BioSimSpace.IO.readPDB

BioSimSpace.IO.readPDB(id, pdb4amber=False, work_dir=None, show_warnings=False, property_map={})[source]

Read a molecular system from a Protein Data Bank (PDBP) ID in the RSCB PDB website.

Parameters:

  • id (str) – The PDB ID string, or path to a PDB file.

  • pdb4amber (bool) – Whether to process the PDB file using pdb4amber. This reformats the file such that it can be handled by the AMBER suite of tools.

  • show_warnings (bool) – Whether to show any warnings raised during parsing of the input files.

  • work_dir (str) – The working directory used to run pdb4amber.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Returns:

system – A molecular system.

Return type:

System

Examples

Create a molecular system from the deoxy human haemoglobin Protein Data Bank (PDB) record.

>>> import BioSimSpace as BSS
>>> system = BSS.IO.readPDB("1a3n")

Create a molecular system from a PDB file on disk and re-format so that it is compatible with the AmberTools suite. Data Bank (PDB) record.

>>> import BioSimSpace as BSS
>>> system = BSS.IO.readPDB("file.pdb", pdb4amber=True)