Dyna Repo Inria MDPosit
Collection
Collection of datasets describing Inria's MDPosit
•
3 items
•
Updated
Dataset Preview
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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: Couldn't cast array of type struct<tag: string, message: string> to null
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1831, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 644, in write_table
pa_table = table_cast(pa_table, self._schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2272, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2223, in cast_table_to_schema
arrays = [
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2224, in <listcomp>
cast_array_to_feature(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in wrapper
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in <listcomp>
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2001, in cast_array_to_feature
arrays = [
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2002, in <listcomp>
_c(array.field(name) if name in array_fields else null_array, subfeature)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2052, in cast_array_to_feature
casted_array_values = _c(array.values, feature.feature)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2086, in cast_array_to_feature
return array_cast(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1950, in array_cast
raise TypeError(f"Couldn't cast array of type {_short_str(array.type)} to {_short_str(pa_type)}")
TypeError: Couldn't cast array of type struct<tag: string, message: string> to null
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1456, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1055, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 894, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 970, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1702, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1858, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
project_identifier
string | accession
string | published
bool | md_index
int64 | md_name
string | analyses
list | chains
list | metadata
dict | files
list |
|---|---|---|---|---|---|---|---|---|
A000A
|
A000A
| true
| 0
|
replica 1
|
[
"clusters",
"clusters-00",
"clusters-01",
"dist-perres",
"energies",
"fluctuation",
"hbonds",
"interactions",
"pca",
"pockets",
"rgyr",
"rmsd-pairwise",
"rmsd-perres",
"rmsds",
"sasa",
"tmscores"
] |
[] |
{
"NAME": "Dynarepo 1AK4",
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
"AUTHORS": [
"Omid Mokhtari",
"Hamed Khakzad",
"Yasaman Karami"
],
"GROUPS": [
"Delta team, Inria center at the University of Lorraine"
],
"CONTACT": "[email protected]",
"PROGRAM": "GROMACS",
"VERSION": "2024.2",
"TYPE": "trajectory",
"METHOD": "Classical MD",
"LICENSE": "Apache License 2.0",
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
"CITATION": "DynaRepo citation",
"THANKS": "DynaRepo Acknowledgements",
"LINKS": null,
"PDBIDS": [
"1AK4"
],
"FORCED_REFERENCES": null,
"REFERENCES": [
"P62937",
"P12497"
],
"INPUT_LIGANDS": null,
"LIGANDS": [],
"LIGANDNAMES": null,
"PROTSEQ": [
"PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMY",
"MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE"
],
"NUCLSEQ": [],
"DOMAINS": [
"Peptidyl-prolyl cis-trans isomerase A",
"Peptidyl-prolyl cis-trans isomerase A, N-terminally processed",
"PPIase cyclophilin-type",
"Gag-Pol polyprotein",
"Capsid protein p24",
"Interaction with human PPIA/CYPA and NUP153",
"Dimerization/Multimerization of capsid protein p24",
"Cleavage; by viral protease",
"Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA"
],
"FRAMESTEP": 0.1,
"TIMESTEP": 2,
"TEMP": 310,
"ENSEMBLE": "NPT",
"FF": [
"CHARMM36m"
],
"WAT": "TIP3P",
"BOXTYPE": "Dodecahedron",
"SYSTATS": 4763,
"SYSTRES": 310,
"PROTATS": 4763,
"PROTRES": 310,
"NUCLATS": 0,
"NUCLRES": 0,
"LIPIATS": 0,
"LIPIRES": 0,
"CARBATS": 0,
"CARBRES": 0,
"SOLVATS": 0,
"SOLVRES": 0,
"COUNCAT": 0,
"COUNANI": 0,
"COUNION": 0,
"INTERACTIONS": [
