def test_slice(self):
traj1 = TrajectoryIterator(filename="data/Tc5b.x",
top="./data/Tc5b.top")
frame_indices = slice(9, 6, -1)
traj0 = pt.load(filename="./data/Tc5b.x",
top=pt.load_topology("./data/Tc5b.top"),
frame_indices=frame_indices)
aa_eq(traj0[0].xyz, traj1[9].xyz)
aa_eq(traj0[1].xyz, traj1[8].xyz)
aa_eq(traj0[2].xyz, traj1[7].xyz)
assert traj0[0].rmsd(traj1[9]) < 1E-4
rmsdlist = []
ref = traj1[0].copy()
for frame in traj1:
rmsdlist.append(frame.rmsd(ref))
nparr = np.array(rmsdlist)
# make sure we don't suport other frame_indices
traj2 = Trajectory()
traj2 = pt.load(
filename="./data/Tc5b.x",
top=pt.load_topology("./data/Tc5b.top"),
frame_indices=list(range(4)) + list(range(9, 5, -1)) + [4, ])
aa_eq(traj2[-1].xyz, traj1[4].xyz)
def test_traj_topology(self):
traj = pt.TrajectoryIterator()
assert traj.top.is_empty() == True
traj.top = pt.load_topology("./data/Tc5b.top")
assert traj.top.is_empty() == False
traj._load("./data/Tc5b.x")
# use toplogy
traj = pt.TrajectoryIterator()
assert traj.topology.is_empty() == True
traj.topology = pt.load_topology("./data/Tc5b.top")
assert traj.topology.is_empty() == False
traj._load("./data/Tc5b.x")
def test_indexing(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj2 = pt.TrajectoryIterator()
traj2.top = pt.load_topology(fn('Tc5b.top'))
traj2._load(fn('Tc5b.x'))
farray = traj2[[0, 9, 1]]
assert farray.n_frames == 3
aa_eq(traj2[0].atom(0), farray[0].atom(0))
aa_eq(traj2[9].atom(0), farray[1].atom(0))
aa_eq(traj2[1].atom(0), farray[2].atom(0))
arr = np.asarray(traj2[0]._buffer1d[:])
frame0 = traj2[0]
arr0 = np.asarray(frame0._buffer1d[:])
mat0 = np.asmatrix(arr0).reshape(304, 3)
mat0[:, 0] = np.asmatrix(list(range(304))).reshape(304, 1)
assert frame0[0, 0] == 0.
assert frame0[1, 0] == 1.
assert frame0[2, 0] == 2.
# raise if size = 0
traj3 = pt.Trajectory()
assert traj3.n_frames == 0, 'empty Trajectory, n_frames must be 0'
with pytest.raises(IndexError):
traj3[0]
with pytest.raises(IndexError):
traj3.__setitem__(0, traj[3])
def main():
args = get_argument()
#check_input_data(args)
print(f'Current working directory: {os.getcwd()}')
#if not check_config_file(args.config, args.verbose):
# sys.exit(1)
#configfile = configparser.ConfigParser()
#configfile.read(f'{args.config}')
#hdlr = logging.FileHandler(
# f'framework_{strftime("%Y-%m-%d__%H-%M-%S", localtime())}.log')
#logging.root.addHandler(hdlr)
#logging.root.setLevel(logging.INFO)
#logging.root.setLevel(logging.DEBUG)
#logging.info(f'***Output from framework*** {strftime("%Y-%m-%d__%H-%M-%S", localtime())} \n')
#logging.info(f'#Protein : {args.protein} -> protein.pdb \n')
