def to_molsysmt_MolSys(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'pytraj.Trajectory')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from molsysmt.native.molsys import MolSys
from . import to_molsysmt_Topology
from . import to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(item,
atom_indices=atom_indices,
check=False)
tmp_item.structures = to_molsysmt_Structures(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
return tmp_item
def to_openmm_Modeller(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'file:mol2')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import to_openmm_Topology
from . import get_coordinates_from_atom, get_box_from_system
from ..openmm_Topology import to_openmm_Modeller as openmm_Topology_to_openmm_Modeller
tmp_item = to_openmm_Topology(item, atom_indices=atom_indices, check=False)
coordinates = get_coordinates_from_atom(
item,
indices=atom_indices,
structure_indices=structure_indices,
check=False)
box = get_box_from_system(item,
structure_indices=structure_indices,
check=False)
tmp_item = openmm_Topology_to_openmm_Modeller(tmp_item,
coordinates=coordinates,
box=box,
check=False)
return tmp_item
def to_string_pdb_text(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'string:pdb_id')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from ..file_pdb import download as download_file_pdb
from ..string_pdb_text import extract as extract_string_pdb_text
from os import remove
tmp_item = download_file_pdb(item.replace('pdb_id:', ''), output_filename)
tmp_file = tmp_item
fff = open(tmp_item, 'r')
tmp_item = fff.read()
fff.close()
remove(tmp_file)
tmp_item = extract_string_pdb_text(tmp_item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False,
check=False)
return tmp_item
def to_mdtraj_Trajectory(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'parmed.Structure')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import to_mdtraj_Topology
from . import get_coordinates_from_atom, get_box_from_system
from ..mdtraj_Topology import to_mdtraj_Trajectory as openmm_Topology_to_openmm_Modeller
tmp_item = to_mdtraj_Topology(item, atom_indices=atom_indices, check=False)
coordinates = get_coordinates_from_atom(
item,
indices=atom_indices,
structure_indices=structure_indices,
check=False)
box = get_box_from_system(item,
structure_indices=structure_indices,
check=False)
tmp_item = mdtraj_Topology_to_mdtraj_Trajectory(tmp_item,
coordinates=coordinates,
box=box,
check=False)
return tmp_item
def extract(item,
atom_indices='all',
structure_indices='all',
copy_if_all=True,
check=True):
if check:
digest_item(item, 'mdtraj.Trajectory')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
if (atom_indices is 'all') and (structure_indices is 'all'):
if copy_if_all:
from copy import deepcopy
tmp_item = deepcopy(item)
else:
tmp_item = item
else:
tmp_item = item
if atom_indices is not 'all':
tmp_item = tmp_item.atom_slice(atom_indices)
if structure_indices is not 'all':
tmp_item = tmp_item.slice(structure_indices)
return tmp_item
def to_openmm_Modeller(item,
atom_indices='all',
coordinates=None,
box=None,
check=True):
if check:
digest_item(item, 'openmm.Topology')
atom_indices = digest_atom_indices(atom_indices)
coordinates = digest_coordinates(coordinates)
box = digest_box(box)
from . import extract
from molsysmt import puw
from openmm.app import Modeller
tmp_item = extract(item,
atom_indices=atom_indices,
copy_if_all=False,
check=False)
positions = puw.convert(coordinates[0], 'nm', to_form='openmm.unit')
tmp_item = Modeller(tmp_item, positions)
return tmp_item
def to_openmm_Simulation(item, atom_indices='all', structure_indices='all',
forcefield=None, non_bonded_method='no_cutoff', non_bonded_cutoff='1.0 nm', constraints=None,
rigid_water=True, remove_cm_motion=True, hydrogen_mass=None, switch_distance=None,
flexible_constraints=False, integrator='Langevin', temperature='300.0 K',
collisions_rate='1.0 1/ps', integration_timestep='2.0 fs', platform='CUDA', check=True):
if check:
digest_item(item, 'file:pdb')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import to_openmm_Modeller
from ..openmm_Modeller import to_openmm_Simulation as openmm_Modeller_to_openmm_Simulation
tmp_item = to_openmm_Modeller(item, atom_indices=atom_indices, structure_indices=structure_indices, check=False)
tmp_item = openmm_Modeller_to_openmm_Simulation(tmp_item,
forcefield=forcefield, non_bonded_method=non_bonded_method,
non_bonded_cutoff=non_bonded_cutoff, constraints=constraints,
rigid_water=rigid_water, remove_cm_motion=remove_cm_motion,
hydrogen_mass=hydrogen_mass, switch_distance=switch_distance,
flexible_constraints=flexible_constraints, integrator=integrator,
