Commit ef86f5f0 authored by jdurrant's avatar jdurrant
Browse files

Removed all my test files from the directory.

parent a795aae1
from __future__ import absolute_import
import scoria
from scoria.Test import FileIOBenchmarks
FileIOBenchmarks()
echo "Python with numpy"
python benchmarks.py
echo "Python without numpy"
python benchmarks.py NODEPENS
echo "PyPy without numpy"
pypy benchmarks.py
from __future__ import absolute_import
from __future__ import print_function
import scoria
from scoria import dumbpy as numpy
import time
from .six.moves import range
t1 = time.time()
mol = scoria.Molecule()
mol.load_pdb_into("scoria/sample-files/single_frame.pdb", False, False, False, False)
for t in range(500):
mol.translate_molecule(numpy.array([1.0, 0.0, 0.0]))
mol.save_pdb("test.pdb")
print((time.time() - t1))
from __future__ import absolute_import
from __future__ import print_function
import scoria
from scoria import dumbpy as numpy
import time
from six.moves import range
t1 = time.time()
for t in range(50000000):
pass
mol = scoria.Molecule()
mol.load_pdb_into("scoria/sample-files/single_frame.pdb", False, False, False, False)
print((time.time() - t1))
# NEVER MIND THIS FILE FOR NOW. MDANALYSIS CONSTRUCTOR STILL BEING CREATED...
from __future__ import absolute_import
import scoria
#mol = scoria.Molecule()
#mol.load_pdb_into("scoria/sample-files/single_frame.pdb", False, False, False)
#print mol.information.get_trajectory_frame_count()
# Load PSF and DCD files.
#mol = scoria.Molecule()
#mol.load_via_MDAnalysis("./scoria/sample-files/M2_traj.psf", "./scoria/sample-files/M2_traj.dcd")
#print mol.save_pdb("test.pdb")
mol = scoria.Molecule()
#mol.load_pdb_into("test.pdb", is_trajectory = True)
#mol.fileio.load_pdb_trajectory_into("test.pdb")
mol.fileio.load_pdbqt_trajectory_into("scoria/sample-files/vina.out")
#mol.load_pdbqt_into("scoria/sample-files/vina.out", is_trajectory = True)
#print mol.information.get_trajectory_frame_count()
#print mol.information.__trajectory
#print list(mol.get_coordinates())
import pdb; pdb.set_trace()
\ No newline at end of file
import numpy
import scoria
m1 = scoria.Molecule()
m2 = scoria.Molecule()
m1.load_pdb_into("test.pdb", False, False, False, False)
m2.load_pdb_into("test.pdb", False, False, False, False)
# move m2 so an alignment is needed.
m2.translate_molecule(numpy.array([15.0, 15.0, 15.0]))
m2.rotate_molecule_around_a_line_between_atoms(1, 25, 23.4)
# Now define the tethers.
CA1 = m1.select_atoms({"name": "CA"})
CA2 = m2.select_atoms({"name": "CA"})
tethers = zip(CA1, CA2)
m3 = m1.get_other_molecules_aligned_to_this(m2, tethers)
m1.save_pdb("aligned1.pdb")
m3.save_pdb("aligned2.pdb")
# aligned1.pdb and aligned2.pdb are right on top of each other.
This diff is collapsed.
for line in f:
import scoria as pymol
mol = pymol.Molecule("PDB","scoria/sample-files/single_frame.pdb")
sel = {"bad":"thing"}
mol.select_atoms(sel)
from __future__ import absolute_import
import scoria
mol = scoria.Molecule()
mol.load_pdb_into("test.pdb", False, False, False, False)
mol.save_pdb("testttt.pdb")
# Mac OSX Sierra (10.12.1)
# Python 2.7.12 |Anaconda 2.2.0 OR PyPy 1.8.0
# NumPy 1.11.0
# SciPy 0.16.0
# MDAnalysis 0.15.0
echo "TRYING WITH TRADITIONAL PYTHON"
python unit_tests.py
echo "TRYING WITH PYPY"
pypy unit_tests.py
\ No newline at end of file
import scoria
test = scoria.UnitTests()
test.run_all()
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