#logging.info(f'#Ligand : {args.ligand} {configfile["LIGAND"]["name"]} \n')
#logging.info(f'#Tunnel: {args.tunnel} \n')
pdb = pt.load("protein_with_tunnel.pdb")
pdb_topology = pt.load_topology('protein_with_tunnel.pdb')
restraint_residue = []
for i in range(1, pdb_topology.n_residues):
#print(f'\':{i} FIL T\'')
string_index = f':{i} :FIL T'
if pt.distance(pdb, string_index) < 12.0:
# simp_top = pdb_topology.simplify()
#name = simp_top.residue()
restraint_residue.append(f'{pdb_topology.residue(i).index},')
#string_residues.join(f':{pdb_topology.residue(i).index}')
#restraint_residue.append(name)
string_residues = ' '.join([str(elem) for elem in restraint_residue])
print(string_residues)
def _assign_filter(self, sel_filter=None):
if sel_filter is not None:
print("Assigning sel_filter membership(bflt,aflt,tflt): '" +
self.topofile + "'")
data_len = len(self.nodes)
pdb = pt.load_topology(self.topofile)
H_indices = pdb.select(sel_filter)
for i in range(1, data_len + 1):
# Get selected atoms # in bond
if self.nodes[i].a2 != -1:
self.nodes[i].bflt = 0
if self.nodes[i].a2 - 1 in H_indices:
self.nodes[i].bflt += 1
if self.nodes[i].a1 - 1 in H_indices:
self.nodes[i].bflt += 1
# Get selected atoms # in angle
if not (self.nodes[i].a2 == -1 or self.nodes[i].a3 == -1):
self.nodes[i].aflt = 0
if self.nodes[i].a3 - 1 in H_indices:
self.nodes[i].aflt += 1
if self.nodes[i].a1 - 1 in H_indices:
self.nodes[i].aflt += 1
# Get selected atoms # in torsion
if not (self.nodes[i].a2 == -1 or self.nodes[i].a3 == -1
or self.nodes[i].a4 == -1):
self.nodes[i].tflt = 0
if self.nodes[i].a1 - 1 in H_indices:
self.nodes[i].tflt += 1
if self.nodes[i].a2 - 1 in H_indices:
self.nodes[i].tflt += 1
if self.nodes[i].a3 - 1 in H_indices:
self.nodes[i].tflt += 1
if self.nodes[i].a4 - 1 in H_indices:
self.nodes[i].tflt += 1
def test_mass_atomic_number_dict():
top = pt.load_topology(fn("tz2.parm7"))
mass_list = []
for atom in top:
mass_list.append(mass_atomic_number_dict[atom.atomic_number])
aa_eq(mass_list, top.mass, decimal=2)
def test_indexing(self):
traj = pt.iterload('data/Tc5b.x', 'data/Tc5b.top')
traj2 = pt.TrajectoryIterator()
traj2.top = pt.load_topology("./data/Tc5b.top")
traj2._load("./data/Tc5b.x")
farray = traj2[[0, 9, 1]]
assert farray.n_frames == 3
assert traj2[0].atom(0) == farray[0].atom(0)
assert traj2[9].atom(0) == farray[1].atom(0)
assert traj2[1].atom(0) == farray[2].atom(0)
arr = np.asarray(traj2[0]._buffer1d[:])
frame0 = traj2[0]
arr0 = np.asarray(frame0._buffer1d[:])
mat0 = np.asmatrix(arr0).reshape(304, 3)
mat0[:, 0] = np.asmatrix(list(range(304))).reshape(304, 1)
assert frame0[0, 0] == 0.
assert frame0[1, 0] == 1.
assert frame0[2, 0] == 2.
