def get_rmsds(traj_fn, native_fn='native.pdb', aindices_fn="project/AtomIndices.dat"):
aindices = np.loadtxt(aindices_fn, dtype='int')
native = mdtraj.load(native_fn, atom_indices=aindices)
traj = mdtraj.load(traj_fn, atom_indices=aindices)
native = mdtraj.rmsd_cache(native)
traj = mdtraj.rmsd_cache(traj)
rmsds = traj.rmsds_to(native, 0)
return rmsds
def __init__(
self, wildtype_counts, wildtype_states_fn, wildtype_topology_fn, mutant_topology_fn, lag_time, simulation
):
"""Create an OpenMM sampler
Parameters
----------
wildtype_counts : np.ndarray, shape=(n_states, n_states)
The number of observed transition counts in the base
protein
wildtype_states_fn : string
Path to a trajectory file giving the states at the
centers of each state, for the wildtype topology.
The states must be defined by RMSD.
wildtype_topology_fn : string
Path to a file giving the topology of the wildtype.
Should be a pdb.
mutant_topology_fn : string
Path to a file giving the topology of the mutant.
Should be a pdb.
lag_time : simtk.unit.Quantity
The msm lag time, in real time units.
simulation : simtk.openmm.app.Simulation
A simulation object, set up for the mutant.
"""
self._wt_states = md.load(wildtype_states_fn)
wt_backbone_inds = [a.index for a in self._wt_states.topology.atoms if a.name in ["C", "CA", "CB", "N", "O"]]
assert len(wt_backbone_inds) > 0
wt_backbone = md.load(wildtype_states_fn, atom_indices=wt_backbone_inds)
self._wt_rmsd_cache = md.rmsd_cache(wt_backbone)
self._wt_topology = app.PDBFile(wildtype_topology_fn).topology
self._lag_time = lag_time
self._mutant_topology = app.PDBFile(mutant_topology_fn).topology
self._mutant_backbone_inds = [
a.index for a in self._mutant_topology.atoms() if a.name in ["C", "CA", "CB", "N", "O"]
]
if not len(list(self._wt_topology.atoms())) == self._wt_states.n_atoms:
raise ValueError("wt topology fn must have same # of states as wt state file")
self._simulation = simulation
super(OpenMMMutantSampler, self).__init__(wildtype_counts, verbose=True)
crystal = md.load(crystal_fn)
trajectory = md.load(trajectory_fn, top=crystal) # load the xtc. the crystal structure defines the topology
print trajectory
# Let's also try loading only the heavy atoms from disk, because calculating
# RMSD with exchangeable hydrogen atoms is generally not a good idea
heavy_atoms = [atom.index for atom in crystal.topology.atoms if atom.element.symbol != 'H']
heavy_crystal = md.load(crystal_fn, atom_indices=heavy_atoms)
heavy_trajectory = md.load(trajectory_fn, top=crystal, atom_indices=heavy_atoms)
print heavy_trajectory
# Format the data for the RMSD calculation by building an RMSDCache.
crystal_cache = md.rmsd_cache(crystal)
trajectory_cache = md.rmsd_cache(trajectory)
crystal_heavy_cache = md.rmsd_cache(heavy_crystal)
trajectory_heavy_cache = md.rmsd_cache(heavy_trajectory)
rmsds_to_crystal = trajectory_cache.rmsds_to(crystal_cache, 0)
heavy_rmds_to_crystal = trajectory_heavy_cache.rmsds_to(crystal_heavy_cache, 0)
# Plot the results
import matplotlib.pyplot as pp
pp.figure();
pp.plot(trajectory.time, rmsds_to_crystal, 'r', label='all atom');
pp.plot(heavy_trajectory.time, heavy_rmds_to_crystal, 'b', label='heavy atom');
pp.legend();
pp.title('RMSDs to crystal');
pp.xlabel('simulation time (ps)');
import mdtraj as md
import numpy as np
atom_indices = np.loadtxt('data/AtomIndices.dat', int)
t1 = md.load('data/trj-00000.nc', top='data/input.pdb', atom_indices=atom_indices)
t2 = md.load('data/trj-00001.nc', top='data/input.pdb', atom_indices=atom_indices)
t = t1 + t2
r = md.rmsd_cache(t, 'axis')
print "Coords"
print r.cords[0]
print 'RMSDs\n', r.rmsds_to(r, 0)
print 'G\n', r._g[:len(t1)]
print r._g[len(t1):]
# In this example, we cluster our alanine dipeptide trajectory using
# the RMSD distance and Ward's algorithm.
import mdtraj as md
import numpy as np
import scipy.cluster.hierarchy
# Lets load up our trajectory. This is the trajectory that we generated in
# the "Running a simulation in OpenMM and analyzing the results with mdtraj"
# example. The first step is to build the rmsd cache, which precalculates
# some values for the rmsd computation.
traj = md.load('ala2.h5')
print traj
engine = md.rmsd_cache(traj)
# Lets compute all pairwise rmsds between conformations.
distances = np.empty((traj.n_frames, traj.n_frames))
for i in range(traj.n_frames):
distances[i] = engine.rmsds_to(engine, i)
print 'Max pairwise rmsd: %f nm' % np.max(distances)
# scipy.cluster implements the ward linkage
# algorithm (among others)
linkage = scipy.cluster.hierarchy.ward(distances)
# Lets plot the resulting dendrogram.
"""
Little script to find all-atom generators from the dimensionality reduced
generators.
"""
import mdtraj as md
import numpy as np
import mdtraj.compatibility
trjs = md.load('Trajectories/trj0.lh5')
trjs.restrict_atoms(np.loadtxt('AtomIndices.dat', int))
rc = md.rmsd_cache(trjs)
gens = md.rmsd_cache(md.load('Data_RMSD2_5A/Gens.lh5'))
ks = []
for i in range(len(gens)):
k = np.argmin(rc.rmsds_to(gens, i))
ks.append(k)
t = md.load('Trajectories/trj0.lh5')
print 'Done'
md.Trajectory(xyz=t.xyz[ks], topology=t.topology).save('Data_RMSD2_5A/Gens.h5')