adding_stats_to_mmcif's Introduction

adding_stats_to_mmcif

Adds sequence and scaling data to an mmCIF file in preparation for submission to the wwPDB deposition system.

typical usage

INPUT: Aimless XML file, Any STAR/CIF/mmCIF file, OUTPUT: updated cifFile

from adding_stats_to_mmcif import run_process

aimless_xml_file = 'input.xml'
fasta_sequence_file = 'sequence.fasta'
input_mmcif = 'input.cif'
output_mmcif = 'output.cif'
worked = run_process(input_mmcif=input_mmcif, output_mmcif=output_mmcif,
                             fasta_file=fasta_sequence_file,
                             xml_file=aimless_xml_file)

where aimless_xml_file is the output XML file from Aimless input_cif is an existing mmCIF file from Refmac fasta_sequence_file is a fasta file containing the sequence of the polymers in Fasta format output_cif is the output modified mmCIF file which data from the aimless XML file.

Testing

To run tests

python -m unittest

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adding_stats_to_mmcif's Issues

handle non standard residues in polymer sequence

currently non-standard residues are given their parent ID, but they should be given the non-canonical three letter code in entity_poly for submission.

add detection if internet connect is present or not

only do remote calls when internet connection is present

link to the active fork?

How about a prominent link in README to https://github.com/wwPDB/py-adding_stats_to_mmcif
which I understand is the official continuation of this project?

Add an option to change the experimental method

Add an option to change the experimental method - default to X-ray if not provided

remove requirements to call wwPDB validation API and move to a separate package

add to mmCIF which ligands are new in refinement

This should be an input option to add to the mmCIF.

add option to input software provide as a argument

Add an option to input software in the following format
[{'pgm': 'aimless', 'version': 'v....'}]

either empty value of missing tag if nothing known.
will need mmcif dictionary parsing to get correct case and classification for software.

Add major issues from deposition interface to this project

output html

add parsing of mmCIF dictionary

_reflns.B_iso_Wilson_estimate present in phenix output

.. interferes, under current wwpdb validation, with addition of other items in the '_reflns.' category. Speculation: wwpdb validation claims duplication of the category even though no actual items are duplicated, but the category's items may be dispersed throughout the cif block. Would such dispersion actually violate the format definition?