temperature=temperature, collisions_rate=collisions_rate,
integration_timestep=integration_timestep, platform=platform, check=False)
return tmp_item
def to_molsysmt_MolSys(item,
selection='all',
structure_indices='all',
syntaxis='MolSysMT'):
if check:
digest_item(item, 'openmm.GromacsGroFile')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from molsysmt.native.molsys import MolSys
from .to_molsysmt_Topology import to_molsysmt_Topology
from .to_molsysmt_Structures import to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
tmp_item.structures = to_molsysmt_Structures(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
return tmp_item
def to_pdbfixer_PDBFixer(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'mdtraj.Trajectory')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import to_openmm_Topology
from . import get_coordinates_from_atom
from ..openmm_Topology import to_pdbfixer_PDBFixer as openmm_Topology_to_pdbfixer_PDBFixer
tmp_item = to_openmm_Topology(item, atom_indices=atom_indices, check=False)
coordinates = get_coordinates_from_atom(
item,
indices=atom_indices,
structure_indices=structure_indices,
check=False)
tmp_item = openmm_Topology_to_pdbfixer_PDBFixer(tmp_item,
coordinates=coordinates,
check=False)
return tmp_item
def to_pytraj_Trajectory(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'file:pdb')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
try:
from pytraj import load
except:
raise LibraryNotFoundError('pytraj')
from ..pytraj_Trajectory import extract as extract_pytraj_Trajectory
tmp_item = load(item)
tmp_item = extract_pytraj_Trajectory(tmp_item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False,
check=False)
return tmp_item
def to_mdanalysis_Universe(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'file:mmtf')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
try:
from MDAnalysis import Universe
except:
raise LibraryNotFoundError('MDAnalysis')
from ..mdanalysis_Universe import extract as extract_mdanalysis_Universe
tmp_item = Universe(item)
tmp_item = extract_mdanalysis_Universe(tmp_item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False,
check=False)
return tmp_item
def extract(item,
atom_indices='all',
structure_indices='all',
copy_if_all=True,
check=True):
if check:
digest_item(item, 'parmed.Structure')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
if (atom_indices is 'all') and (structure_indices is 'all'):
if copy_if_all:
from copy import deepcopy
tmp_item = deepcopy(item)
else:
tmp_item = item
else:
from molsysmt._private.atom_indices import atom_indices_to_AmberMask
from molsysmt._private.atom_indices import complementary_atom_indices
tmp_atom_indices = complementary_atom_indices(item, atom_indices)
mask = atom_indices_to_AmberMask(item, tmp_atom_indices)
tmp_item = copy(item)
tmp_item.strip(
atom_indices2AmberMask(atom_indices, len(item.atoms),
inverse=True))
return tmp_item
def add(to_item, item, check=True):
if check:
digest_item(item, 'pytraj.Trajectory')
digest_item(to_item, 'pytraj.Trajectory')
raise NotImplementedMethodError()
def add(to_item, item, check=True):
if check:
digest_item(item, 'mdanalysis.Universe')
digest_item(to_item, 'mdanalysis.Universe')
raise NotImplementedMethodError()
def add(to_item, item, check=True):
if check:
digest_item(item, 'mdtraj.Topology')
digest_item(to_item, 'mdtraj.Topology')
raise NotImplementedMethodError()
def add(to_item, item, check=True):
if check:
digest_item(item, 'mdtraj.HDF5TrajectoryFile')
digest_item(to_item, 'mdtraj.HDF5TrajectoryFile')
raise NotImplementedMethodError()
def to_openmm_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'openmm.GromacsTopFile')
atom_indices = digest_atom_indices(atom_indices)
tmp_item = item.topology
return tmp_item
def append_structures(item, step=None, time=None, coordinates=None, box=None, check=True):
if check:
digest_item(item, 'mdtraj.Trajectory')
step = digest_step(step)
time = digest_time(time)
coordinates = digest_coordinates(coordinates)
box = digest_box(box)
raise NotImplementedMethodError()
def to_mdanalysis_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'file:pdb')
atom_indices = digest_atom_indices(atom_indices)
from . import to_mdanalysis_topology_PDBParser
from ..mdanalysis_topology_PDBParser import to_mdanalysis_Topology as mdanalysis_topology_PDBParser_to_mdanalysis_Topology
tmp_item = to_mdanalysis_topology_PDBParser(item, check=False)
tmp_item = mdanalysis_topology_PDBParser_to_mdanalysis_Topology(tmp_item, atom_indices=atom_indices, check=False)
return tmp_item
def to_molsysmt_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'file:gro')