# raise if size = 0
traj3 = pt.Trajectory()
assert traj3.n_frames == 0, 'empty Trajectory, n_frames must be 0'
self.assertRaises(IndexError, lambda: traj3[0])
self.assertRaises(IndexError, lambda: traj3.__setitem__(0, traj[3]))
def test_basic(self):
'''slicing, select'''
top = pt.load_topology(fn('Tc5b.top'))
#
assert isinstance(top[0], Atom)
assert isinstance(top[:2], pt.Topology)
assert isinstance(top[:1], pt.Topology)
assert isinstance(top[range(10)], pt.Topology)
assert isinstance(top[list(range(10))], pt.Topology)
assert isinstance(top[np.array(range(10))], pt.Topology)
assert top[0].name == top['@1'][0].name
# mask, AtomMask, python array, list
atm = top("@CA")
indices = atm.indices
for a1, a2, a3, a4 in zip(top['@CA'], top[atm], top[indices],
top[list(indices)]):
assert a1.name == a2.name == a3.name == a4.name == 'CA'
# check len
assert len(top[:]) == top.n_atoms
assert len(top[:10]) == 10
# API
top.bond_indices
top.angle_indices
top.dihedral_indices
def test_0(self):
top = pt.load_topology("./data/ala3.psf")
reslit = top.residuelist
atm = AtomMask("@CA")
top.set_integer_mask(atm)
atm.invert_mask()
frame = Frame(atm.n_atoms)
frame[:10] = np.asarray(array('d', list(range(30)))).reshape(10, 3)
def test_get_iter(self):
top = pt.load_topology("./data/DOPC.parm7")
s = [atom.name for atom in top[":PC@H*"]]
atom0 = top[":PC@H*"][0]
old_natoms = top.n_atoms
self.assertRaises(ValueError, lambda: top.join(top))
top.join(top.copy())
assert top.n_atoms == 2 * old_natoms
def test_blind_load(self):
top = pt.load_topology("./data/Tc5b.top")
assert isinstance(top, Topology) == True
traj = pt.iterload(filename="./data/Tc5b.x", top="./data/Tc5b.top")
is_traj = (isinstance(traj, TrajectoryIterator)
or isinstance(traj, Trajectory))
assert is_traj
def test_slice_basic(self):
traj2 = pt.Trajectory()
traj2.top = pt.load_topology("./data/Tc5b.top")
traj2.load("./data/Tc5b.x")
traj2.load("./data/Tc5b.x")
traj2.load("./data/Tc5b.x")
traj2.load("./data/Tc5b.x")
fsub = traj2[2:10]
fsub[0][0] = 100.
def test_blind_load():
top = pt.load_topology(tc5b_top)
assert isinstance(top, Topology) == True
traj = pt.iterload(filename=tc5b_trajin, top=tc5b_top)
is_traj = (isinstance(traj, TrajectoryIterator)
or isinstance(traj, Trajectory))
assert is_traj
def test_get_iter(self):
top = pt.load_topology("./data/DOPC.parm7")
s = [atom.name for atom in top[":PC@H*"]]
atom0 = top[":PC@H*"][0]
old_natoms = top.n_atoms
self.assertRaises(ValueError, lambda: top.join(top))
top.join(top.copy())
assert top.n_atoms == 2 * old_natoms
def test_psf(self):
top = pt.load_topology(fn('ala3.psf'))
list(top.residues)
atm = AtomMask("@CA")
top._set_integer_mask(atm)
atm.invert_mask()
frame = Frame(atm.n_atoms)
frame[:10] = np.asarray(array('d', list(range(30)))).reshape(10, 3)
def test_slice_basic(self):
traj2 = pt.Trajectory()
traj2.top = pt.load_topology(fn('Tc5b.top'))
traj2.load(fn('Tc5b.x'))
traj2.load(fn('Tc5b.x'))
traj2.load(fn('Tc5b.x'))
traj2.load(fn('Tc5b.x'))
fsub = traj2[2:10]
fsub[0][0] = 100.
def test_get_iter(self):
top = pt.load_topology(fn('DOPC.parm7'))
[atom.name for atom in top[":PC@H*"]]
top[":PC@H*"][0]
old_natoms = top.n_atoms
with pytest.raises(ValueError):
top.join(top)
top.join(top.copy())
assert top.n_atoms == 2 * old_natoms
def test_tleap(self):
from pytraj.testing import amberhome
if amberhome and os.path.exists(amberhome + '/bin/tleap'):
from pytraj.amber_wrapper import prmtop_from_tleap
t0 = prmtop_from_tleap('./data/tz2.pdb')
t1 = pt.load_topology('./data/tz2.pdb')
print(t0, t1)
assert t0.n_atoms == t1.n_atoms
else:
print("does not have AMBERHOME. skip")
