def run(project, pdb, traj_fn, atom_indices, alt_indices, permute_indices):
#project = Project.load_from_hdf(options.projectfn)
traj = Trajectory.load_trajectory_file(traj_fn, Conf=project.Conf)
# you could replace this with your own metric if you like
metric = LPRMSD(atom_indices, permute_indices, alt_indices)
ppdb = metric.prepare_trajectory(pdb)
ptraj = metric.prepare_trajectory(traj)
print ppdb['XYZList'].shape
print ptraj['XYZList'].shape
distances, xout = metric.one_to_all_aligned(ppdb, ptraj, 0)
print distances
return distances
def run(project, pdb, traj_fn, atom_indices, alt_indices, permute_indices):
#project = Project.load_from_hdf(options.projectfn)
traj = Trajectory.load_trajectory_file(traj_fn, Conf=project.Conf)
# you could replace this with your own metric if you like
metric = LPRMSD(atom_indices, permute_indices, alt_indices)
ppdb = metric.prepare_trajectory(pdb)
ptraj = metric.prepare_trajectory(traj)
print ppdb['XYZList'].shape
print ptraj['XYZList'].shape
distances, xout = metric.one_to_all_aligned(ppdb, ptraj, 0)
print distances
return distances
def run(project, assignments, conformations_per_state, states, output_dir,
gens_file, atom_indices, permute_indices, alt_indices, total_memory):
if states == "all":
states = np.arange(assignments.max() + 1)
# This is a dictionary: {generator : ((traj1, frame1), (traj1, frame3), (traj2, frame1), ... )}
inverse_assignments = defaultdict(lambda: [])
for i in xrange(assignments.shape[0]):
for j in xrange(assignments.shape[1]):
inverse_assignments[assignments[i, j]].append((i, j))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
print "Setting up the metric."
rmsd_metric = LPRMSD(atom_indices, permute_indices, alt_indices)
# This trickery allows us to get the correct number of leading
# zeros in the output file name no matter how many generators we have
digits = len(str(max(states)))
# Create a trajectory of generators and prepare it.
if os.path.exists(gens_file):
gens_traj = Trajectory.load_trajectory_file(gens_file)
p_gens_traj = rmsd_metric.prepare_trajectory(gens_traj)
formstr_pdb = '\"Generator-%%0%ii.pdb\"' % digits
formstr_xtc = '\"Cluster-%%0%ii.xtc\"' % digits
print "Loading up the trajectories."
traj_nfiles, traj_bytes = get_size(project['TrajFilePath'])
LoadAll = 0
MaxMem = 0.0
# LPW This is my hack that decides whether to load trajectories into memory, or to read them from disk.
if (
traj_bytes * 5
) < total_memory * 1073741824: # It looks like the Python script uses roughly 5x the HDF file size in terms of memory.
print "Loading all trajectories into memory."
LoadAll = 1
AllTraj = [project.LoadTraj(i) for i in np.arange(project["NumTrajs"])]
#print "After loading trajectories, memory usage is % .3f GB" % (float(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) / 1048576)
if not os.path.exists(gens_file):
if not 'AllTraj' in locals():
raise Exception((
'To get away with not supplying a Gens.lh5 structure to align to for each state '
'you need to have enough memory to load all the trajectories simultaniously. This could be worked around...'
))
print 'Randomly Sampling from state for structure to align everything to'
centers_list = []
for s in states:
chosen = inverse_assignments[np.random.randint(
len(inverse_assignments[s]))]
centers_list.append(AllTraj[chosen[0]][chosen[1]])
gens_traj = concatenate_trajectories(centers_list)
p_gens_traj = rmsd_metric.prepare_trajectory(gens_traj)
formstr_pdb = '\"Center-%%0%ii.pdb\"' % digits
cluster_traj = project.GetEmptyTrajectory()
# Loop through the generators.
for s in states:
if len(inverse_assignments[s]) == 0:
raise ValueError('No assignments to state! %s' % s)
if conformations_per_state == 'all':
confs = inverse_assignments[s]
else:
random.shuffle(inverse_assignments[s])
if len(inverse_assignments[s]) >= conformations_per_state:
confs = inverse_assignments[s][0:conformations_per_state]
else:
confs = inverse_assignments[s]
print 'Not enough assignments in state %s' % s
FrameDict = {}
for (traj, frame) in confs:
FrameDict.setdefault(traj, []).append(frame)
# Create a single trajectory corresponding to the frames that
# belong to the current generator.
if "XYZList" in cluster_traj:
cluster_traj.pop("XYZList")
print "Generator %i" % s,
TrajNums = set([i[0] for i in confs])
for i in TrajNums:
if LoadAll:
T = AllTraj[i][np.array(FrameDict[i])]
else:
T = project.LoadTraj(i)[np.array(FrameDict[i])]
cluster_traj += T
print " loaded %i conformations, aligning" % len(cluster_traj),
# Prepare the trajectory, align to the generator, and reassign the coordinates.
p_cluster_traj = rmsd_metric.prepare_trajectory(cluster_traj)
rmsd, xout = rmsd_metric.one_to_all_aligned(p_gens_traj,
p_cluster_traj, s)
p_cluster_traj['XYZList'] = xout.copy()
