A Node.js API for the RCSB Protein Data Bank (PDB)
A Node.js API for the RCSB Protein Data Bank (PDB)
npm install pdbmine
Just require the package.
var miner = require('pdbmine');
You can query the PDB with a string, and a callback function. The result will be an array of PDB ID strings.
miner.query('ribozyme', function(result){
console.log(result);
});
You can also just get a list of all the PDB IDs:
miner.get_all_ids(function(result){
console.log(result);
});
You can download a pdb or cif format file of the structure of interest:
miner.download('5k7c', 'pdb', function(data){
fs = require('fs');
fs.writeFileSync('5k7c.pdb', data);
});
You can also get info on certain structures by calling the following function. You pass in either a single PDB-ID or a list, a single parameter or a list of parameters, and a callback function.
miner.describe_pdb(['100D','4OJI'], ['depositionDate', 'macromoleculeType'], function(result){
console.log(result);
});
Valid parameters can be accessed via miner.fields. They are also listed at the bottom of this README
You can filter the results from describe_pdb() using the standard Array filtering method:
miner.describe_pdb(['100D','4OJI'], ['depositionDate', 'macromoleculeType'], function(result){
filtered_result = result.filter(obj => obj.macromoleculeType == 'Protein');
console.log(filtered_result);
});
Don’t like callback functions? You can avoid passing in callback functions and instead use Promises as follows:
miner.query('ribozyme')
.then(results => miner.describe_pdb(results, ['macromoleculeType']))
.then(descriptions => descriptions.filter(obj => obj.macromoleculeType == 'RNA'))
.then(rnas => {
console.log(rnas);
});
| Report Name | Field Name |
|---|---|
| Structure Summary Report (StructureSummary) | atomSiteCount |
| authors | |
| classification | |
| depositionDate | |
| experimentalTechnique | |
| macromoleculeType | |
| ndbId | |
| pdbDoi | |
| releaseDate | |
| residueCount | |
| resolution | |
| revisionDate | |
| structureMolecularWeight | |
| structureTitle | |
| Sequence Report (Sequence) | chainLength |
| db_code | |
| db_name | |
| entityId | |
| entityMacromoleculeType | |
| kabschSander | |
| molecularWeight | |
| sequence | |
| Ligand Report (Ligands) | InChI |
| InChIKey | |
| ligandFormula | |
| ligandId | |
| ligandImage | |
| ligandMolecularWeight | |
| ligandName | |
| ligandSmiles | |
| Binding Affinity Report (BindingAffinity) | EC50 |
| IC50 | |
| Ka | |
| Kd | |
| Ki | |
| deltaG | |
| deltaH | |
| deltaS | |
| hetId | |
| Biological Detail Report (BiologicalDetails) | biologicalProcess |
| cellularComponent | |
| compound | |
| ecNo | |
| expressionHost | |
| molecularFunction | |
| plasmid | |
| source | |
| taxonomyId | |
| Cluster Entity Report (ClusterEntity) | authorAssignedEntityName |
| clusterNumber100 | |
| clusterNumber30 | |
| clusterNumber40 | |
| clusterNumber50 | |
| clusterNumber70 | |
| clusterNumber90 | |
| clusterNumber95 | |
| entityId | |
| geneName | |
| idNum | |
| rankNumber100 | |
| rankNumber30 | |
| rankNumber40 | |
| rankNumber50 | |
| rankNumber70 | |
| rankNumber90 | |
| rankNumber95 | |
| synonym | |
| taxonomy | |
| taxonomyId | |
| uniprotAcc | |
| uniprotAlternativeNames | |
| uniprotRecommendedName | |
| Domains Report (Domains) | cathDescription |
| cathId | |
| pfamAccession | |
| pfamDescription | |
| pfamId | |
| scopDomain | |
| scopFold | |
| scopId | |
| Crystallization Report (Crystallization) | crystallizationMethod |
| crystallizationTempK | |
| densityMatthews | |
| densityPercentSol | |
| pdbxDetails | |
| phValue | |
| Unit Cell Dimension Report (UnitCellDimensions) | Z_PDB |
| lengthOfUnitCellLatticeA | |
| lengthOfUnitCellLatticeB | |
| lengthOfUnitCellLatticeC | |
| spaceGroup | |
| unitCellAngleAlpha | |
| unitCellAngleBeta | |
| unitCellAngleGamma | |
| Data Collection Detail Report (DataCollectionDetails) | collectionDate |
| collectionTemperature | |
| device | |
| diffractionSource | |
| diffrnId | |
| Refinement Detail Report (RefinementDetails) | averageBFactor |
| rAll | |
| rFree | |
| rObserved | |
| rWork | |
| refinementResolution | |
| Refinement Parameter Report (refinementParameters) | highResolutionLimit |
| reflectionsForRefinement | |
| structureDeterminationMethod | |
| Software Report (NmrSoftware) | authors |
| name | |
| version | |
| NMR Spectrometer Report (NmrSpectrometer) | fieldStrength |
| manufacturer | |
| model | |
| nmrExperimentalSampleConditions Report (NMRExperimentalSampleConditions) | contents |
| ionicStrength | |
| ph | |
| pressure | |
| pressureUnits | |
| solventSystem | |
| temperature | |
| type | |
| NMR Representative Report (NmrRepresentative) | conformerId |
| selectionCriteria | |
| NMR Refine Report (NMRRefinement) | details |
| method | |
| NMR Ensemble Report (NmrEnsemble) | conformerSelectionCriteria |
| totalConformersCalculated | |
| totalConformersSubmitted | |
| EM Structure Report (EMStructure) | emResolution |
| emDiffractionResolution | |
| reconstructionMethod | |
| symmetryType | |
| pointSymmetry | |
| aggregationState | |
| embedding | |
| staining | |
| vitrification | |
| emdbMap | |
| additionalMap | |
| Citation Report (Citation) | abstractTextShort |
| authors | |
| doi | |
| firstPage | |
| journalName | |
| lastPage | |
| meshTerms | |
| pmc | |
| publicationYear | |
| pubmedId | |
| title | |
| volumeId | |
| Other Citation Report (OtherCitations) | authors |
| firstPage | |
| journalName | |
| pmc | |
| publicationYear | |
| pubmedId | |
| title | |
| volumeId | |
| Structural Genomics Centers Report (SGProject) | centerInitial |
| centerName | |
| projectName |