def test_tleap(self):
from pytraj.testing import amberhome
if amberhome and os.path.exists(amberhome + '/bin/tleap'):
from pytraj.amber_wrapper import prmtop_from_tleap
t0 = prmtop_from_tleap('./data/tz2.pdb')
t1 = pt.load_topology('./data/tz2.pdb')
print(t0, t1)
assert t0.n_atoms == t1.n_atoms
else:
print("does not have AMBERHOME. skip")
def test_simplifed_topology(self):
'''simplify'''
top = pt.load_topology("./data/Tc5b.top")
sim_top = top.simplify()
for atom, sim_atom in zip(top.atoms, sim_top.atoms):
assert atom.resname == sim_atom.resname, 'equal resname'
assert atom.name == sim_atom.name, 'equal resname'
assert atom.type == sim_atom.type, 'equal resname'
assert atom.charge == sim_atom.charge, 'equal resname'
assert atom.mass == sim_atom.mass, 'equal resname'
def test_simplifed_topology(self):
'''simplify'''
top = pt.load_topology("./data/Tc5b.top")
sim_top = top.simplify()
for atom, sim_atom in zip(top.atoms, sim_top.atoms):
assert atom.resname == sim_atom.resname, 'equal resname'
assert atom.name == sim_atom.name, 'equal resname'
assert atom.type == sim_atom.type, 'equal resname'
assert atom.charge == sim_atom.charge, 'equal resname'
assert atom.mass == sim_atom.mass, 'equal resname'
def pack(traj, mol, n_copies, unitcells=None, ig=8888, grid_spacing=0.2):
'''
Parameters
----------
traj : pytraj.Trajectory
mol : pytraj.Trajectory
unitcells : None or np.ndarray, dim=2
if None, use box info from traj else use it
n_copies : number of `mol`
ig : int
randome seed
grid_spacing : float
'''
add_to_box_exe = amberbin('AddToBox') or 'AddToBox'
input_pdb = 'input.pdb'
mol_pdb = 'mol.pdb'
out_pdb = 'out.pdb'
assert mol.n_frames == 1
total_n_atoms = traj.n_atoms + mol.n_atoms * n_copies
new_traj_xyz = np.empty((traj.n_frames, total_n_atoms, 3), dtype='f8')
with tempfolder():
mol.save(mol_pdb, overwrite=True)
for index, frame in enumerate(traj):
pytraj.write_traj(input_pdb, traj=frame, top=traj.top, overwrite=True)
parm = parmed.load_file(input_pdb)
if unitcells is not None:
parm.box = unitcells[index]
else:
assert frame.has_box(), 'must have box info'
parm.box = frame.box
# add remark 290
parm.save(input_pdb, overwrite=True)
command = [
add_to_box_exe,
'-c', input_pdb,
'-a', mol_pdb,
'-na', str(n_copies),
'-IG', str(ig),
'-G', str(grid_spacing),
'-o', out_pdb
]
try:
subprocess.check_output(command, stderr=subprocess.STDOUT)
new_traj_xyz[index] = pytraj.load(out_pdb).xyz
except subprocess.CalledProcessError as e:
return e.output.decode()
top = pytraj.load_topology(out_pdb)
return pytraj.Trajectory(xyz=new_traj_xyz, top=top)
def prmtop_from_tleap(filename, leapin=None, verbose=False):
'''make prmtop file from pdb
Parameters
----------
filename : str, pdb filename
leapin : str, optional, default None
leap input
if None, use::
source leaprc.ff14SB
set default PBradii mbondi3
x = loadpdb {pdbfile}
saveamberparm x {pdbfile}.prmtop {pdbfile}.rst7
quit
verbose : bool, default False
if False, suppress tleap output
'''
import os
import subprocess
import pytraj as pt
if leapin is None:
leapin = leap_template
amberhome = os.environ.get('AMBERHOME')
if amberhome is None:
raise RuntimeError('must set AMBERHOME')
tleap = amberhome + '/bin/tleap'
filename = os.path.abspath(filename)
with tempfolder():
leapin = leapin.format(pdbfile=filename)
with open("tmp_leap.in", 'w') as f:
f.write(leapin)
with open(os.devnull, 'wb') as devnull:
if not verbose:
subprocess.check_call(
[tleap, ' -f tmp_leap.in'],
stdout=devnull,
stderr=subprocess.STDOUT)
else:
x = subprocess.check_call([tleap, ' -f tmp_leap.in'])
if verbose:
print(x)