{
"name": "protein-protein interaction B-A",
"agent_1": "protein B",
"agent_2": "protein A",
"selection_1": "chain A",
"selection_2": "chain B",
"type": "protein-protein"
}
],
"PBC_SELECTION": null,
"CHAINNAMES": null,
"MEMBRANES": null,
"CUSTOMS": null,
"ORIENTATION": null,
"PTM": [],
"MULTIMERIC": null,
"COLLECTIONS": "dynarepo",
"WARNINGS": [],
"BOXSIZEX": 10.6979,
"BOXSIZEY": 10.6979,
"BOXSIZEZ": 7.58653,
"mdName": "replica 1",
"mdAtoms": 4763,
"mdFrames": 5001
}
|
[
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}
},
{
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"metadata": {
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},
{
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},
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A000A
|
A000A
| true
| 1
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replica 2
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[
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"clusters-01",
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"pca",
"pockets",
"rgyr",
"rmsd-pairwise",
"rmsd-perres",
"rmsds",
"sasa",
"tmscores"
] |
[] |
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A000A
|
A000A
| true
| 2
|
replica 3
|
[
"clusters",
"clusters-00",
"clusters-01",
"dist-perres",
"energies",
"fluctuation",
"hbonds",
"interactions",
"pca",
"pockets",
"rgyr",
"rmsd-pairwise",
"rmsd-perres",
"rmsds",
"sasa",
"tmscores"
] |
[] |
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A000B
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A000B
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A000B
|
A000B
| true
| 1
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replica 2
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[
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"pockets",
"rgyr",
"rmsd-pairwise",
"rmsd-perres",
"rmsds",
"sasa",
"tmscores"
] |
[] |
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] |
A000B
|
A000B
| true
| 2
|
replica 3
| ["clusters","clusters-00","clusters-01","clusters-02","clusters-03","clusters-04","clusters-05","clu(...TRUNCATED)
|
[] | {"NAME":"Dynarepo 1AKJ","DESCRIPTION":"PPI from PDBbind, Classical MD simulations, 3 replicates of 5(...TRUNCATED)
| [{"name":"topology.tpr","downloadUrl":"/projects/A000B/files/topology.tpr","length":2921512,"content(...TRUNCATED)
|
A000C
|
A000C
| true
| 0
|
replica 1
| ["clusters","clusters-00","clusters-01","dist-perres","energies","fluctuation","hbonds","interaction(...TRUNCATED)
|
[] | {"NAME":"Dynarepo 1AVA","DESCRIPTION":"PPI from PDBbind, Classical MD simulations, 3 replicates of 5(...TRUNCATED)
| [{"name":"topology.tpr","downloadUrl":"/projects/A000C/files/topology.tpr","length":2711500,"content(...TRUNCATED)
|
A000C
|
A000C
| true
| 1
|
replica 2
| ["clusters","clusters-00","clusters-01","dist-perres","energies","fluctuation","hbonds","interaction(...TRUNCATED)
|
[] | {"NAME":"Dynarepo 1AVA","DESCRIPTION":"PPI from PDBbind, Classical MD simulations, 3 replicates of 5(...TRUNCATED)
| [{"name":"topology.tpr","downloadUrl":"/projects/A000C/files/topology.tpr","length":2711500,"content(...TRUNCATED)
|
A000C
|
A000C
| true
| 2
|
replica 3
| ["clusters","clusters-00","clusters-01","dist-perres","energies","fluctuation","hbonds","interaction(...TRUNCATED)
|
[] | {"NAME":"Dynarepo 1AVA","DESCRIPTION":"PPI from PDBbind, Classical MD simulations, 3 replicates of 5(...TRUNCATED)
| [{"name":"topology.tpr","downloadUrl":"/projects/A000C/files/topology.tpr","length":2711500,"content(...TRUNCATED)
|
A000D
|
A000D
| true
| 0
|
replica 1
| ["clusters","clusters-00","clusters-01","dist-perres","energies","fluctuation","hbonds","interaction(...TRUNCATED)
|
[] | {"NAME":"Dynarepo 1AY7","DESCRIPTION":"PPI from PDBbind, Classical MD simulations, 3 replicates of 5(...TRUNCATED)
| [{"name":"topology.tpr","downloadUrl":"/projects/A000D/files/topology.tpr","length":1068892,"content(...TRUNCATED)
|
End of preview.
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