def make_fake_topology(n_atoms):
'''make fake Topology, just for writing xyz array to supported formats
(netcdf, dcd, trr, ...)
>>> import pytraj as pt
>>> top = pt.tools.make_fake_topology(100)
>>> top.n_atoms
100
>>> isinstance(top, pt.Topology)
True
>>> import numpy as np
>>> xyz = np.random.rand(10*100*3).reshape(10, 100, 3)
>>> traj0 = pt.Trajectory(xyz=xyz, top=top)
>>> pt.write_traj('output/test.nc', traj0, overwrite=True)
>>> traj = pt.iterload('output/test.nc', top=top)
>>> traj.n_atoms
100
'''
from pytraj import Atom, Residue, Topology
top = Topology()
for _ in range(n_atoms):
atom = Atom(name='X', type='X', charge=0., mass=0., resid=0)
residue = Residue('Y', 0)
top.add_atom(atom, residue)
return top
def make_fake_topology(n_atoms):
'''make fake Topology, just for writing xyz array to supported formats
(netcdf, dcd, trr, ...)
>>> import pytraj as pt
>>> top = pt.tools.make_fake_topology(100)
>>> top.n_atoms
100
>>> isinstance(top, pt.Topology)
True
>>> import numpy as np
>>> xyz = np.random.rand(10*100*3).reshape(10, 100, 3)
>>> traj0 = pt.Trajectory(xyz=xyz, top=top)
>>> pt.write_traj('output/test.nc', traj0, overwrite=True)
>>> traj = pt.iterload('output/test.nc', top=top)
>>> traj.n_atoms
100
'''
from pytraj import Atom, Residue, Topology
top = Topology()
for _ in range(n_atoms):
atom = Atom(name='X', type='X', charge=0., mass=0., resid=0)
residue = Residue('Y', 0)
top.add_atom(atom, residue)
return top
def _load_Topology(filename):
from pytraj import Topology, ParmFile
top = Topology()
parm = ParmFile()
parm.read(filename, top)
return top
def test_empty_top(self):
top = Topology()
assert top.is_empty() == True
top = pt.load_topology(tc5b_top)
assert top.is_empty() == False
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_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 to_pytraj_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'molsysmt.Topology')
atom_indices = digest_atom_indices(atom_indices)
try:
from pytraj import Topology
from pytraj import Atom as pytraj_atom, Residue as pytraj_residue
except:
raise LibraryNotFound('pytraj')
from molsysmt.physico_chemical_properties import mass as get_mass
from molsysmt.physico_chemical_properties import charge as get_charge
from molsysmt import puw
n_atoms = item.atoms_dataframe.shape[0]
atom_index_array = item.atoms_dataframe["atom_index"].to_numpy()
atom_name_array = item.atoms_dataframe["atom_name"].to_numpy()
atom_id_array = item.atoms_dataframe["atom_id"].to_numpy()
atom_type_array = item.atoms_dataframe["atom_type"].to_numpy()
group_index_array = item.atoms_dataframe["group_index"].to_numpy()
group_name_array = item.atoms_dataframe["group_name"].to_numpy()
group_id_array = item.atoms_dataframe["group_id"].to_numpy()
group_type_array = item.atoms_dataframe["group_type"].to_numpy()
chain_index_array = item.atoms_dataframe["chain_index"].to_numpy()
chain_name_array = item.atoms_dataframe["chain_name"].to_numpy()
chain_id_array = item.atoms_dataframe["chain_id"].to_numpy()
chain_type_array = item.atoms_dataframe["chain_type"].to_numpy()
bonds_atom1 = item.bonds_dataframe["atom1_index"].to_numpy()
bonds_atom2 = item.bonds_dataframe["atom2_index"].to_numpy()
mass_atom_array = puw.get_value(get_mass(item))
try:
charge_atom_array = get_charge(molecular_system)
except:
charge_atom_array = np.zeros(shape=[n_atoms])
tmp_item = Topology()
former_group_index = -1
list_new_atoms = []
for ii in range(n_atoms):
atom_index = atom_index_array[ii]
atom_name = atom_name_array[ii]
atom_id = atom_id_array[ii]
atom_type = atom_type_array[ii]
atom_charge = atom_charge_array[ii]
atom_mass = atom_mass_array[ii]
group_index = group_index_array[ii]
chain_index = chain_index_array[ii]
new_group = (former_group_index != group_index)
if new_group:
residue_name = group_name_array[ii]
residue_id = group_id_array[ii]
residue = pytraj_residue(residue_name,
resid=group_index,
icode=residue_id,
chainID=chain_index)
former_group_index = group_index
atom = pytraj_atom(name=atom_name,
type=atom_type,
resid=group_index,
mass=atom_mass,
charge=atom_charge)
list_new_atoms.append(atom)
tmp_item.add_atom(atom, residue)
bonds = np.column_stack(bonds_atom1, bonds_atom2)
tmp_item.add_bonds(bonds)
return tmp_item