def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_openmm_AmberInpcrdFile
from ..openmm_AmberInpcrdFile import get_step_from_system as aux_get
tmp_item = to_openmm_AmberInpcrdFile(item, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_openmm_Topology
from ..openmm_Topology import get_box_from_system as aux_get
tmp_item = to_openmm_Topology(item, structure_indices=structure_indices, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_openmm_PDBFile
from ..openmm_PDBFile import get_chain_index_from_atom as aux_get
tmp_item = to_openmm_PDBFile(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_bond_type_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_openmm_AmberPrmtopFile
from ..openmm_AmberPrmtopFile import get_bond_type_from_bond as aux_get
tmp_item = to_openmm_AmberPrmtopFile(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_bond_type_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
tmp_indices = get_bond_index_from_bond(item, indices=indices, check=False)
bond = list(item.bonds())
output = [bond[ii].type for ii in tmp_indices]
output = _np.array(output)
del (bond)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_mdtraj_Topology
from ..mdtraj_Topology import get_chain_index_from_atom as aux_get
tmp_item = to_mdtraj_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_molecule_name_from_molecule(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
n_molecules = get_n_molecules_from_system(item)
output = _np.full(n_molecules, None, dtype=object)
else:
output = _np.full(indices.shape[0], None, dtype=object)
return output
def get_entity_type_from_entity(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_pytraj_Topology
from ..pytraj_Topology import get_entity_type_from_entity as aux_get
tmp_item = to_pytraj_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from .to_molsysmt_MolSys import to_molsysmt_MolSys
from ..molsysmt_MolSys import get_step_from_system as aux_get
tmp_item = to_molsysmt_MolSys(item, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_atom_index_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_openmm_Topology
from ..openmm_Topology import get_atom_index_from_bond as aux_get
tmp_item = to_openmm_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_string_pdb_text
from ..string_pdb_text import get_step_from_system as aux_get
tmp_item = to_string_pdb_text(item, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_bond_type_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_molsysmt_Topology
from ..molsysmt_Topology import get_bond_type_from_bond as aux_get
tmp_item = to_molsysmt_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from .to_molsysmt_MolSys import to_molsysmt_MolSys
from ..molsysmt_MolSys import get_chain_index_from_atom as aux_get
tmp_item = to_molsysmt_MolSys(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_mmtf_MMTFDecoder
from ..mmtf_MMTFDecoder import get_chain_index_from_atom as aux_get
tmp_item = to_mmtf_MMTFDecoder(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_atom_index_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_mdtraj_Trajectory
from ..mdtraj_Trajectory import get_atom_index_from_bond as aux_get
tmp_item = to_mdtraj_Trajectory(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_group_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
tmp_indices = get_atom_index_from_atom(item, indices=indices, check=False)
atom = list(item.atoms())
output = [atom[ii].residue.index for ii in tmp_indices]
output = _np.array(output)
del (atom)
return output
def get_group_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_mdtraj_HDF5TrajectoryFile
from ..mdtraj_HDF5TrajectoryFile import get_group_index_from_atom as aux_get
tmp_item = to_mdtraj_HDF5TrajectoryFile(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_chain_type_from_chain(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
n_indices = get_n_chains_from_system(item, check=False)
indices = range(n_indices)
output = [None for ii in indices]
output = _np.array(output)
return output
def get_coordinates_from_atom(item, indices='all', structure_indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_mdtraj_XTCTrajectoryFile
from ..mdtraj_XTCTrajectoryFile import get_coordinates_from_atom as aux_get
tmp_item = to_mdtraj_XTCTrajectoryFile(item, check=False)
output = aux_get(tmp_item, indices=indices, structure_indices=structure_indices, check=False)
return output
def set_atom_name_to_atom(item,
indices='all',
structure_indices='all',
value=None,
check=True):
if check:
_digest_item(item, 'molsysmt.Topology')
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
item.atoms_dataframe.loc[indices, 'atom_name'] = value
pass
def get_box_shape_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt.pbc import box_shape_from_box_vectors
output = None
box = get_box_from_system(item,
structure_indices=structure_indices,
check=False)
if box is not None:
output = box_shape_from_box_vectors(box)
return output
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(indices)
from . import to_mmtf_MMTFDecoder
from ..mmtf_MMTFDecoder import get_step_from_system as aux_get
tmp_item = to_mmtf_MMTFDecoder(item, check=False)
output = aux_get(tmp_item,
structure_indices=structure_indices,
check=False)
return output
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_mdtraj_HDF5TrajectoryFile
from ..mdtraj_HDF5TrajectoryFile import get_step_from_system as aux_get
tmp_item = to_mdtraj_HDF5TrajectoryFile(item, check=False)
output = aux_get(tmp_item,
structure_indices=structure_indices,
check=False)
return output
def get_n_components_from_system(item, check=True):
if check:
_digest_item(item, _form)
component_index_from_atom = get_component_index_from_atom(item,
indices='all')
if component_index_from_atom[0] is None:
n_components = 0
else:
output = _np.unique(component_index_from_atom)
n_components = output.shape[0]
return n_components
def get_coordinates_from_atom(item, indices='all', structure_indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
coordinates= _puw.quantity(item.xyz * 0.1, unit='nm')
if indices is not 'all':
coordinates = coordinates[:, atom_indices, :]
if structure_indices is not 'all':
coordinates = coordinates[structure_indices,:,:]
return coordinates
def get_n_inner_bonds_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_openmm_GromacsGroFile
from ..openmm_GromacsGroFile import get_n_inner_bonds_from_atom as aux_get
tmp_item = to_openmm_GromacsGroFile(item, check=False)
output = aux_get(tmp_item,
indices=indices,
structure_indices=structure_indices,
check=False)
return output
def get_group_name_from_group(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
n_indices = get_n_groups_from_system(item, check=False)
indices = range(n_indices)
group = list(item.residues())
output = [group[ii].name for ii in indices]
del (group)
output = _np.array(output, dtype=object)
return output
def get_chain_id_from_chain(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
n_indices = get_n_chains_from_system(item, check=False)
indices = range(n_indices)
chain = list(item.chains())
output = [chain[ii].id for ii in indices]
del (chain)
output = _np.array(output)
return output
def get_component_type_from_component(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from molsysmt.element.component import get_component_type_from_group_names
output = []
group_names_from_component = get_group_name_from_component(item,
indices=indices,
check=False)
for group_name in group_names_from_component:
output.append(get_component_type_from_group_names(aux))
output = _np.array(output, dtype=object)
return output
def get_atom_index_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
n_bonds = get_n_bonds_from_system(item, check=False)
indices = _np.arange(n_bonds)
bond = list(item.bonds())
output = [[bond[ii].atom1.index, bond[ii].atom2.index] for ii in indices]
output = _np.array(output)
del (bond)
return output
