Command Line Example #2
NatureGeorge
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More demo command...pdb_profiling --folder $your_output_folder \
sifts-mapping --input $id_file \
--output $out_file \
--func pipe_select_ho \
--kwargs 'dict(check_pdb_status=False, select_mo_kwargs=dict(sort_cols=[\"bs_score\",\"-BINDING_LIGAND_COUNT\",\"1/resolution\",\"revision_date\",\"id_score\"], infer_new_col=True))' |
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Code Versionfrom pdb_profiling import default_config
from pdb_profiling.processors import Identifiers
from pdb_profiling.utils import a_concat
from tqdm import tqdm
default_config(your_folder)
demo_unps = ('Q5VST9', 'Q5JWF2', 'P21359', 'P68871', 'P63092')
Identifiers(demo_unps).query_from_DB_with_unps('ALTERNATIVE_PRODUCTS').run(tqdm).then(a_concat).result()Commandline Versionpdb_profiling --folder $your_folder id-mapping ... (building) |
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from pdb_profiling import default_config
from pdb_profiling.processors import Identifiers
from pdb_profiling.utils import a_concat
from tqdm import tqdm
default_config(your_folder)
demo_unps = ('P21359','P01116','P68871')
Identifiers(demo_unps).query_from_DB_with_unps('INFO').run(tqdm).then(a_concat).result()
Identifiers(demo_unps).query_from_DB_with_unps('DB_REFERENCES').run().then(a_concat).result()
|
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from pandas import DataFrame
from pdb_profiling import default_config
from pdb_profiling.processors import PDB, PDBs
default_config(your_folder)
pdb_objects = PDBs(['1a01', '2xyn', '3hl2', '4hho'])
exp_res = pdb_objects.fetch(PDBs.fetch_exp_pipe).run().result()
DataFrame(
(j for i in exp_res for j in i),
columns=['pdb_id',
'resolution',
'experimental_method_class',
'experimental_method',
'multi_method',
'-r_factor',
'-r_free']) |
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from pdb_profiling.utils import a_concat
SIFTSs(('P21359', 'Q5VST9', 'P21359-5')).fetch('pipe_base').then_func=SIFTS.to_dataframe).run().then(a_concat).result()pdb_profiling --folder $your_output_folder sifts-mapping --input $id_file --output $output_file --func pipe_base |
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Map Genomic Coordinates
from pdb_profiling import default_config
from pdb_profiling.processors import Identifier
from pdb_profiling.utils import a_load_json
default_config()
Identifier('P21359-3').fetch_from_proteins_api('coordinates/location/', ':550').then(a_load_json).result()['locations'][0]# output
{'accession': 'P21359-3',
'taxid': 9606,
'chromosome': '17',
'ensemblTranslationId': 'ENSP00000491589',
'proteinStart': 550,
'geneStart': 31219125,
'proteinEnd': 550,
'geneEnd': 31219127}# reverse direction
Identifier('9606/17').fetch_from_proteins_api('coordinates/', ':31219125-31219127').then(a_load_json).result() |
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Folder Tree
To starts with, you need to choose a folder as the output dir of PDB-Profiling. The current path would be the default arg and you don't have to specify
--folderarg if you intend to use the current path.Click to view tree
Map from transcript/protein identifier to UniProt Isoform
Demo content for
$id_fileThe mapping results are stored in the
$your_output_folder/local/CustomDB.db's IDMapping Table.If your
$id_filehas column name(s), you can add--column $column_name, and the command becomes this:Map from UniProt Isoform to available PDB Chain instance
By default, this command would load UniProt Isoforms from the
$your_output_folder/local/CustomDB.db's IDMapping Table and perform the SIFTS mapping procedure.Noted that if you start a new task in the same folder, you should delete
$your_output_folder/local/CustomDB.db's IDMapping Table or the complete DB file.Load External File to process
If you already have a file containing UniProt Isoform identifiers, you can directly run the
sifts-mappingcommand without running theid-mappingcommand:Still, if you have column name(s) in your
$id_file, you can add--column $column_name.Noted that you should drop duplicate identifiers by yourself.
Perform Selection
sifts-mapping --func pipe_select_mo(default)sifts-mapping --func pipe_select_hosifts-mapping --func pipe_select_heProtein-Ligand Interaction Pair(Obsoleted due to the bug of PISA API)sifts-mapping --func pipe_select_else --kwargs '{"func": "pipe_protein_ligand_interface", "focus_assembly_ids": (0,)}'Protein-Nucleotide Interaction Pair(Obsoleted due to the bug of PISA API)sifts-mapping --func pipe_select_else --kwargs '{"func": "pipe_protein_nucleotide_interface"}'sifts-mapping --func pipe_select_else --kwargs 'func="Protein/NA"'Retrieve SMR Data
Map from PDB to UniProt Isoform
Demo content for
$id_fileResidue Mapping expanded from SIFTS mapping results
Noted that the default separator is
\t, if your input file has another separator, you can add--sep $your_sepDemo content for
$sifts_fileDownload Complete PDB Structure from PDB Archive
.pdbformatBy default, the file suffix would be
.ent.gz. You can specify the file suffix you want..cifformatCollect PDB-Based Annotations
From SIFTS Resources
Sequence Domain
api/mappings/interpro/api/mappings/pfam/Structrual Domain
api/mappings/scop/api/mappings/cath/api/mappings/cath_b/Others
api/mappings/go/api/mappings/ec/api/mappings/hmmer/api/pdb/entry/secondary_structure/From PDBe Graph Database (PDBe Graph API/Aggregated API)
FunPDBe Resources
graph-api/pdb/funpdbe_annotation/graph-api/pdb/funpdbe_annotation/depth/,graph-api/pdb/funpdbe_annotation/cath-funsites/,graph-api/pdb/funpdbe_annotation/3Dcomplex/,graph-api/pdb/funpdbe_annotation/akid/,graph-api/pdb/funpdbe_annotation/3dligandsite/,graph-api/pdb/funpdbe_annotation/camkinet/,graph-api/pdb/funpdbe_annotation/canSAR/,graph-api/pdb/funpdbe_annotation/ChannelsDB/,graph-api/pdb/funpdbe_annotation/dynamine/,graph-api/pdb/funpdbe_annotation/FoldX/,graph-api/pdb/funpdbe_annotation/MetalPDB/,graph-api/pdb/funpdbe_annotation/M-CSA/,graph-api/pdb/funpdbe_annotation/p2rank/,graph-api/pdb/funpdbe_annotation/Missense3D/,graph-api/pdb/funpdbe_annotation/POPScomp_PDBML/,graph-api/pdb/funpdbe_annotation/ProKinO/,graph-api/pdb/funpdbe_annotation/14-3-3-pred/Others
graph-api/pdb/bound_molecules/graph-api/pdb/bound_molecule_interactionsgraph-api/pdb/sequence_conservation/graph-api/uniprot/sequence_conservation/graph-api/uniprot/annotations/Code:
Command line:
pdb_profiling sifts-mapping \ --input pdbs.dat \ --func fetch_from_pdbe_api \ --kwargs 'dict(api_suffix="api/mappings/interpro/")' \ --chunksize 50 \ --skip_pdbs ''Beta Was this translation helpful? Give feedback.
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