mmtfPyspark.io.mmtfReader module¶

mmtfReader.py: Methods for reading and downloading structures in MMTF file formats. The data are returned as a PythonRDD with the structure id (e.g. PDB ID) as the key and the structural data as the value.

Supported operations and file formats: - Read directory of MMTF-Hadoop sequence files in full and reduced representation - Download MMTF full and reduced representations using web service (mmtf.rcsb.org) - Read directory of MMTF files (.mmtf, mmtf.gz)

download_full_mmtf_files(pdbIds)[source]¶

Download and reads the specified PDB entries in full mmtf format using MMTF web services

Parameters:	path : str Path to PDB files
Returns:	data structure data as keywork/value pairs

download_mmtf_files(pdbIds, reduced=False)[source]¶

Download and reads the specified PDB entries using MMTF web services with either full or reduced format

Parameters:	path : str Path to PDB files reduced : bool flag to indicate reduced or full file format
Returns:	data structure data as keywork/value pairs

download_reduced_mmtf_files(pdbIds)[source]¶

Download and reads the specified PDB entries in reduced mmtf format using MMTF web services

Parameters:	path : str Path to PDB files
Returns:	data structure data as keywork/value pairs

get_mmtf_full_path()[source]¶

Returns the path to the full MMTF-Hadoop sequence file. It looks for the environmental variable “MMTF_FULL”, if not set, an error message will be shown.

Returns:	str path to the mmtf_full directory

get_mmtf_reduced_path()[source]¶

Returns the path to the reduced MMTF-Hadoop sequence file. It looks for the environmental variable “MMTF_REDUCED”, if not set, an error message will be shown.

Returns:	str path to the mmtf_reduced directory

read_full_sequence_file(pdbId=None, fraction=None, seed=123)[source]¶

Reads a MMTF-Hadoop Sequence file using the default file location. The default file location is determined by get_mmtf_full_path()

To download mmtf files: https://mmtf.rcsb.org/download.html

Parameters:	pdbID : list, optional List of structures to read fraction : float, optional fraction of structure to read seed : int, optional random seed

read_mmtf_files(path)[source]¶

Read the specified PDB entries from a MMTF file

Parameters:	path : str Path to MMTF files
Returns:	data structure data as keywork/value pairs

read_reduced_sequence_file(pdbId=None, fraction=None, seed=123)[source]¶

Reads a MMTF-Hadoop Sequence file using the default file location. The default file location is determined by get_mmtf_reduced_path()

To download mmtf files: {https://mmtf.rcsb.org/download.htm}

Parameters:	pdbID : list, optional List of structures to read fraction : float, optional fraction of structure to read seed : int, optional random seed

read_sequence_file(path, pdbId=None, fraction=None, seed=123)[source]¶

Reads an MMTF Hadoop Sequence File. Can read all files from path, randomly rample a fraction, or a subset based on input list. See <a href=”http://mmtf.rcsb.org/download.html”> for file download information</a>

Parameters:	path : str path to file directory pdbID : list List of structures to read fraction : float fraction of structure to read seed : int random seed
Raises:	Exception file path does not exist