atom_indices = digest_atom_indices(atom_indices)
from . import to_openmm_GromacsGroFile
from ..openmm_GromacsGroFile import to_molsysmt_Topology as openmm_GromacsGroFile_to_molsysmt_Topology
tmp_item = to_openmm_GromacsGroFile(item, check=False)
tmp_item = openmm_GromacsGroFile_to_molsysmt_Topology(tmp_item, atom_indices=atom_indices, check=False)
return tmp_item
def to_string_aminoacids1(item, group_indices='all', check=True):
if check:
digest_item(item, 'mdtraj.Topology')
atom_indices = digest_atom_indices(atom_indices)
from . import to_string_aminoacids3
from ..string_aminoacids3 import to_string_aminoacids1 as string_aminoacids3_to_string_aminoacids1
tmp_item = to_string_aminoacids3(item, group_indices=group_indices, check=False)
tmp_item = string_aminoacids3_to_string_aminoacids1(tmp_item, check=False)
return tmp_item
def to_mdtraj_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'file:mol2')
atom_indices = digest_atom_indices(atom_indices)
from mdtraj import load_mol2
from ..mdtraj_Topology import extract as extract_mdtraj_Topology
tmp_item = load_mol2(item).topology
tmp_item = extract_mdtraj_Topology(tmp_item)
return tmp_item
def to_parmed_Structure(item, atom_indices='all', check=True):
if check:
digest_item(item, 'mdtraj.Topology')
atom_indices = digest_atom_indices(atom_indices)
from . import to_openmm_Topology
from .openmm_Topology import to_parmed_Structure as openmm_Topology_to_parmed_Structure
tmp_item = to_openmm_Topology(item, atom_indices=atom_indices, check=False)
tmp_item = openmm_Topology_to_parmed_Structure(tmp_item, check=False)
return tmp_item
def to_openmm_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'mdtraj.HDF5TrajectoryFile')
atom_indices = digest_atom_indices(atom_indices)
from . import to_mdtraj_Topology
from ..mdtraj_Topology import to_openmm_Topology as mdtraj_Topology_to_openmm_Topology
tmp_item = to_mdtraj_Topology(item, atom_indices=atom_indices, check=False)
tmp_item = mdtraj_Topology_to_openmm_Topology(item, check=False)
return tmp_item
def to_molsysmt_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'file:mol2')
atom_indices = digest_atom_indices(atom_indices)
from . import to_mdtraj_Topology
from ..mdtraj_Topology import to_molsysmt_Topology as mdtraj_Topology_to_molsysmt_Topology
tmp_item = to_mdtraj_Topology(item, atom_indices=atom_indices, check=False)
tmp_item = mdtraj_Topology_to_molsysmt_Topology(tmp_item, check=False)
return tmp_item
def to_string_aminoacids3(item, group_indices='all', check=True):
if check:
digest_item(item, 'file:mmtf.MMTFDecoder')
group_indices = digest_group_indices(atom_indices)
from . import to_molsysmt_Topology
from ..molsysmt_Topology import to_string_aminoacids3 as molsysmt_Topology_to_string_aminoacids3
tmp_item = to_molsysmt_Topology(item, check=False)
tmp_item = molsysmt_Topology_to_string_aminoacids3(tmp_item, group_indices=group_indices, check=False)
return tmp_item
def to_mdanalysis_topology_PDBParser(item, atom_indices='all', check=True):
if check:
digest_item(item, 'file:pdb')
atom_indices = digest_atom_indices(atom_indices)
try:
from MDAnalysis.topology import PDBParser
except:
raise LibraryNotFoundError('MDAnalysis')
tmp_item = PDBParser.PDBParser(item)
return tmp_item
def to_file_xyznpy(item, atom_indices='all', structure_indices='all', output_filename=None, check=True):
if check:
digest_item(item, 'XYZ')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
tmp_item = output_filename
with open(tmp_item, 'wb') as fff:
np.save(fff, item.shape, allow_pickle=True)
np.save(fff, puw.get_value(item, to_unit='nm'), allow_pickle=True)
return tmp_item
def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', check=True):
if check:
digest_item(item, 'file:xtc')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import to_mdtraj_XTCTrajectoryFile
from ..mdtraj_XTCTrajectoryFile import to_molsysmt_Structures as mdtraj_XTCTrajectoryFile_to_molsysmt_Structures
tmp_item = to_mdtraj_XTCTrajectoryFile(item, check=False)
tmp_item = mdtraj_XTCTrajectoryFile_to_molsysmt_Structures(tmp_item, atom_indices=atom_indices, structure_indices=structure_indices, check=False)
return tmp_item
def to_file_pdb(item, atom_indices='all', structure_indices='all', output_filename=None, check=True):
if check:
digest_item(item, 'mmtf.MMTFDecoder')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import to_molsysmt_MolSys
from ..molsysmt_MolSys import to_file_pdb as molsysmt_MolSys_to_file_pdb
tmp_item = to_molsysmt_MolSys(item, atom_indices=atom_indices, structure_indices=structure_indices)
tmp_item = molsysmt_MolSys_to_file_pdb(tmp_item, output_filename=output_filename)
return tmp_item
