def test_1(self):
l = [1., 2., 3.]
Vec3(l)
from parmed.vec3 import Vec3 as chem_v3
cv3 = chem_v3.__new__(chem_v3, *l)
Vec3(cv3)
def get_forces_from_xvg(frcfile):
with open(frcfile, 'r') as f:
frc = [float(x) for x in f.readline().split()[1:]]
return [
Vec3(frc[i], frc[i + 1], frc[i + 2])
for i in range(0, len(frc), 3)
]
def test_1(self):
l = [1., 2., 3.]
v1 = Vec3(l)
from parmed.vec3 import Vec3 as chem_v3
cv3 = chem_v3.__new__(chem_v3, *l)
v2 = Vec3(cv3)
def has_old_vec3():
from parmed.vec3 import Vec3
v1 = Vec3(1, 2, 3)
if not hasattr(v1, 'x') or v1.x != 1:
return True
try:
v2 = -v1
except TypeError:
return True
return False
def reduce_box_vectors(a, b, c):
"""
This function puts three unit cell vectors in a reduced form where a is
"mostly" in x, b is "mostly" in y, and c is "mostly" in z. This form is
necessary for some programs (notably OpenMM and Gromacs)
Parameters
----------
a : 3-element collection of float
First unit cell vector
b : 3-element collection of float
Second unit cell vector
c : 3-element collection of float
Third unit cell vector
Returns
-------
red_a, red_b, red_c : Vec3, Vec3, Vec3
The reduced unit cell vectors in units of angstroms
Notes
-----
The implementation here is taken from the OpenMM Python application layer
written by Peter Eastman
"""
if u.is_quantity(a):
a = a.value_in_unit(u.angstroms)
if u.is_quantity(b):
b = b.value_in_unit(u.angstroms)
if u.is_quantity(c):
c = c.value_in_unit(u.angstroms)
a = Vec3(*a)
b = Vec3(*b)
c = Vec3(*c)
c = c - b * round(c[1] / b[1])
c = c - a * round(c[0] / a[0])
b = b - a * round(b[0] / a[0])
return a, b, c
def zero_ep_frc(frc, struct):
vec0 = Vec3(0.0, 0.0, 0.0)
for i, atom in enumerate(struct.atoms):
if isinstance(atom, ExtraPoint):
frc[i] = vec0
def positions(self):
return [Vec3(*xyz) for xyz in self.coordinates[0]]
def positions(self):
return [Vec3(*xyz) for xyz in self._coordinates[0]] * u.angstroms
def positionsold(self):
""" Old atomic positions with units """
return [Vec3(*xyz) for xyz in self.coordsold[0]] * u.angstroms
def positions(self):
""" Atomic positions with units """
return [Vec3(*xyz) for xyz in self.coords[0]] * u.angstroms
def positions(self):
"""
Atomic coordinates with units attached to them with the shape (natom, 3)
"""
return [Vec3(*xyz) for xyz in self.coordinates[0]] * u.angstroms