def rel2sim(self, relFrames):
""" Converts trajectory index-frame pairs into Sim-frame pairs
Parameters
----------
relFrames : 2D np.ndarray
An array containing in each row trajectory index and frame pairs
Returns
-------
frames : np.ndarray
An array of :class:`Frame <htmd.simlist.Frame>` objects containing the simulation object, the trajectory
piece ID and the frame index.
Examples
--------
>>> simframes = data.rel2sim([100, 56]) # 100th simulation frame 56
"""
from htmd.simlist import Frame
sims = []
frames = []
for i in range(np.size(relFrames, 0)):
trajID = relFrames[i, 0]
trajFrame = relFrames[i, 1]
sims.append(self.simlist[trajID])
frames.append(
Frame(self.simlist[trajID], self.ref[trajID][trajFrame, 0],
self.ref[trajID][trajFrame, 1]))
return np.array(frames)
def rel2sim(self, relFrames, simlist=None):
""" Converts trajectory index-frame pairs into Sim-frame pairs
Parameters
----------
relFrames : 2D np.ndarray
An array containing in each row trajectory index and frame pairs
simlist : numpy.ndarray of :class:`Sim <htmd.simlist.Sim>` objects
Optionally pass a different (but matching, i.e. filtered) simlist for creating the Frames.
Returns
-------
frames : np.ndarray
An array of :class:`Frame <htmd.simlist.Frame>` objects containing the simulation object, the trajectory
piece ID and the frame index.
Examples
--------
>>> simframes = data.rel2sim([100, 56]) # 100th simulation frame 56
"""
from htmd.simlist import Frame
if simlist is None:
simlist = self.simlist
else:
if len(simlist) != len(self.simlist):
raise AttributeError(
'Provided simlist has different number of trajectories than the one used by this object.'
)
relFrames = np.array(relFrames)
if relFrames.ndim == 1:
relFrames = relFrames[np.newaxis, :]
sims = []
frames = []
for i in range(np.size(relFrames, 0)):
trajID = relFrames[i, 0]
trajFrame = relFrames[i, 1]
sims.append(simlist[trajID])
ref = self.trajectories[trajID].reference
frames.append(
Frame(simlist[trajID], ref[trajFrame, 0], ref[trajFrame, 1]))
return np.array(frames)
md.datapath = path.join(home(), 'data', 'adaptive', 'data')
md.run()
# Cleaning up
inputodel = glob(path.join(home(), 'data', 'adaptive', 'input', 'e2*'))
for i in inputodel:
shutil.rmtree(i, ignore_errors=True, acemd='/shared/acemd/bin/acemd')
os.remove(path.join(home(), 'data', 'adaptive', 'input', 'e2_writeinputs.log'))'''
import htmd
import os
import shutil
from htmd.queues.localqueue import LocalGPUQueue
from htmd.simlist import Frame, simlist
from htmd.util import tempname
filedir = htmd.home.home() + '/data/adaptive/'
sims = simlist(glob(os.path.join(filedir, 'data', '*', '')),
glob(os.path.join(filedir, 'input', '*', '')),
glob(os.path.join(filedir, 'input', '*', '')))
outf = tempname()
os.makedirs(outf)
f = Frame(sims[0], 0, 5)
_writeInputsFunction(1, f, 2, outf, 'input.coor')
mol = Molecule(sims[0])
mol.read(os.path.join(outf, 'e2s2_e1s1p0f5', 'input.coor'))
shutil.rmtree(outf)