=51.975, model='1', z=56.907, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C2',
symmetry='1_555', component_number='118', chain='B', y=58.033,
x=50.991, model='1', z=57.814, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N2',
symmetry='1_555', component_number='118', chain='B', y=58.557,
x=51.138, model='1', z=59.032, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N3',
symmetry='1_555', component_number='118', chain='B', y=57.299,
x=49.949, model='1', z=57.556, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C4',
symmetry='1_555', component_number='118', chain='B', y=56.828,
x=49.974, model='1', z=56.301, pdb='1GID')
]
self.res = Component(some_atoms, type='rna', pdb='1GID', model=1,
chain='A', sequence='G', number=50,
symmetry='6_555')
def test_can_get_distance_between_atoms(self):
val = self.atom.distance(Atom(x=1, y=0, z=0))
self.assertEqual(2.0, val)
def setUp(self):
self.atom = Atom(pdb='1GID', model=1, chain='A', component_id='C',
component_number=50, name="C1'", symmetry='6_555',
x=-1, y=0, z=0)
