本文整理汇总了Python中mdtraj.load方法的典型用法代码示例。如果您正苦于以下问题:Python mdtraj.load方法的具体用法?Python mdtraj.load怎么用?Python mdtraj.load使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类mdtraj
的用法示例。
在下文中一共展示了mdtraj.load方法的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: func
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def func(args, parser):
# delay import of the rest of the module to improve `mdentropy -h` performance
import pickle
import mdtraj as md
import pandas as pd
from ..utils import parse_files
from ..metrics import DihedralMutualInformation
files = parse_files(args.traj)
traj = md.load(files, top=args.top, stride=args.stride)
mi = DihedralMutualInformation(n_bins=args.nbins, types=args.types,
method=args.method, threads=args.n_threads,
normed=True)
M = mi.partial_transform(traj, shuffle=iter, verbose=True)
df = pd.DataFrame(M, columns=mi.labels)
pickle.dump(df, open(args.out, 'wb'))
示例2: func
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def func(args, parser):
# delay import of the rest of the module to improve `mdentropy -h`
# performance
import pickle
import mdtraj as md
import pandas as pd
from ..utils import parse_files
from ..metrics import DihedralTransferEntropy
f1, f2 = parse_files(args.current), parse_files(args.past)
current = md.load(f1, top=args.top, stride=args.stride)
past = md.load(f2, top=args.top, stride=args.stride)
tent = DihedralTransferEntropy(n_bins=args.nbins, types=args.types,
method=args.method, threads=args.n_threads,
normed=True)
T = tent.partial_transform((past, current), shuffle=iter, verbose=True)
df = pd.DataFrame(T, columns=tent.labels)
pickle.dump(df, open(args.out, 'wb'))
示例3: test_convex_find_pockets
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def test_convex_find_pockets(self):
"""Test that some pockets are filtered out."""
current_dir = os.path.dirname(os.path.realpath(__file__))
protein_file = os.path.join(current_dir, "1jld_protein.pdb")
ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")
import mdtraj as md
protein = md.load(protein_file)
finder = dc.dock.ConvexHullPocketFinder()
all_pockets = finder.find_all_pockets(protein_file)
pockets = finder.find_pockets(protein_file)
# Test that every atom in pocket maps exists
n_protein_atoms = protein.xyz.shape[1]
for pocket in pockets:
assert isinstance(pocket, box_utils.CoordinateBox)
assert len(pockets) < len(all_pockets)
示例4: visualize_complex
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def visualize_complex(complex_mdtraj):
ligand_atoms = [a.index for a in complex_mdtraj.topology.atoms if "LIG" in str(a.residue)]
binding_pocket_atoms = md.compute_neighbors(complex_mdtraj, 0.5, ligand_atoms)[0]
binding_pocket_residues = list(set([complex_mdtraj.topology.atom(a).residue.resSeq for a in binding_pocket_atoms]))
binding_pocket_residues = [str(r) for r in binding_pocket_residues]
binding_pocket_residues = " or ".join(binding_pocket_residues)
traj = nglview.MDTrajTrajectory( complex_mdtraj ) # load file from RCSB PDB
ngltraj = nglview.NGLWidget( traj )
ngltraj.representations = [
{ "type": "cartoon", "params": {
"sele": "protein", "color": "residueindex"
} },
{ "type": "licorice", "params": {
"sele": "(not hydrogen) and (%s)" % binding_pocket_residues
} },
{ "type": "ball+stick", "params": {
"sele": "LIG"
} }
]
return ngltraj
示例5: prepare_example
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def prepare_example():
"""
Prepare the host-guest example relative calculation.
"""
#load in the host and guest molecules
host_traj = extract_molecule(host_guest_path, "HST")
guest_traj = extract_molecule(host_guest_path, "GST")
#convert the trajs to mols
host_mol = convert_mdtraj_to_oemol(host_traj)
guest_mol = convert_mdtraj_to_oemol(guest_traj)
#make the other guest molecule:
new_guest_molecule = iupac_to_oemol(alternate_guest)
#write out the host molecule:
write_host(host_mol, host_vacuum_path)
#write out the guest molecules:
write_guest_molecules(guest_mol, new_guest_molecule, guests_vacuum_path)
示例6: _initialise_frame
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def _initialise_frame(self, frame):
"""
Parse a GROMACS GRO file and create Residues/Atoms
Required before reading coordinates from XTC file
:param frame: Frame instance to initialise from GRO file
"""
import mdtraj
top = mdtraj.load(self._topname)
frame.name = ""
self.num_atoms = top.n_atoms
frame.natoms = top.n_atoms
frame.residues = [Residue(name=res.name, num=res.resSeq) for res in top.topology.residues]
for atom in top.topology.atoms:
new_atom = Atom(name=atom.name, num=atom.serial,
coords=top.xyz[0][atom.index])
frame.residues[atom.residue.index].add_atom(new_atom)
frame.box = top.unitcell_lengths[0]
示例7: _load_to_position
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def _load_to_position(spec, arr_shape):
'''
Load a specified file into a specified position by spec. The
arr_shape parameter lets us know how big the final array should be.
