Tutorials on configuring cazy_webscraper to retrieve data from PDB

cazy_webscraper can be configured to retrieve protein structures files user specified sets of CAZymes in a local CAZyme database. Many of the same configuration options apply to the retrieval of protein data from CAZy, UniProt, GenBank and PDB.

BioPython is used to perform the retrieval of protein structure files from PDB. The retrieved structure files are written to the disk, not into the local CAZyme database.

> Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., … others. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423.

cazy_webscraper can be configured via the command line and/or via a YAML configuration file.

This page runs through examples of how to combine the various ‘filters’ that can be applied, to fully customised the retrieval of protein structured from PDB. These tutorials are designed for those with less experience using command-line tools.

Note

If you installed cazy_webscraper using bioconda or pip to invoke cazy_webscraper to retrieve PDB data call it using cw_get_pdb_structures - this is the method used in this tutorial. If you installed cazy_webscraper from source then you will need to invoke cazy_webscraper from the root of the repo using the command python3 cazy_webscraper/expand/pdb/get_pdb_structures.py.

Note

PDB structure files are retrieved for the PDB accessions that are in a local CAZyme database created using cazy_webscraper. A freshly built CAZyme database only contains NCBI protein accessions, taxonomic kingdoms, source organisms, and CAZy family annotations. Therefore, the cw_get_uniprot_data command must be used to retrieve PDB accessions from the UniProt database prior to using the cw_get_pdb_structures command.

From this point on, we will be discussed the cw_get_pdb_structures, which is the entry point for retrieving data from PDB. We also presume you are comfortable configuring cazy_webscraper for the scraping of data from CAZy.

Configuration via the command line

cw_get_pdb_structures has two required argument: * The path to the local CAZyme database created using cazy_webscraper * The structure file formats to retrieve the data from PDB in

The accepted structure file formats are: * mmCif (default, PDBx/mmCif file), * pdb (format PDB), * xml (PDBML/XML format), * mmtf (highly compressed), * bundle (PDB formatted archive for large structure}

Any combination of file formats can be provided to cw_get_pdb_structures to download every file type for each PDB accession in the local CAZyme database. To list multiple file formats, separate each file format with a single space (’ ‘). For example, to download the mmCif and xml files for every PDB accession in a local CAZyme database (located at cazy/cazyme_db.db), use the following command:

cw_get_pdb_structures cazy/cazyme_db.db mmCif xml

Warning

The file formats are case sensitive. For example, make sure to use ‘mmCif’ not ‘mmcif’.

When no optional arguments are provided, the default behaviour is invoked. The default behaviour is to: Retrieve protein data for all CAZymes in the local CAZyme db

Options configurable at the command line

CAZymes of interest can be defined via providing:

  • A set of GenBank accessions

  • A set of UniProt accessions

  • CAZy classes

  • CAZy families

  • Taxonomic kingdoms

  • Genera

  • Species

  • Strains

  • EC numbers

Here you can find a full list of the command-line flags and options.

Retrieving protein structures for specific CAZy classes and families

The --classes and --families flags from scraping data from CAZy are applied in the extact same way for retrieving protein structure files from PDB.

For instance, if instead of retrieving protein data for all CAZymes in your local CAZyme database, you want to retrieve protein data for CAZymes in specific CAZy classes then add the --classes flag followed by the classes you want to retrieve protein data for.

Tip

To list multiple classes, separate the classes with a single comma.

For example, if you want to retrieve protein data for all CAZymes from Glycoside Hydrolase and Carbohydrate Esterases then use the command:

cw_get_pdb_structures cazy/cazyme.db mmCif --classes GH,CE

OR

cw_get_pdb_structures cazy/cazyme.db mmCif --classes Glycoside Hydrolases,Carbohydrate Esterases

Retrieving protein data for proteins from specific specific CAZy families is achieved using the --families flag. For example, to retrieve protein data for all proteins in PL1, PL2 and PL3 in the local CAZyme database, in mmCif and PDB format, use the following command:

cw_get_pdb_structures cazy/cazyme.db mmCif pdb --families PL1,PL2,PL3

Warning

cw_get_pdb_structures only accpets families written in the proper CAZy family syntax. GH1 is accepted. gh1 and GlycosideHydrolases1 are not accepted.

As with scraping data from CAZy, the --classes and --families flags can be combined. To retrieve protein data for all CAZymes in PL1, PL2, PL3 and all of GH and CE both:

cw_get_pdb_structures cazy/cazyme.db mmCif pdb --families PL1,PL2,PL3 --classes GH,CE

AND

cw_get_pdb_structures cazy/cazyme.db mmCif pdb --classes GH,CE --families PL1,PL2,PL3

are accepted.

Applying taxonomic

The --kingdoms, --genera, --species and --strains flags can be used to refine the dataset of proteins to retrieve protein data by taxonomy. These flags are applied in the exact same way as they are used for the scraping of data from CAZy. Only proteins in the local CAZyme database and matching at least on of the provided taxonomy criteria will have protein data retrieved from PDB.

For example, if you want to retrieve protein data for all CAZymes in a local CAZyme database from bacterial and eukaryotic species, in pdb and xml formats, then use the command

cw_get_pdb_structures cazy/cazyme.db pdb xml --kingdoms bacteria,eukaryota

Warning

The kingdoms must be spelt the same way CAZy spells them, for example use ‘eukaryot**a**’ instead of ‘eukaryot**e**’.

Note

The kingdoms are not case sensitive, therefore, both bacteria and Bacteria are accepted.

Note

You can list the kingdoms in any order. Thus, both bacteria,eukaryota and eukaryota,bacteria are accepted.

