def dimensions(self):
"""unitcell dimensions (A, B, C, alpha, beta, gamma)
GRO::
8.00170 8.00170 5.65806 0.00000 0.00000 0.00000 0.00000 4.00085 4.00085
PDB::
CRYST1 80.017 80.017 80.017 60.00 60.00 90.00 P 1 1
XTC: c.trajectory.ts._unitcell::
array([[ 80.00515747, 0. , 0. ],
[ 0. , 80.00515747, 0. ],
[ 40.00257874, 40.00257874, 56.57218552]], dtype=float32)
"""
# unit cell line (from http://manual.gromacs.org/current/online/gro.html)
# v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
# 0 1 2 3 4 5 6 7 8
# This information now stored as _ts_order_x/y/z to keep DRY
x = self._unitcell[self._ts_order_x]
y = self._unitcell[self._ts_order_y]
z = self._unitcell[self._ts_order_z] # this ordering is correct! (checked it, OB)
return triclinic_box(x, y, z)
def dimensions(self):
# This information now stored as _ts_order_x/y/z to keep DRY
x = self._unitcell[self._ts_order_x]
y = self._unitcell[self._ts_order_y]
z = self._unitcell[self._ts_order_z]
# this ordering is correct! (checked it, OB)
return triclinic_box(x, y, z)
def dimensions(self):
"""unitcell dimensions (A, B, C, alpha, beta, gamma)
GRO::
8.00170 8.00170 5.65806 0.00000 0.00000 0.00000 0.00000 4.00085 4.00085
PDB::
CRYST1 80.017 80.017 80.017 60.00 60.00 90.00 P 1 1
XTC: c.trajectory.ts._unitcell::
array([[ 80.00515747, 0. , 0. ],
[ 0. , 80.00515747, 0. ],
[ 40.00257874, 40.00257874, 56.57218552]], dtype=float32)
"""
# unit cell line (from http://manual.gromacs.org/current/online/gro.html)
# v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
# 0 1 2 3 4 5 6 7 8
# This information now stored as _ts_order_x/y/z to keep DRY
x = self._unitcell[self._ts_order_x]
y = self._unitcell[self._ts_order_y]
z = self._unitcell[self._ts_order_z] # this ordering is correct! (checked it, OB)
return triclinic_box(x, y, z)
def dimensions(self):
"""
Unit cell dimensions ``[A,B,C,alpha,beta,gamma]``.
"""
x = self._unitcell[0:3]
y = self._unitcell[3:6]
z = self._unitcell[6:9]
return triclinic_box(x, y, z)
def dimensions(self):
"""
Unit cell dimensions ``[A,B,C,alpha,beta,gamma]``.
"""
x = self._unitcell[0:3]
y = self._unitcell[3:6]
z = self._unitcell[6:9]
return triclinic_box(x, y, z)
def dimensions(self):
"""unitcell dimensions (*A*, *B*, *C*, *alpha*, *beta*, *gamma*)
lengths *A*, *B*, *C* are in the MDAnalysis length unit (Å), and
angles are in degrees.
Setting dimensions will populate the underlying native format
description (triclinic box vectors). If `edges
<https://nongnu.org/h5md/h5md.html#simulation-box>`_ is a matrix,
the box is of triclinic shape with the edge vectors given by
the rows of the matrix.
"""
return core.triclinic_box(*self._unitcell)
def dimensions(self):
"""unitcell dimensions (A, B, C, alpha, beta, gamma)
- A, B, C are the lengths of the primitive cell vectors e1, e2, e3
- alpha = angle(e1, e2)
- beta = angle(e1, e3)
- gamma = angle(e2, e3)
"""
# Layout of unitcell is [X, Y, Z] with the primitive cell vectors
x = self._unitcell[0]
y = self._unitcell[1]
z = self._unitcell[2]
return triclinic_box(x, y, z)
def dimensions(self):
"""unitcell dimensions (A, B, C, alpha, beta, gamma)
- A, B, C are the lengths of the primitive cell vectors e1, e2, e3
- alpha = angle(e1, e2)
- beta = angle(e1, e3)
- gamma = angle(e2, e3)
"""
# Layout of unitcell is [X, Y, Z] with the primitive cell vectors
x = self._unitcell[0]
y = self._unitcell[1]
z = self._unitcell[2]
return triclinic_box(x, y, z)
def dimensions(self):
"""unitcell dimensions (A, B, C, alpha, beta, gamma)"""
x = self._unitcell['x']
y = self._unitcell['y']
z = self._unitcell['z']
return triclinic_box(x, y, z)
def dimensions(self):
"""unitcell dimensions (A, B, C, alpha, beta, gamma)"""
x = self._unitcell['x']
y = self._unitcell['y']
z = self._unitcell['z']
return triclinic_box(x, y, z)