'''
(position, filename, load_kwargs) = spec
xyz = md.load(filename, **load_kwargs).xyz
# mp.Array must be converted to numpy array and reshaped
arr = _tonumpyarray(shared_array).reshape(arr_shape)
# dump coordinates in.
arr[position:position+len(xyz)] = xyz
return xyz.shape
示例8: test_assign_to_nearest_center_few_centers
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def test_assign_to_nearest_center_few_centers():
# assign_to_nearest_center takes two code paths, one for
# n_centers > n_frames and one for n_frames > n_centers. This tests
# the latter.
trj = md.load(get_fn('frame0.xtc'), top=get_fn('native.pdb'))
center_frames = [0, int(len(trj)/3), int(len(trj)/2)]
assigns, distances = util.assign_to_nearest_center(
trj, trj[center_frames], md.rmsd)
alldists = np.zeros((len(center_frames), len(trj)))
for i, center_frame in enumerate(trj[center_frames]):
alldists[i] = md.rmsd(trj, center_frame)
assert_allclose(np.min(alldists, axis=0), distances, atol=1e-3)
assert_array_equal(np.argmin(alldists, axis=0), assigns)
示例9: test_reassign_script
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def test_reassign_script():
topologies = [get_fn('native.pdb'), get_fn('native.pdb')]
trajectories = [get_fn('frame0.xtc'), get_fn('frame0.xtc')]
centers = [c for c in md.load(trajectories[0], top=topologies[0])[::50]]
with tempfile.NamedTemporaryFile(suffix='.pkl') as ctrs_f:
pickle.dump(centers, ctrs_f)
ctrs_f.flush()
runhelper(
['--centers', ctrs_f.name,
'--trajectories', trajectories[0], trajectories[1],
'--atoms', '(name N or name C or name CA or name H or name O)',
'--topology', topologies])
示例10: test_load_as_concatenated_stride
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def test_load_as_concatenated_stride(self):
t1 = md.load(self.trj_fname, top=self.top)
t2 = md.load(self.trj_fname, top=self.top)
t3 = md.load(self.trj_fname, top=self.top)
print(len(t1))
print(len(md.load(self.trj_fname, top=self.top, stride=10)))
lengths, xyz = load_as_concatenated(
[self.trj_fname]*3,
top=self.top,
stride=10,
processes=2)
expected = np.concatenate([t1.xyz[::10],
t2.xyz[::10],
t3.xyz[::10]])
self.assertTrue(np.all(expected == xyz))
self.assertEqual(expected.shape, xyz.shape)
示例11: test_selection_load_as_concatenated
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def test_selection_load_as_concatenated(self):
'''
**kwargs should work with load_as_concatenated
Verify that when *kwargs is used in load_as_concatenated, it is
applied to each trajectory as it's loaded (e.g. for the purposes
of selection).
'''
selection = np.array([1, 3, 6])
t1 = md.load(self.trj_fname, top=self.top, atom_indices=selection)
t2 = md.load(self.trj_fname, top=self.top, atom_indices=selection)
t3 = md.load(self.trj_fname, top=self.top, atom_indices=selection)
lengths, xyz = load_as_concatenated(
[self.trj_fname]*3,
top=self.top,
atom_indices=selection,
processes=3)
expected = np.concatenate([t1.xyz, t2.xyz, t3.xyz])
self.assertTrue(np.all(expected == xyz))
self.assertEqual(expected.shape, xyz.shape)
示例12: load_trajs
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def load_trajs(args):
""" Creates a generator object that can be then passed to the CARDS framework.
"""
trajectories = args.trajectories[0]
topology = args.topology[0]
#filenames = glob(trajectories)
targets = {os.path.basename(topf): "%s files" % len(trjfs) for topf, trjfs
in zip(args.topology, args.trajectories)}
logger.info("Starting CARDS; targets:\n%s",
json.dumps(targets, indent=4))
#gen = (md.load(traj, top=topology) for traj in args.trajectories)
gen = load_trajectory_generator(trajectories, topology)
logger.info("Created generator")
return gen
示例13: read_xtc
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def read_xtc(trajfile, top, **kwargs):
""" read the trajectrory using mdtraj module from the xtc file """
print("Read trajectory file: ", trajfile)
print("Read topology from: ", top)
t1 = time.time()
trajectory = md.load(trajfile, top=top)
t2 = time.time() - t1
nframes, natoms = trajectory.xyz.shape[:2]
print("# frames: ", nframes)
print("# atoms: ", natoms)
print("Read trajecory in %.0f s\n" % t2)
return trajectory
示例14: featurize
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def featurize(self, protein_file, pockets):
"""
Calculate atomic coodinates.
Params
------
protein_file: str
Location of PDB file. Will be loaded by MDTraj
pockets: list[CoordinateBox]
List of `dc.utils.CoordinateBox` objects.
Returns
-------
A numpy array of shale `(len(pockets), n_residues)`
"""
import mdtraj
protein_coords = rdkit_util.load_molecule(
protein_file, add_hydrogens=False, calc_charges=False)[0]
mapping = boxes_to_atoms(protein_coords, pockets)
protein = mdtraj.load(protein_file)
n_pockets = len(pockets)
n_residues = len(BindingPocketFeaturizer.residues)
res_map = dict(zip(BindingPocketFeaturizer.residues, range(n_residues)))
all_features = np.zeros((n_pockets, n_residues))
for pocket_num, pocket in enumerate(pockets):
pocket_atoms = mapping[pocket]
for ind, atom in enumerate(pocket_atoms):
atom_name = str(protein.top.atom(atom))
# atom_name is of format RESX-ATOMTYPE
# where X is a 1 to 4 digit number
residue = atom_name[:3]
if residue not in res_map:
logger.info("Warning: Non-standard residue in PDB file")
continue
atomtype = atom_name.split("-")[1]
all_features[pocket_num, res_map[residue]] += 1
return all_features
示例15: visualize_ligand
# 需要导入模块: import mdtraj [as 别名]
# 或者: from mdtraj import load [as 别名]
def visualize_ligand(ligand_mdtraj):
traj = nglview.MDTrajTrajectory( ligand_mdtraj ) # load file from RCSB PDB
ngltraj = nglview.NGLWidget( traj )
ngltraj.representations = [
{ "type": "ball+stick", "params": {"sele": "all" } } ]
return ngltraj