schrodinger.application.matsci.hdfutils module¶

Contains functionality related to hdf files

class schrodinger.application.matsci.hdfutils.HDFIO¶

Bases: object

Class describing HDF5 input and output methods

readHDF(filename, key)¶

Reads a HDF file

Parameters

filename (str) – The filename
key (str) – The key to read

Return type

pandas.core.frame.DataFrame

Returns

Pandas data frame stored in the passed key

getKeys(filename, clean_text=None)¶

Gets the keys in HDF file

Parameters: filename – The filename
Return type: list
Returns: list of keys in the file

setData(filename, data)¶

Puts the pandas dataframes in the HDF file.

Parameters

filename (str) – The filename
data (dict) – The dictionary where the key is the key for the values of pandas dataframe

class schrodinger.application.matsci.hdfutils.HDFProxyPickleIO¶

Bases: object

Class describing pickle input and output methods which act as a proxy for HDF5 file

readHDF(filename, key)¶

Reads a pickle file

Parameters

filename (str) – The filename
key (str) – The key to read

Return type

pandas.core.frame.DataFrame

Returns

Pandas data frame stored in the passed key

getKeys(filename, clean_text=None)¶

Gets the keys of data stored in the pickle file

Parameters: filename – The filename
Return type: list
Returns: list of keys in the file

setData(filename, data)¶

Puts the pandas dataframes in the HDF file.

Parameters

filename (str) – The filename
data (dict) – The dictionary where the key is the key for the values of pandas dataframe

schrodinger.application.matsci.hdfutils.generate_hierarchial_key(*args)¶

Generates a hierarchial key for a hdf file

Parameters: args (list) – the list of strings which will form the key
Return type: str
Returns: the hierarchial key

schrodinger.application.matsci.hdfutils.get_filename(basename)¶

Gets the filename with proper extension

Parameters: basename (str) – The basename
Returns: The filename
Return type: str

schrodinger.application.matsci.hdfutils.get_hdf_io(filename)¶

Gets the i/o class associated with the extension of the filename

Parameters: filename (str) – The filename
Returns: The i/o class
Return type: HDFIO or HDFProxyPickleIO

schrodinger.application.matsci.hdfutils.get_hdf_keys(filename, clean_text=None)¶

Gets the keys of data stored in the file

Parameters

filename (str) – The filename
clean_text (str or NoneType) – The str used to replace KEY_SEPARATOR in keys

Return type

list

Returns

list of keys in the file

schrodinger.application.matsci.hdfutils.read_hdf(filename, key)¶

Reads the data in the file associated with the key

Parameters

filename (str) – The filename
key (str) – The key to read

Return type

pandas.core.frame.DataFrame

Returns

Pandas data frame stored in the passed key

schrodinger.application.matsci.hdfutils.HDFStore(filename, mode='w')¶

Context manager for hdf/hdf proxy file.

Parameters

filename (str) – The filename
mode (str) – The mode for opening the file. Only writing is supported.