SOAPify.HDF5er.HDF5To

This submodule gives the user some function to extract data from the hdf5 files

Functions

HDF52AseAtomsChunckedwithSymbols(groupTraj, ...)

generates an ase trajectory from an hdf5 trajectory

createUniverseFromSlice(trajectoryGroup[, ...])

Creates a MDanalysis.Universe from a trajectory group

getXYZfromMDA(filelike, trajToExport[, ...])

generate an xyz-file in a IO object from an MDA trajectory

getXYZfromTrajGroup(filelike, group[, ...])

generate an xyz-file in a IO object from a trajectory group in an hdf5

saveXYZfromTrajGroup(filename, group[, ...])

Saves "filename" as an xyz file
SOAPify.HDF5er.HDF5To.HDF52AseAtomsChunckedwithSymbols(groupTraj, chunkTraj, chunkBox, symbols)[source]

generates an ase trajectory from an hdf5 trajectory

Parameters

  • groupTraj (h5py.Group) – the group within the hdf5 file where the trajectroy is stored

  • chunkTraj (tuple[slice]) – the list of the chunks of the trajectory within the given group

  • chunkBox (tuple[slice]) – the list of the chunks of the frame boxes within the given group

  • symbols (list[str]) – the list of the name of the atoms

Returns

the trajectory stored in the given group

Return type

list[ase.Atoms]

SOAPify.HDF5er.HDF5To.createUniverseFromSlice(trajectoryGroup, useSlice=slice(None, None, None))[source]

Creates a MDanalysis.Universe from a trajectory group

Parameters

  • trajectoryGroup (h5py.Group) – the given trajectory group

  • useSlice (_type_, optional) – the asked slice from wich create an universe. Defaults to slice(None).

Returns

an universe containing the wnated part of the trajectory

Return type

MDAnalysis.Universe

SOAPify.HDF5er.HDF5To.getXYZfromMDA(filelike, trajToExport, framesToExport=slice(None, None, None), allFramesProperty='', perFrameProperties=None, **additionalColumns)[source]

generate an xyz-file in a IO object from an MDA trajectory

the additionalColumns arguments are added as extra columns to the file, they must be numpy.ndarray with shape (nofFrames,NofAtoms) for 1D data or (nofFrames,NofAtoms,Nvalues) for multidimensional data this will add one or more columns to the xyz file

Parameters

  • filelike (IO) – the IO destination, can be a file

  • group (MDAnalysis.Universe | MDAnalysis.AtomGroup) – the universe or the selection of atoms to export

  • frames (List or slice or None, optional) – the frames to export. Defaults to None.

  • allFramesProperty (str, optional) – A comment string that will be present in all of the frames. Defaults to “”.

  • perFrameProperties (list[str], optional) – A list of comment. Defaults to None.

  • additionalColumns() – the additional columns to add to the file: each new keyword arguments will add a column to the xyz file

SOAPify.HDF5er.HDF5To.getXYZfromTrajGroup(filelike, group, framesToExport=slice(None, None, None), allFramesProperty='', perFrameProperties=None, **additionalColumns)[source]

generate an xyz-file in a IO object from a trajectory group in an hdf5

the additionalColumns arguments are added as extra columns to the file, they must be numpy.ndarray with shape (nofFrames,NofAtoms) for 1D data or (nofFrames,NofAtoms,Nvalues) for multidimensional data this will add one or more columns to the xyz file, named after the keyword argument

Parameters

  • filelike (IO) – the IO destination, can be a file

  • group (h5py.Group) – the trajectory group

  • frames (List or slice or None, optional) – the frames to export. Defaults to None.

  • allFramesProperty (str, optional) – A comment string that will be present in all of the frames. Defaults to “”.

  • perFrameProperties (list[str], optional) – A list of comment. Defaults to None.

  • additionalColumns() – the additional columns to add to the file: each new keyword arguments will add a column to the xyz file

SOAPify.HDF5er.HDF5To.saveXYZfromTrajGroup(filename, group, framesToExport=slice(None, None, None), allFramesProperty='', perFrameProperties=None, **additionalColumns)[source]

Saves “filename” as an xyz file

see saveXYZfromTrajGroup this calls getXYZfromTrajGroup and treats the inputs in the same way

Parameters

  • filename (str) – name of the file

  • group (h5py.Group) – the trajectory group

  • additionalColumsn() – the additional columns to add to the file

  • allFramesProperty (str, optional) – A comment string that will be present in all of the frames. Defaults to “”.

  • perFrameProperties (list[str], optional) – A list of comment. Defaults to None.