org.pdb.ws.general

Interface PdbWebService

All Superinterfaces:

Remote

public interface PdbWebService
extends Remote

The Interface for the RCSB PDB WebService. A number of different functions are provided. The most important one is the runXmlQuery(java.lang.String), which allows to run any of the RCSB advanced queries via SOAP.

runXmlQuery

String[] runXmlQuery(String xmlQuery)
                     throws RemoteException

This is the most important web service call provided by RCSB-PDB, since it allows to access all of the advanced search functionality via a web service. Runs any RCSB advanced query. This works by posting the XML representation of an advanced query. The XML representation of a query can be found by pressing the show query details link on the left hand menu. To generate a query XML, use the RCSB PDB web site to build a query, then choose the "Show Query Details" link in the left-hand navigation menu.

See also the RESTful web service documentation: /pdb/rest.

Parameters:

xmlQuery - The XML representing a RCSB advanced query.

Returns:

An array of PDB IDs

Throws:

RemoteException

blastPDB

String blastPDB(String sequence,
                double eCutOff,
                String matrix,
                String outputFormat)
                throws RemoteException

BLASTs the given sequence against the sequences in the RCSB PDB and returns the output

Parameters:

sequence - A protein sequence

eCutOff - See BLAST documentation for details

matrix - See BLAST documentation for details

outputFormat - See BLAST documentation for details

Returns:

The output of the BLAST program

Throws:

RemoteException

blastPDB

String blastPDB(String structureId,
                String chainId,
                double eCutOff,
                String matrix,
                String outputFormat)
                throws RemoteException

BLASTs the sequence of the given chain against the sequences in the RCSB PDB and returns the output

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier

eCutOff - See BLAST documentation for details

matrix - See BLAST documentation for details

outputFormat - See BLAST documentation for details

Returns:

The output of the BLAST program

Throws:

RemoteException

blastQueryXml

String blastQueryXml(String sequence,
                     double eCutOff)
                     throws RemoteException

BLASTs the given sequence against the sequences in the RCSB PDB and returns the output as XML

Parameters:

sequence - A protein sequence

eCutOff - See BLAST documentation for details

Returns:

The output of the BLAST program as XML

Throws:

RemoteException

blastStructureIdQueryXml

String blastStructureIdQueryXml(String structureId,
                                String chainId,
                                double eCutOff)
                                throws RemoteException

BLASTs the sequence of the given chain against the sequences in the RCSB PDB and returns the output as XML

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier

eCutOff - See BLAST documentation for details

Returns:

The output of the BLAST program as XML

Throws:

RemoteException

fastaQuery

String[] fastaQuery(String sequence,
                    double eCutOff)
                    throws RemoteException

Runs FASTa against the given sequence and returns an array of matching PDB IDs

Parameters:

sequence - A protein sequence

eCutOff - See FASTa documentation for details

Returns:

An array of matching PDB Structure Identifiers (aka PDB IDs)

Throws:

RemoteException

fastaStructureIdQuery

String[] fastaStructureIdQuery(String structureId,
                               String chainId,
                               double eCutOff)
                               throws RemoteException

Runs FASTa against the sequence of the given chain and returns an array of matching PDB IDs

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier

eCutOff - See FASTa documentation for details

Returns:

An array of matching PDB Structure Identifiers (aka PDB IDs)

Throws:

RemoteException

getAtomSite

Atom_siteWS getAtomSite(String structureId)
                        throws RemoteException

Returns the first atom site object for a structure. Not really useful except for testing.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

An atom site object. Probably not the optimal representation of an atom site - it has 86 fields!

Throws:

RemoteException

getAtomSites

Atom_siteWS[] getAtomSites(String structureId)
                           throws RemoteException

Returns the atom site objects for a structure.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

An array of atom site objects. Probably not the optimal representation of an atom site - it has 86 fields!

Throws:

RemoteException

getChainLength

int getChainLength(String structureId,
                   String chainId)
                   throws RemoteException

Finds the length of the given chain.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier

Returns:

The length of the given chain

Throws:

RemoteException

getChains

String[] getChains(String structureId)
                   throws RemoteException

Finds all the chain identifiers for a given structure.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

The author-assigned chain identifiers for the given structure

Throws:

RemoteException

getCifChain

String getCifChain(String structureId,
                   String chainId)
                   throws RemoteException

Converts author-assigned chain identifiers into their corrected (mmCIF) equivalents.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An Author-Assigned Chain Identifier

Returns:

The chain identifier (mmCIF) of the given chain

Throws:

RemoteException

getPdbChain

String getPdbChain(String in0,
                   String in1)
                   throws RemoteException

Finds the length of the given chain, where the chain identifier is the mmCIF version.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An mmCIF Chain Identifier

Returns:

The length of the given chain

Throws:

RemoteException

getCifChainLength

int getCifChainLength(String structureId,
                      String chainId)
                      throws RemoteException

Throws:

RemoteException

getCifChains

String[] getCifChains(String structureId)
                      throws RemoteException

Finds all the mmCIF chain identifiers for a given structure.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

The mmCIF chain identifiers for the given structure. Note that these are NOT the author-assigned identifiers, although often they can match. For an example, check out the mmCIF file for 1AEW.