return pt.load_topology("tmp.top")
def test_0(self):
atm = AtomMask("@CA")
assert atm.n_atoms == 0
top = pt.load_topology("./data/Tc5b.top")
top.set_integer_mask(atm)
assert atm.n_atoms == 20
top2 = top._modify_state_by_mask(atm)
assert top2.n_atoms == 20
for atom in top2:
assert atom.name == 'CA'
atm.invert_mask()
top3 = top._modify_state_by_mask(atm)
assert top3.n_atoms == top.n_atoms - 20
def test_0(self):
atm = AtomMask("@CA")
assert atm.n_atoms == 0
top = pt.load_topology(fn('Tc5b.top'))
top._set_integer_mask(atm)
assert atm.n_atoms == 20
top2 = top._modify_state_by_mask(atm)
assert top2.n_atoms == 20
for atom in top2:
assert atom.name == 'CA'
atm.invert_mask()
top3 = top._modify_state_by_mask(atm)
assert top3.n_atoms == top.n_atoms - 20
def get_atom_num_and_pos(topology, mask, trajectory=None):
'''retrun an array with a list of atom positions and numbers (starting at 1)
corresponding to a cpptraj mask rerurns a tuple of
coords and atom_numbers'''
if isinstance(topology, basestring) == True:
topology = pt.load_topology(topology)
atom_numbers = topology.select(mask)+1
if trajectory is not None:
if isinstance(trajectory, basestring) == True:
trajectory = pt.iterload(trajectory, topology)
coords = np.array(trajectory[mask][-1].xyz)
else:
coords = None
return coords, atom_numbers
def test_6_speed(self):
import numpy as np
from pytraj import AtomMask
# test constructor from list/array/python array
top = pt.load_topology(fn('DOPC.parm7'))
indices = top.select(":WAT")
atm1 = AtomMask(indices)
atm2 = AtomMask(list(indices))
atm3 = AtomMask(np.asarray(indices))
# use max_atoms
atm4 = AtomMask(np.asarray(indices), 1000)
import numpy as np
assert np.all(atm1.indices == atm2.indices)
assert np.all(atm3.indices == atm4.indices)
def test_6_speed(self):
import numpy as np
from pytraj import AtomMask
# test constructor from list/array/python array
top = pt.load_topology("./data/DOPC.parm7")
indices = top.select(":WAT")
atm1 = AtomMask(indices)
atm2 = AtomMask(list(indices))
atm3 = AtomMask(np.asarray(indices))
# use max_atoms
atm4 = AtomMask(np.asarray(indices), 1000)
import numpy as np
assert np.all(atm1.indices == atm2.indices)
assert np.all(atm3.indices == atm4.indices)
def test_5_speed(self):
top = pt.load_topology(fn('DOPC.parm7'))
from time import time
t0 = time()
indices = top(":WAT").indices
time() - t0
t0 = time()
_indices_view = top(":WAT")._indices_view
time() - t0
count = 0
for i, j in zip(indices, _indices_view):
if not i == j:
count += 1
assert count == 0
def test_5_speed(self):
top = pt.load_topology("./data/DOPC.parm7")
from time import time
t0 = time()
indices = top(":WAT").indices
gap_0 = time() - t0
t0 = time()
_indices_view = top(":WAT")._indices_view
gap_1 = time() - t0
count = 0
for i, j in zip(indices, _indices_view):
if not i == j:
count += 1
assert count == 0
def test_1(self):
top = pt.load_topology(tc5b_top)
#
top.strip("!@CA")
assert top.n_atoms == 20
for atom in top.atoms:
pass
for res in top.residues:
pass
for mol in top.mols:
pass
for idx, atom in enumerate(top.atoms):
pass
assert idx + 1 == top.n_atoms
def test_trajectory_writer_open_close():
farray = pt.load(
fn("Tc5b.x"), fn("Tc5b.top"), frame_indices=list(range(10)))
frame0 = farray[0]
with tempfolder():
trajout = TrajectoryWriter()
trajout.open(filename="test.x", top=farray.top, overwrite=True)
trajout.write(frame0)
# add more frames
for i in range(5, 8):
trajout.write(farray[i])
trajout.close()
farray = Trajectory()
farray.top = pt.load_topology(fn('Tc5b.top'))
farray.load("test.x")
def get_atomdicts_pytraj(topology):
