Chemical shift prediction dataset
Project description
Data for NMR GNN
This contains the parsing scripts and data used for our GNN chemical shift predictor model.
Install
pip install nmrgnn-data
Numpy Error
If you see this error:
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Try re-install numpy
pip uninstall -y numpy && pip install numpy
Parsing Scripts
To install with the parsing functionality, use this
conda install -c omnia -c conda-forge rdkit openmm numpy==1.18.5
pip install nmrgnn-data[parse]
Working with Data
All commands below can have additional information printed using the --help
argument.
Find pairs
Find pairs of atoms with chemical shifts that are neighbors and sort them based on distance.
nmrdata find-pairs structure-test.tfrecords-data.tfrecord ALA-H ALA-N
Count Names
Get class/atom name counts:
nmrdata count-names structure-test.tfrecords-data.tfrecord
Validate
Check that records are consistent with embeddings
nmrdata validate-embeddings structure-test.tfrecords-data.tfrecord
Check that neighbor lists are consistent with embeddings
nmrdata validate-nlist structure-test.tfrecords-data.tfrecord
Check that peaks are reasonable (no nans, no extreme values, no bad masks)
nmrdata validate-peaks structure-test.tfrecords-data.tfrecord
Output Lables
To extract labels ordered by PDB and residue:
nmrdata write-peak-labels test-structure-shift-data.tfrecord test-structure-shift-record-info.txt labels.txt
Making New Data
See commands parse-shiftml
, parse-metabolites
, parse-shiftx
which are parsers for various databases.
From RefDB Files
This requires a pickled python object called data.pb
to be in the directory. It is
a list of dict
s containing pdb_file
(path to PDB), pdb
(PDB ID), corr
(path to .corr
file), and chain
(which chain).
chain
can be _
to indicate use first chain.
nmrparse parse-refdb directory name --pdb_filter exclude_ids.txt
Citation
Please cite Predicting Chemical Shifts with Graph Neural Networks
@article{yang2021predicting,
title={Predicting Chemical Shifts with Graph Neural Networks},
author={Yang, Ziyue and Chakraborty, Maghesree and White, Andrew D},
journal={Chemical Science},
year={2021},
publisher={Royal Society of Chemistry}
}
Project details
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