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