def test_xvg_comments(self):
data = file_io.load_xvg('files/test_file_io/data_&comments.xvg',
dims=3,
comments=('#', '@', '&'))
self.assertEqual(data.shape[0], 6)
self.assertEqual(data.shape[1], 10)
self.assertEqual(data.shape[2], 3)
def test_xvg_return_time(self):
data, time = file_io.load_xvg('files/test_file_io/data_3D.xvg',
dims=3,
return_time_data=True)
self.assertEqual(time.size, 6)
def test_fakedata_3D(self):
# make sure reordering is correct, values actually right
data = file_io.load_xvg('files/test_file_io/fake_3D_data.xvg', dims=3)
self.assertEqual(data[1, 1, 0], 10)
self.assertEqual(data[1, 1, 1], 11)
self.assertEqual(data[1, 1, 2], 12)
def test_xvg_3D(self):
data = file_io.load_xvg('files/test_file_io/data_3D.xvg', dims=3)
self.assertEqual(data.shape[0], 6)
self.assertEqual(data.shape[1], 10)
self.assertEqual(data.shape[2], 3)
F = -kX (kX to keep a particle at a specific distance from reference)
Parameters
-displacements - n_frames * n_particles * xyz
-spring constant - force constant that keeps dummy particles in place. Gromacs units are k=kJ/(mol nm^2)
Returns
- forces - n_frames * n_particles * xyz - dimensional components of forces
'''
return spring_constant * displacements
if __name__ == '__main__':
# testing
prefix = '/home/kevin/hdd/Projects/software_validation/dummy_particles/flat_bilayer/dummy_3.6nm/'
top_force = file_io.load_xvg(prefix + 'freeze/data/dummy_top_force.xvg',
dims=3)
dummy_ref = md.load(prefix + 'pos_res/dummy_ref.pdb')
dummy_traj = md.load_xtc(prefix + 'pos_res/dummy_coords.xtc',
top=prefix + 'pos_res/dummy_firstframe.pdb')
dummy_ref_dims = dummy_ref.unitcell_lengths
dummy_traj_dims = dummy_traj.unitcell_lengths
a = calc_posres_forces(dummy_traj.xyz,
dummy_ref.xyz,
1000,
scaling=True,
traj_dims=dummy_traj_dims,
ref_dims=dummy_ref_dims)
def test_xvg_2D(self):
data = file_io.load_xvg('files/testFileIO/data_2D.xvg', dims=2)
self.assertEqual(data.shape[0], 6)
self.assertEqual(data.shape[1], 10)
self.assertEqual(data.shape[2], 2)