pdbmine

A Node.js API for the RCSB Protein Data Bank (PDB)

Installation

npm install pdbmine

If you plan on using pdbmine in your research/project please cite us at https://arxiv.org/abs/1904.03801

Usage

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);
	 });

Parameters

| 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 |