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): """ 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)""" x = self._unitcell['x'] y = self._unitcell['y'] z = self._unitcell['z'] return triclinic_box(x, y, z)