'''pytrajdict being created via top = pt.load_topology(topologyfile)
pytrajdict = top.to_dict()'''
top = pt.load_topology(topology)
pytrajdict = top.to_dict()
atom_names = pytrajdict['atom_name']
resids = pytrajdict['resid']
chainids = pytrajdict['mol_number']
mydictlist = []
for number, (name, res, chain) in enumerate(zip(atom_names,
resids,
chainids)):
if chain+1 == 3:
break
mydictlist.append(dict(atom_number=str(number+1),
atom_name=str(name),
res=res+1, chain=chain+1))
return mydictlist
def to_pytraj_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'file:pdb')
atom_indices = digest_atom_indices(atom_indices)
try:
from pytraj import load_topology
except:
raise LibraryNotFoundError('pytraj')
from ..pytraj_Topology import extract as extract_pytraj_Topology
tmp_item = load_topology(item)
tmp_item = extract_pytraj_Topology(tmp_item, atom_indices=atom_indices,
structure_indices=structure_indices, copy_if_all=False, check=False)
return tmp_item
def test_simplifed_topology(self):
'''simplify'''
top = pt.load_topology(fn('Tc5b.top'))
sim_top = top.simplify()
assert sim_top.select('@CA').tolist() == top.select('@CA').tolist()
for atom, sim_atom in zip(top.atoms, sim_top.atoms):
assert atom.resname == sim_atom.resname
assert atom.name == sim_atom.name
assert atom.type == sim_atom.type
assert atom.charge == sim_atom.charge
assert atom.mass == sim_atom.mass
# API
atom = sim_top.atoms[0]
atom.residue
atom.residue.name
atom.residue.index
atom.bond_partners
def filter_seperated(trajectory, topology, targetdir, separated_frame, masks,
outprefix):
cwd = os.getcwd()
trajectory = lib.paths_for_there(trajectory, targetdir)
topology = lib.paths_for_there(topology, targetdir)
separated_frame = lib.paths_for_there(separated_frame, targetdir)
os.system('mkdir -p ' + targetdir)
os.chdir(targetdir)
cpptrajtext = ('parm ' + topology + ' \n'
'trajin ' + trajectory + ' \n'
'reference ' + separated_frame + ' [ref] \n'
'nativecontacts ' + masks + ' distance 3.3 out '
'contacts series ref [ref] \n'
'go \n')
with open('cpptraj.in', 'w') as f:
f.write(cpptrajtext)
os.system('mpirun -np 4 cpptraj.MPI -i cpptraj.in')
top = pt.load_topology(topology)
traj = pt.iterload(trajectory, top)
d = np.loadtxt('contacts', usecols=(0, 2), dtype=int)
nocontact = []
contact = []
for i, k in d:
if k == 0:
nocontact.append(i - 1)
else:
contact.append(i - 1)
pt.write_traj('nocont_' + outprefix + '.nc',
traj[nocontact],
top=top,
overwrite=True)
conttraj = 'cont_' + outprefix + '.nc'
pt.write_traj(conttraj, traj[contact], top=top, overwrite=True)
os.chdir(cwd)
return lib.paths_for_here(targetdir, conttraj)
def compress_traj_pt(trajs,
top,
targetdir,
cutoff_fraction,
compression,
outfile_name=None):
'''cutoff_fraction is the fraction of frames left out at the beginning
compression = 1 will give no compression'''
top = pt.load_topology(top)
noexttraj = os.path.splitext(os.path.basename(trajs[0]))[0]
traj = pt.iterload(trajs, top)
if cutoff_fraction > 1:
traj = traj[len(traj) / cutoff_fraction::compression]
else:
traj = traj[::compression]
if outfile_name is None:
outfile_name = 'compress_' + noexttraj + '.nc'
os.system('mkdir -p ' + targetdir)
traj.save(targetdir + '/' + outfile_name, overwrite=True)
return lib.paths_for_here(targetdir, outfile_name)
def test_1(self):
datadir = "./data/"
filename = "./data/Tc5b.top"
top = pt.load_topology(filename)
#
top.strip("!@CA")
assert top.n_atoms == 20
for atom in top.atoms:
pass
for res in top.residues:
pass
for mol in top.mols:
pass
for idx, atom in enumerate(top.atoms):
pass
assert idx + 1 == top.n_atoms
def test_1(self):
datadir = "./data/"
