def get_step_from_system(item, structure_indices='all', check=True): if check: _digest_item(item, _form) structure_indices = _digest_structure_indices(structure_indices) return None
def set_coordinates_to_system(item, indices='all', structure_indices='all', value=None, check=True): if check: _digest_item(item, 'molsysmt.MolSys') indices = _digest_indices(indices) structure_indices = _digest_structure_indices(structure_indices) return set_coordinates_to_atom(item, indices='all', structure_indices=structure_indices, value=value, check=False)
def set_box_to_system(item, indices='all', structure_indices='all', value=None, check=True): if check: _digest_item(item, 'molsysmt.MolSys') indices = _digest_indices(indices) structure_indices = _digest_structure_indices(structure_indices) item.trajectory.box = value pass
def set_atom_name_to_atom(item, indices='all', structure_indices='all', value=None, check=True): if check: _digest_item(item, 'molsysmt.MolSys') indices = _digest_indices(indices) structure_indices = _digest_structure_indices(structure_indices) from ..molsysmt_Topology import set_atom_name_to_atom as aux_set return aux_set(item.topology, indices=indices, structure_indices=structure_indices, value=value, check=True)
def get_step_from_system(item, structure_indices='all', check=True): if check: _digest_item(item, _form) structure_indices = _digest_structure_indices(structure_indices) if structure_indices is 'all': output = item.step else: output = item.step[structure_indices] return output
def get_coordinates_from_system(item, structure_indices='all', check=True): if check: _digest_item(item, _form) structure_indices = _digest_structure_indices(structure_indices) if structure_indices is 'all': output = item.coordinates else: output = item.coordinates[structure_indices, :, :] 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) raise NotImplementedMethodError()
def get_box_from_system(item, structure_indices='all', check=True): if check: _digest_item(item, _form) structure_indices = _digest_structure_indices(structure_indices) box = item.getPeriodicBoxVectors() unit = _puw.get_unit(box) box = _np.expand_dims(puw.get_value(box), axis=0) box = _puw.standardize(box * unit) return box
def get_box_angles_from_system(item, structure_indices='all', check=True): if check: _digest_item(item, _form) structure_indices = _digest_structure_indices(structure_indices) tmp_box_angles = item.get_box_angles() if structure_indices is 'all': output = tmp_box_angles else: output = tmp_box_angles[structure_indices, :] return output
def get_time_from_system(item, structure_indices='all', check=True): if check: _digest_item(item, _form) structure_indices = _digest_structure_indices(structure_indices) output = _puw.quantity(item.time, unit='ps') if structure_indices is not 'all': output = output[structure_indices] 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) box = getBoxVectors(asNumpy=True) unit = _puw.get_unit(box) box = _np.expand_dims(box, axis=0) box = _puw.standardize(box * unit) return box
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_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_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_box_from_system(item, structure_indices='all', check=True): if check: _digest_item(item, _form) structure_indices = _digest_structure_indices(structure_indices) output = None if item.box is not None: if structure_indices is 'all': output = item.box else: output = item.box[structure_indices, :, :] 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_XTCTrajectoryFile from ..mdtraj_XTCTrajectoryFile import get_step_from_system as aux_get tmp_item = to_mdtraj_XTCTrajectoryFile(item, check=False) output = aux_get(tmp_item, 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_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_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_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 .to_molsysmt_MolSys import to_molsysmt_MolSys from ..molsysmt_MolSys import get_coordinates_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_box_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_vectors_from_box_lengths_and_angles lengths = _puw.quantity(item.unitcells[:,0:3]*0.1, unit='nm') angles = _puw.quantity(item.unitcells[:,3:6], unit='degrees') if structure_indices is not 'all': lengths = lengths[structure_indices,:] angles = angles[structure_indices,:] output = box_vectors_from_box_lengths_and_angles(lengths, angles) 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) box = item.getPeriodicBoxVectors() output = None if box is not None: unit = _puw.get_unit(box) box = _np.array(_puw.get_value(box)) box = box.reshape(1, box.shape[0], box.shape[1]) box = box * unit output = _puw.standardize(box) 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) tmp_coordinates = item.coordinates if structure_indices is not 'all': tmp_coordinates = tmp_coordinates[structure_indices, :, :] if indices is not 'all': tmp_coordinates = tmp_coordinates[:, indices, :] return tmp_coordinates
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_openmm_GromacsGroFile from ..openmm_GromacsGroFile import get_coordinates_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_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_Trajectory from ..mdtraj_Trajectory import get_coordinates_from_atom as aux_get tmp_item = to_mdtraj_Trajectory(item, check=False) output = aux_get(tmp_item, indices=indices, structure_indices=structure_indices, check=False) 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 molsysmt._private.math import serie_to_chunks if structure_indices is 'all': n_structures = get_n_structures_from_system(item) structure_indices = _np.arange(n_structures) starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices) xyz_list = [] for start, size in zip(starts_serie_frames, size_serie_frames): item.seek(start) if indices is 'all': xyz, _, _, _ = item.read(n_structures=size) else: xyz, _, _, _ = item.read(n_structures=size, atom_indices=indices) xyz_list.append(xyz) xyz = _np.concatenate(xyz_list) del (xyz_list) xyz = xyz.astype('float64') xyz = xyz * _puw.unit(item.distance_unit) xyz = _puw.standardize(xyz) return xyz
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) unit = _puw.get_unit(item.positions) coordinates = _np.array(_puw.get_value(item.getPositions(asNumpy=True))) coordinates = coordinates.reshape(1, coordinates.shape[0], coordinates.shape[1]) if structure_indices is not 'all': coordinates = coordinates[structure_indices,:,:] if indices is not 'all': coordinates = coordinates[:,indices,:] coordinates = coordinates * unit coordinates = _puw.standardize(coordinates) return coordinates
def set_box_to_system(item, structure_indices='all', value=None, check=True): if check: _digest_item(item, 'openmm.Topology') structure_indices = _digest_structure_indices(structure_indices) box = _digest_box(value) box = _puw.convert(value, to_unit='nanometers', to_form='openmm.unit') n_structures = box.shape[0] if n_structures == 1: item.setPeriodicBoxVectors(box[0]) else: raise ValueError( "The box to set in to a openmm.Topology has more than a frame") pass