def test_correct_output_ions():
"""
Ions such as sodium or potassium are not parametrized. However,
their formal charge is taken as partial charge since they are not
involved in covalent bonding.
Hence, it is expected that no warning is raised.
The test is performed with a sodium ion.
"""
sodium = Atom([0, 0, 0], element="NA")
sodium_array = array([sodium])
# Sodium possesses a formal charge of +1
sodium_array.charge = np.array([1])
# Sodium is not involved in covalent bonding
sodium_array.bonds = BondList(sodium_array.array_length())
with pytest.warns(None) as record:
partial_charges(sodium_array, iteration_step_num=1)
assert len(record) == 0
def test_gro_id_overflow():
# Create an oversized AtomArray where atom_id > 100000 and res_id > 10000
num_atoms = 100005
atoms = array([
Atom([1, 2, 3],
atom_name="CA",
element="C",
res_name="X",
res_id=i + 1) for i in range(num_atoms)
])
atoms.box = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# Write .gro file
tmp_file_name = biotite.temp_file(".gro")
io.save_structure(tmp_file_name, atoms)
# Read .gro file
gro_file = gro.GROFile.read(tmp_file_name)
s = gro_file.get_structure()
assert s.array_length() == num_atoms
def test_gro_no_box():
"""
.gro file format requires valid box parameters at the end of each
model. However, if we read such a file in, the resulting object should not
have an assigned box.
"""
# Create an AtomArray
atom = Atom([1, 2, 3], atom_name="CA", element="C", res_name="X", res_id=1)
atoms = array([atom])
# Write .gro file
tmp_file_name = biotite.temp_file(".gro")
io.save_structure(tmp_file_name, atoms)
# Read in file
gro_file = gro.GROFile.read(tmp_file_name)
s = gro_file.get_structure()
# Assert no box with 0 dimension
assert s.box is None
import numpy as np
from biotite.structure.info import residue
from biotite.structure import Atom
from biotite.structure import array
from biotite.structure import BondList
from biotite.structure import partial_charges
# Test the partial charge of carbon in the molecules given in table
# 3 of the Gasteiger-Marsili publication
# Since some of the molecules are not available in the Chemical
# Components Dictionary, the respective AtomArrays are constructed via
# Biotite and the coordinates are arbitrarily set to the origin since
# the relevant information is the BondList
# Creating atoms to build molecules with
carbon = Atom([0, 0, 0], element="C")
hydrogen = Atom([0, 0, 0], element="H")
oxygen = Atom([0, 0, 0], element="O")
nitrogen = Atom([0, 0, 0], element="N")
fluorine = Atom([0, 0, 0], element="F")
sulfur = Atom([0, 0, 0], element="S")
# Building molecules
methane = array([carbon, hydrogen, hydrogen, hydrogen, hydrogen])
methane.bonds = BondList(methane.array_length(),
np.array([[0, 1], [0, 2], [0, 3], [0, 4]]))
import numpy as np
from numpy import float32, int32
from biotite.sequence import CodonTable
from biotite.sequence.align import SubstitutionMatrix
import pytest
__author__ = "Maximilian Greil"
@pytest.mark.parametrize("repr_object",
[NucleotideSequence("AACTGCTA"),
NucleotideSequence("AACTGCTA", ambiguous=True),
ProteinSequence("BIQTITE"),
Alphabet(["X", "Y", "Z"]),
GeneralSequence(Alphabet(["X", "Y", "Z"]), "XYZ"),
LetterAlphabet(["X", "Y", "Z"]),
Location(98, 178),
Feature("CDS", [Location(98, 178)], qual={"gene": "test1"}),
Annotation([Feature("CDS", [Location(98, 178)], qual={"gene": "test1"})]),
AnnotatedSequence(Annotation([Feature("CDS", [Location(98, 178)], qual={"gene": "test1"})]),
NucleotideSequence("AACTGCTA")),
Alignment([NucleotideSequence("CGTCAT", ambiguous=False), NucleotideSequence("TCATGC", ambiguous=False)],
np.array([[0, -1], [1, -1], [2, 0], [3, 1], [4, 2], [5, 3], [-1, 4], [-1, 5]]), score=-20),
Atom([1, 2, 3], chain_id="A"),
CodonTable.default_table(),
SubstitutionMatrix(Alphabet(["foo", "bar"]), Alphabet([1, 2, 3]),
{("foo", 1): 5, ("foo", 2): 10, ("foo", 3): 15, ("bar", 1): 42,
("bar", 2): 42, ("bar", 3): 42})])
def test_repr(repr_object):
assert eval(repr(repr_object)) == repr_object