filename = "./data/Tc5b.top"
top = pt.load_topology(filename)
#
top.strip("!@CA")
assert top.n_atoms == 20
for atom in top.atoms:
pass
for res in top.residues:
pass
for mol in top.mols:
pass
for idx, atom in enumerate(top.atoms):
pass
assert idx + 1 == top.n_atoms
def test_basic(self):
'''slicing, select'''
top = pt.load_topology("./data/Tc5b.top")
#
assert isinstance(top[0], Atom)
assert isinstance(top[:2], pt.Topology)
assert isinstance(top[:1], pt.Topology)
assert isinstance(top[range(10)], pt.Topology)
assert isinstance(top[list(range(10))], pt.Topology)
assert isinstance(top[np.array(range(10))], pt.Topology)
assert top[0].name == top['@1'][0].name
# mask, AtomMask, python array, list
atm = top("@CA")
indices = atm.indices
for a1, a2, a3, a4 in zip(top['@CA'], top[atm], top[indices],
top[list(indices)]):
assert a1.name == a2.name == a3.name == a4.name == 'CA'
# check len
assert len(top[:]) == top.n_atoms
assert len(top[:10]) == 10
def test_iter_basic(self):
traj = pt.TrajectoryIterator()
traj.top = pt.load_topology("./data/Tc5b.top")
traj._load("./data/Tc5b.x")
for frame in traj:
pass
#!/usr/bin/env python
import os
import pytraj as pt
from glob import iglob, glob
fns = iglob('min*rst7')
parmlist = glob('*.parm7')
if not parmlist:
parmlist = glob('../*.parm7')
top = pt.load_topology(parmlist[0])
failed = []
for fn in fns:
traj = pt.iterload(fn, top)
if traj.n_frames == 0:
failed.append(traj.filename.split('/')[-1])
print('failed', failed)
try:
os.mkdir('old/')
except OSError:
pass
for fn in failed:
os.system('mv {} old/'.format(fn))
def test_3_indexing(self):
top = pt.load_topology("./data/Tc5b.top")
atm = AtomMask("@CA")
top.set_integer_mask(atm)
import pytraj as pt
top = pt.load_topology("../tests/data/Tc5b.top")
# save only CA atoms
pt.write_parm("./output/_Tcb5.onlyCA.top", top["@CA"])
def test_2(self):
"""test open file writen from test_0"""
farray = Trajectory()
farray.top = pt.load_topology('./data/Tc5b.top')
farray.load("./output/test.x")
def test_raise_RuntimeError(self):
self.assertRaises(RuntimeError, lambda: pt.load_topology('dummy'))
def test_select_mask(self):
top = pt.load_topology("./data/Tc5b.top")
arr0 = top.atom_indices("@CA")
def test_empty_top(self):
top = Topology()
assert top.is_empty() == True
filename = "./data/Tc5b.top"
top = pt.load_topology(filename)
assert top.is_empty() == False
def test_del_top(self):
# why here? lazy to make another file
top = pt.load_topology("./data/Tc5b.top")
top2 = top
del top
import pytraj as pt
from netCDF4 import Dataset
from pytraj.testing import Timer
filename = 'GAAC3.5000frames.nc'
top_name = 'GAAC.topo'
top = pt.load_topology(top_name)
@Timer()
def load_netcdf4(filename=filename):
with Dataset(filename, 'r') as fh:
c= fh['coordinates']
return c[:N]
@Timer()
def load_mutable_traj(filename=filename):
with Dataset(filename, 'r') as fh:
c= fh['coordinates']
traj = pt.Trajectory(xyz=c[:N], top=top.copy())
traj.xyz[:] = traj.xyz.astype('f8')
@Timer()
def load_immutable_traj(filename=filename, top_name=top_name):
traj = pt.iterload(filename, top_name)
return traj[:N]
if __name__ == '__main__':
import sys
from collections import OrderedDict
from matplotlib import pyplot as plt
#!/usr/bin/env python
import sys
import parmed as pmd
import pytraj as pt
from collections import Counter
fname = '3gx5.14sb.gaff.parm7'
parm = pmd.load_file(fname)
print('resname set', set(res.name for res in parm.residues))
print('total charge : ', sum(atom.charge for atom in parm.atoms))
print(pmd.tools.summary(parm))
print(pt.load_topology(fname))
print(Counter(res.name for res in parm.residues))