# Now save the generator / cluster to a PDB / XTC file.
outpdb = eval(formstr_pdb) % s
outxtc = eval(formstr_xtc) % s
this_gen_traj = p_gens_traj[s]
print ", saving PDB to %s" % os.path.join(output_dir, outpdb),
this_gen_traj.save_to_pdb(os.path.join(output_dir, outpdb))
print ", saving XTC to %s" % os.path.join(output_dir, outxtc),
p_cluster_traj.save_to_xtc(os.path.join(output_dir, outxtc))
print ", saved"
NowMem = float(resource.getrusage(
resource.RUSAGE_SELF).ru_maxrss) / 1048576
if NowMem > MaxMem:
MaxMem = NowMem
def run(
project,
assignments,
conformations_per_state,
states,
output_dir,
gens_file,
atom_indices,
permute_indices,
alt_indices,
total_memory,
):
if states == "all":
states = np.arange(assignments.max() + 1)
# This is a dictionary: {generator : ((traj1, frame1), (traj1, frame3), (traj2, frame1), ... )}
inverse_assignments = defaultdict(lambda: [])
for i in xrange(assignments.shape[0]):
for j in xrange(assignments.shape[1]):
inverse_assignments[assignments[i, j]].append((i, j))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
print "Setting up the metric."
rmsd_metric = LPRMSD(atom_indices, permute_indices, alt_indices)
# This trickery allows us to get the correct number of leading
# zeros in the output file name no matter how many generators we have
digits = len(str(max(states)))
# Create a trajectory of generators and prepare it.
if os.path.exists(gens_file):
gens_traj = Trajectory.load_trajectory_file(gens_file)
p_gens_traj = rmsd_metric.prepare_trajectory(gens_traj)
formstr_pdb = '"Generator-%%0%ii.pdb"' % digits
formstr_xtc = '"Cluster-%%0%ii.xtc"' % digits
print "Loading up the trajectories."
traj_nfiles, traj_bytes = get_size(project["TrajFilePath"])
LoadAll = 0
MaxMem = 0.0
# LPW This is my hack that decides whether to load trajectories into memory, or to read them from disk.
if (
traj_bytes * 5
) < total_memory * 1073741824: # It looks like the Python script uses roughly 5x the HDF file size in terms of memory.
print "Loading all trajectories into memory."
LoadAll = 1
AllTraj = [project.LoadTraj(i) for i in np.arange(project["NumTrajs"])]
# print "After loading trajectories, memory usage is % .3f GB" % (float(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) / 1048576)
if not os.path.exists(gens_file):
if not "AllTraj" in locals():
raise Exception(
(
"To get away with not supplying a Gens.lh5 structure to align to for each state "
"you need to have enough memory to load all the trajectories simultaniously. This could be worked around..."
)
)
print "Randomly Sampling from state for structure to align everything to"
centers_list = []
for s in states:
chosen = inverse_assignments[np.random.randint(len(inverse_assignments[s]))]
centers_list.append(AllTraj[chosen[0]][chosen[1]])
gens_traj = concatenate_trajectories(centers_list)
p_gens_traj = rmsd_metric.prepare_trajectory(gens_traj)
formstr_pdb = '"Center-%%0%ii.pdb"' % digits
cluster_traj = project.GetEmptyTrajectory()
# Loop through the generators.
for s in states:
if len(inverse_assignments[s]) == 0:
raise ValueError("No assignments to state! %s" % s)
if conformations_per_state == "all":
confs = inverse_assignments[s]
else:
random.shuffle(inverse_assignments[s])
if len(inverse_assignments[s]) >= conformations_per_state:
confs = inverse_assignments[s][0:conformations_per_state]
else:
confs = inverse_assignments[s]
print "Not enough assignments in state %s" % s
FrameDict = {}
for (traj, frame) in confs:
FrameDict.setdefault(traj, []).append(frame)
# Create a single trajectory corresponding to the frames that
# belong to the current generator.
if "XYZList" in cluster_traj:
cluster_traj.pop("XYZList")
print "Generator %i" % s,
TrajNums = set([i[0] for i in confs])
for i in TrajNums:
if LoadAll:
T = AllTraj[i][np.array(FrameDict[i])]
else:
T = project.LoadTraj(i)[np.array(FrameDict[i])]
cluster_traj += T
print " loaded %i conformations, aligning" % len(cluster_traj),
# Prepare the trajectory, align to the generator, and reassign the coordinates.
p_cluster_traj = rmsd_metric.prepare_trajectory(cluster_traj)
rmsd, xout = rmsd_metric.one_to_all_aligned(p_gens_traj, p_cluster_traj, s)
p_cluster_traj["XYZList"] = xout.copy()
# Now save the generator / cluster to a PDB / XTC file.
outpdb = eval(formstr_pdb) % s
outxtc = eval(formstr_xtc) % s
this_gen_traj = p_gens_traj[s]
print ", saving PDB to %s" % os.path.join(output_dir, outpdb),
this_gen_traj.save_to_pdb(os.path.join(output_dir, outpdb))
print ", saving XTC to %s" % os.path.join(output_dir, outxtc),
p_cluster_traj.save_to_xtc(os.path.join(output_dir, outxtc))
print ", saved"
NowMem = float(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) / 1048576
if NowMem > MaxMem:
MaxMem = NowMem