You can combine any combination of the optional flags, including combining the taxonomic filters. For example, you may wish to retrieve protein data for all CAZymes in a local CAZyme database that are derived from all viral species, Aspergillus species, Layia carnosa, Layia chrysanthemoides, Trichoderma reesei QM6a and Trichoderma reesei QM9414. To do this we would combine the respective flags for a single cw_get_pdb_structures command. The command we would use would be:

cw_get_pdb_structures cazy/cazyme.db pdb xml --kingdoms viruses --genera Aspergillus --species Layia carnosa,Layia chrysanthemoides --strains Trichoderma reesei QM6a,Trichoderma reesei QM9414

Note

The order that the flags are used and the order taxa are listed does not matter, and separate multiple taxa names with a single comma with no spaces.

Warning

Use the standard scientific name formating. Captialise the first letter of genus and write a lower case letter for the first letter of the species.

Aspergillus niger is correct

asepergillus niger is incorrect

ASPERGILLUS NIGER is incorrect

Warning

When you specify a species cw_get_pdb_structures will retrieval CAZymes from all strains of the species.

Applying EC number filter

The retrieval of protein data from PDB can also be limited to proteins in a local CAZyme database that are annotated with specific EC numbers.

Having previously retrieved EC number annotations from UniProt and adding them to the local CAZyme database, you may wish to retrieve protein data for CAZymes annotated with specific EC numbers. To do this add the --ec_filter flag to the command, follwed by a list of EC numbers.

cw_get_pdb_structures cazy/cazyme.db pdb --ec_filter "EC1.2.3.4,EC2.3.4.5"

Note

Provide complete EC numbers. Both dashes (‘-’) and asterixes (‘*’) are accepted for missing digits in EC numbers.

EC1.2.3.- and EC1.2.3.* are accepted. EC1.2.3. and EC 1.2.3 are not accepted.

Note

The ‘EC’ prefix is not necessary. EC1.2.3.4 and 1.2.3.4 are accepted.

Warning

If using dashes to represent missing digits in EC numbers, it is recommended to bookend the entire EC number list in single or double quotation marks. Some terminals may misinterpret EC1.2.-.- as trying to invoke the options ‘.’

Note

cw_get_pdb_structures will retrieve the PDB structure files for all proteins in the local CAZyme database that are annotated with at least one of the given EC numbers. Therefore, if multiple EC numbers are given this does not mean PDB structure files will only be retrieved for CAZymes annotated for all provided EC numbers.

--ec_filter is based upon EC number annotations stored within the local CAZyme database. For example, if protein A is annotated with the EC1.2.3.4, but this annotation is not stored in the local CAZyme database, using --ec_filter EC1.2.3.4 will not cause cw_get_pdb_structures to retrieve data for protein A. This is because cw_get_pdb_structures does not know protein A is annotated with EC1.2.3.4, because this annotation is not within its database.

Warning

If --ec_filter is used along side --ec, cw_get_pdb_structures will retrieve all EC number annotations from UniProt for all proteins in the local CAZyme database that are associated with at least one of the EC numbers provided via --ec_filter within the CAZyme database.

Combining all filters

The --classes, --families, --ec_filter, --kingdoms, --genera, --species, and --strains flags can be used in any combination to define a specific subset of proteins in the local CAZyme database for whom protein structure files will be retrieved from PDB.

Below we run through 3 example commands of combining these flags, and the resulting behaviour.

Example 1: To retrieve PDB structure file for all CAZymes in GH, GT, CE1, CE5 and CE8, and which are derived from baceterial species, and retrieve the files in mmCif and xml format we use the command:

cw_get_pdb_structures cazy/cazyme.db mmCif xml --classes GH,CE --families CE1,CE5,CE8 --kingdoms bacteria

Example 2: To retrieve PDB structure files for all CAZymes in GH and which are derived from Aspegillus and Trichoderma species in bundle format we use the command:

cw_get_pdb_structures cazy/cazyme.db bundle --classes GH --genera Aspegillus,Trichoderma

Example 3: To retrieve PDB structure files for all CAZymes in GH,CE and CBM which are derived from baceterial species and are annotated with at least one of EC3.2.1.23, EC3.2.1.37 and EC3.2.1.85, and retrieve the files in pdb and xml format we use the command:

cw_get_pdb_structures cazy/cazyme.db xml pdb --classes GH,CE,CBM --kingdoms bacteria --ec_filter "3.2.1.23,3.2.1.37,3.2.1.85"

Note

The order the structure file formats are provided does not matter.

Providing a list of accessions

Instead of retrieving protein structure files for all CAZymes matching a defined set of criteria, cw_get_pdb_structures can retrieve protein structure files for a set of CAZymes defined by their GenBank and/or UniProt accession.

The flag --genbank_accessions can be used to provide cw_get_pdb_structures a list of GenBank accessions to identify the specific set of CAZymes to retrieve protein structure files for.

The flag --uniprot_accessions can be used to provide cw_get_pdb_structures a list of UniProt accessions to identify the specific set of CAZymes to retrieve protein structure files for.

In both instances (for --genbank_accessions and --uniprot_accessions) the list of respective accessions are provided via a plain text file, with a unique protein accession of each line. The path to this file is then passed to cw_get_pdb_structures via the respective --genbank_accessions and --uniprot_accessions flag.

--genbank_accessions and --uniprot_accessions can be used at the same time to define all CAZymes of interest.

Warning

--genbank_accessions and --uniprot_accessions take president over the filter flags.

When either --genbank_accessions or --uniprot_accessions is used, cw_get_pdb_structures will not retrieve any CAZymes from the local database matching a set of criteria.

Therefore, if --genbank_accessions and --classes are used, cw_get_pdb_structures will ignore the --classes flag and only retrieve PDB structure files for the proteins listed in the file provided via the --genbank_accessions.