pdbnucleicacids 0.2.0

A Biopython based package that constructs and represent all nucleic acids in a PDB structure, with a special focus on base-pair representation.

A Biopython based package that constructs and represent all nucleic acids in a PDB structure, with a special focus on base-pair representation.

• Free software: MIT license

• Documentation: https://pdbnucleicacids.readthedocs.io.

Installation

The official release is found in the Python Package Index (PyPI)

$ pip install pdbnucleicacids

If you want, you can download this repository, change directory into this repository and run

$ make install

If make is not installed, you can run

$ pip install -e .

Get Started

This is a little tutorial on how to use the PDBNucleicAcids module.

You can construct and represent single stranded and double stranded nucleic acids.

>>> from Bio.PDB.PDBList import PDBList
>>> from Bio.PDB.MMCIFParser import MMCIFParser
>>> from PDBNucleicAcids.NucleicAcid import DSNABuilder
>>>
>>> # retrive file from PDB using Biopython
>>> pdbl = PDBList()
>>> pdbl.retrieve_pdb_file(pdb_code="10MH", pdir=".")
>>> pdbl.retrieve_assembly_file(pdb_code="10MH", assembly_num=1, pdir=".")
>>> # ... or else use your own
>>>
>>> # parse and build structure with Biopython
>>> parser = MMCIFParser()
>>> structure = parser.get_structure(
>>>     structure_id="10MH", filename="10mh-assembly1.cif"
>>> )
>>>
>>> # extract DataFrame with basepairs data
>>> builder = DSNABuilder()
>>> dsna_list = builder.build_double_strands(structure)
>>>
>>> # take the first double strand nucleic acid as an example
>>> dsna = dsna_list[0]
>>> dsna.get_dataframe()
    i_chain_id  i_residue_index i_residue_name j_residue_name  j_residue_index j_chain_id
0          B              402             DC             DG              433          C
1          B              403             DC             DG              432          C
2          B              404             DA             DT              431          C
3          B              405             DT             DA              430          C
4          B              406             DG             DC              429          C

In this case we have a gap in the basepairs at i_residue_index 407 and 408. This results in two distinct paired segments of dsDNA.

In reality only 408 is a mispair. 407 is a non-standard 5CM-Guanine pair. It’s ignored by PDBNucleicAcids because it currently supports only standard Watson-Crick basepairs.

TODO

• regarding BasePairsRules:

  • Distinguish between DNA and RNA bases (i.e. Deodyribose Adenine can pair with both Deoxyribose Thyamine or Ribose Thyamine)

  • Code other rules

• Proper tests (WIP)

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.