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Electrostatics / old_pdb

Reading and writing old-format PDB data
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Add support for converting to CIF format #1

Open sobolevnrm opened 3 years ago

sobolevnrm commented 3 years ago

@intendo and @speleo3 -- I decided to create a new repo for PDB support and have it import https://github.com/Electrostatics/mmcif_pdbx instead of adding conversion functionality to mmcif_pdbx.

intendo commented 3 years ago

@sobolevnrm what/where is the new repo?

We have that very simple code to read PQR format that could be easily modified to read in PDB files. The caveat is if you want to read in more than just the ATOM and HETATM.

The PQR reader, https://github.com/Electrostatics/apbs/blob/master/apbs/pqr/reader.py, could be a good chunk of code to copy and change to read in PDB files. Since PDB has an eBNF, we could even make the grammar for parsing a fully PDB pretty quickly.

sobolevnrm commented 3 years ago

@sobolevnrm what/where is the new repo?

We have that very simple code to read PQR format that could be easily modified to read in PDB files. The caveat is if you want to read in more than just the ATOM and HETATM.

The PQR reader, https://github.com/Electrostatics/apbs/blob/master/apbs/pqr/reader.py, could be a good chunk of code to copy and change to read in PDB files. Since PDB has an eBNF, we could even make the grammar for parsing a fully PDB pretty quickly.

You are responding to this issue in the new repo: https://github.com/Electrostatics/old_pdb

This is intended to provide full support for all of the strange PDB old-format records and idiosyncrasies.