def test_trajectory_integer_indexing():
from pyxmolpp2.pdb import PdbFile, AlteredPdbRecords, StandardPdbRecords, RecordName, FieldName
from pyxmolpp2.trjtool import DatFile
from pyxmolpp2.trajectory import Trajectory
records = AlteredPdbRecords(StandardPdbRecords.instance())
records.alter_record(RecordName("ATOM"), FieldName("serial"), [7, 12])
frame = PdbFile("tests_dataset/trjtool/GB1/run00001.pdb",
records).get_frame()
trj = Trajectory(frame, True)
trj.push_trajectory_portion(
DatFile("tests_dataset/trjtool/GB1/run00001.dat"))
n = trj.size
trj[-n]
trj[n - 1]
with pytest.raises(IndexError):
trj[n]
with pytest.raises(IndexError):
trj[-n - 1]
frame1 = trj[0]
frame2 = trj[-n]
assert frame1.index == frame2.index
def test_traj_exceptions():
from pyxmolpp2.pdb import PdbFile, AlteredPdbRecords, StandardPdbRecords, RecordName, FieldName
from pyxmolpp2.polymer import AtomName
from pyxmolpp2.trjtool import DatFile
from pyxmolpp2.trajectory import Trajectory, TrajectoryException
records = AlteredPdbRecords(StandardPdbRecords.instance())
records.alter_record(RecordName("ATOM"), FieldName("serial"), [7, 12])
datfile1 = DatFile("tests_dataset/trjtool/GB1/run00001.dat")
with pytest.raises(TrajectoryException):
frame = PdbFile("tests_dataset/trjtool/GB1/run00001.pdb").get_frame(
records)
frame.asAtoms[0].name = AtomName("XX")
trj = Trajectory(frame, True)
trj.push_trajectory_portion(datfile1)
with pytest.raises(TrajectoryException):
frame = PdbFile("tests_dataset/trjtool/GB1/run00001.pdb").get_frame(
records)
frame.asAtoms[0].delete()
trj = Trajectory(frame, True)
trj.push_trajectory_portion(datfile1)
def test_traj_size():
from pyxmolpp2.pdb import PdbFile, AlteredPdbRecords, StandardPdbRecords, RecordName, FieldName
from pyxmolpp2.trjtool import DatFile
from pyxmolpp2.trajectory import Trajectory
records = AlteredPdbRecords(StandardPdbRecords.instance())
records.alter_record(RecordName("ATOM"), FieldName("serial"), [7, 12])
frame = PdbFile("tests_dataset/trjtool/GB1/run00001.pdb",
records).get_frame()
assert frame.asAtoms.size > 0
trj = Trajectory(frame, True)
trj.push_trajectory_portion(
DatFile("tests_dataset/trjtool/GB1/run00001.dat"))
assert len(trj[0:10]) == 10
assert len(trj[0:10:10]) == 1
assert len(trj[0:10:100]) == 1
assert len(trj[0:100:10]) == 10
assert len(trj[0:100:-10]) == 0
assert len(trj[100:0:-1]) == 100
assert len(trj[0:100:-1]) == 0
def test_read_trjtool():
from pyxmolpp2.pdb import PdbFile, AlteredPdbRecords, StandardPdbRecords, RecordName, FieldName
from pyxmolpp2.trjtool import DatFile
records = AlteredPdbRecords(StandardPdbRecords.instance())
records.alter_record(RecordName("ATOM"), FieldName("serial"), [7,12])
frame = PdbFile("tests_dataset/trjtool/GB1/run00001.pdb",records).get_frame()
assert frame.asAtoms.size > 0
datfile = DatFile("tests_dataset/trjtool/GB1/run00001.dat")
assert datfile.n_frames == 1000
assert datfile.match(frame.asAtoms)
assert datfile.n_atoms_per_frame == frame.asAtoms.size
datfile.set_coordinates(0, frame.asAtoms, list(range(frame.asAtoms.size)))
def test_traj_iteration():
from pyxmolpp2.pdb import PdbFile, AlteredPdbRecords, StandardPdbRecords, RecordName, FieldName
from pyxmolpp2.trjtool import DatFile
from pyxmolpp2.trajectory import Trajectory
records = AlteredPdbRecords(StandardPdbRecords.instance())
records.alter_record(RecordName("ATOM"), FieldName("serial"), [7, 12])
frame = PdbFile("tests_dataset/trjtool/GB1/run00001.pdb").get_frame(
records)
assert frame.asAtoms.size > 0
datfile1 = DatFile("tests_dataset/trjtool/GB1/run00001.dat")
datfile2 = DatFile("tests_dataset/trjtool/GB1/run00002.dat")
trj = Trajectory(frame, True)
trj.push_trajectory_portion(datfile1)
trj.push_trajectory_portion(datfile2)
assert trj.size == datfile1.n_frames + datfile2.n_frames
n = 0
stride = 50
for f in trj[::stride]:
r = f.asAtoms[0].r
n += 1
assert trj.size // stride == n
n = 0
stride = 1
ats = frame.asResidues[0].asAtoms
trj.set_update_list(ats)
for f in trj[::stride]:
n += 1
assert trj.size // stride == n
def test_raise_file_is_empty():
from pyxmolpp2.trjtool import DatFile, unexpected_eof
import os
with pytest.raises(unexpected_eof):
DatFile(os.devnull)
def test_raise_file_does_not_exists():
from pyxmolpp2.trjtool import DatFile, TrjtoolException
with pytest.raises(TrjtoolException):
DatFile("does_not_exists.dat")