def _fb_potential2restraints(self, inputdir):
from moleculekit.molecule import Molecule
restraints = list()
fb_box = np.array(self.fb_box)
# convert fb_box to width
width = list(
np.concatenate(
np.diff(np.array([fb_box[::2], fb_box[1::2]]), axis=0)))
# If fb_box is not symmetrical
if not np.all(fb_box[::2] == -fb_box[1::2]):
# convert fb_box and fb_reference to fbcentre and width
mol = Molecule(os.path.join(inputdir, self.acemd.structure))
mol.read(os.path.join(inputdir, self.acemd.coordinates))
fb_refcentre = mol.get(
'coords', sel=self.fb_reference).mean(axis=0).squeeze()
fbcentre = list(
np.around(
np.mean(np.array([fb_box[::2], fb_box[1::2]]), axis=0) +
fb_refcentre, 3))
restraints.append(
GroupRestraint(self.fb_selection,
width, [(self.fb_k, 0)],
fbcentre=fbcentre))
else:
restraints.append(
GroupRestraint(self.fb_selection,
width, [(self.fb_k, 0)],
fbcentresel=self.fb_reference))
return restraints
def test_acemd3(self):
from htmd.util import tempname
from htmd.home import home
from htmd.units import convert
from glob import glob
import os
from htmd.mdengine.acemd.acemd import GroupRestraint
eq = Equilibration()
eq.runtime = 4
eq.timeunits = "ns"
eq.temperature = 300
eq.restraintsteps = convert(
eq.timeunits, "timesteps", eq.runtime, timestep=eq.acemd.timestep
)
ligres = GroupRestraint(
"resname MOL and noh",
[42, 38, 1],
[(5, 0)],
fbcentre=[-0.178, -0.178, 29.195],
)
eq.restraints = eq.defaultEquilRestraints(1000000) + [ligres]
tmpdir = tempname()
eq.write(
home(dataDir=os.path.join("test-protocols", "build", "protLig")), tmpdir
)
# Compare with reference
refdir = home(
dataDir=os.path.join(
"test-protocols", "equilibration", "acemd3", "protLig", "prerun"
)
)
files = [os.path.basename(f) for f in glob(os.path.join(refdir, "*"))]
self._compareResultFolders(refdir, tmpdir, "protLig")