Throws:

RemoteException

getCifResidue

int getCifResidue(String structureId,
                  String chainId,
                  String residueId)
                  throws RemoteException

Converts an author-assigned residue identifier into its corrected (mmCIF) equivalent.

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier

residueId - An author-assigned Residue Identifier including insertion code (if present)

Returns:

Throws:

RemoteException

getCurrentPdbIds

String[] getCurrentPdbIds()
                          throws RemoteException

Finds all the PDB Identifiers (aka PDB IDs) that are "current" structures - not obsolete, models, etc.

Returns:

An array of current PDB IDs

Throws:

RemoteException

getDomainFragments

DomainFragmentWS[] getDomainFragments(String structureId,
                                      String chainId,
                                      String method)
                                      throws RemoteException

Find all structural protein domain fragments for a given structureId

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier (may be null if domain fragments of all chains are required)

method - A domain prediction method (one of 'SCOP', 'CATH', 'dp' and 'pdp' -- may be null if all are required)

Returns:

an array of DomainFramgentWS objects.

Throws:

RemoteException - if the supplied PDB id is null, or if there was an internal server error

getEcNums

String[] getEcNums()
                   throws RemoteException

Finds all the Enzyme Classification numbers associated with all PDB strucutures

Returns:

An array of strings, where each string contains the PDB ID, the author-assigned chain ID, and the EC number, separated by tabs.

Throws:

RemoteException

getEcNumsForStructures

String[] getEcNumsForStructures(String[] structureIds)
                                throws RemoteException

Finds all the Enzyme Classification numbers associated with the given PDB strucutures.

Parameters:

structureIds - An array of PDB IDs

Returns:

An array of strings, where each string contains the PDB ID, the author-assigned chain ID, and the EC number, separated by tabs.

Throws:

RemoteException

getEntities

int[] getEntities(String structureId)
                  throws RemoteException

Finds the mmCIF entity IDs for a given structure

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

an array of entity IDs

Throws:

RemoteException

getGenomeDetails

String[] getGenomeDetails()
                          throws RemoteException

Finds genome details for all PDB structures

Returns:

An array of strings, where each string contains the PDB ID, the author-assigned chain ID, the locus ID, and the OMIM number, separated by tabs.

Throws:

RemoteException

getIdStatus

String getIdStatus(String structureId)
                   throws RemoteException

Finds the status of the given structure - one of CURRENT, OBSOLETE, UNRELEASED, MODEL, or UNKNOWN

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

one of CURRENT, OBSOLETE, UNRELEASED, MODEL, or UNKNOWN

Throws:

RemoteException

getKabschSander

String getKabschSander(String structureId,
                       String chainId)
                       throws RemoteException

Finds secondary structure for the given chain

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier

Returns:

the Kabsch-Sander secondary structure string

Throws:

RemoteException

getDisorder

String getDisorder(String in0,
                   String in1)
                   throws RemoteException

Throws:

RemoteException

getDbRefIds

String[] getDbRefIds(String in0,
                     String in1,
                     String in2)
                     throws RemoteException

Throws:

RemoteException

getObsoletePdbIds

String[] getObsoletePdbIds()
                           throws RemoteException

Gets the list of obsolete PDB ids

Returns:

An array of PDB IDs for all obsolete structures.

Throws:

RemoteException

getPrimaryCitationTitle

String getPrimaryCitationTitle(String structureId)
                               throws RemoteException

For structures with a primary citation, will find the title of the citation

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

The title of the primary citation

Throws:

RemoteException

getPubmedIdForAllStructures

String[] getPubmedIdForAllStructures()
                                     throws RemoteException

Finds all the Pubmed IDs associated with PDB structures

Returns:

An array of strings, where each string contains the PDB ID and the Pubmed ID, separated by a comma

Throws:

RemoteException

getPubmedIdForStructure

String getPubmedIdForStructure(String structureId)
                               throws RemoteException

Finds a Pubmed ID for the given structure. Not very useful for structures with multiple associated Pubmed IDs.

Parameters:

structureId -

Returns:

A Pubmed ID

Throws:

RemoteException

getReleaseDates

String[] getReleaseDates(String[] structureIds)
                         throws RemoteException

Finds the release dates for the given structures

Parameters:

structureIds - An array of PDB IDs

Returns:

An array of strings, where each string contains the PDB ID and the release date, separated by a tab

Throws:

RemoteException

getSequenceForStructureAndChain

String getSequenceForStructureAndChain(String structureId,
                                       String chainId)
                                       throws RemoteException

Finds the sequence for the given chain

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

chainId - An author-assigned Chain Identifier

Returns:

A sequence

Throws:

RemoteException

getSnpInfo

SnpInfo[] getSnpInfo(String structureId)
                     throws RemoteException

Get SnpInfo for a PDB id

Parameters:

structureId -

Returns:

Throws:

RemoteException

getSnps

String[] getSnps()
                 throws RemoteException

Return all PDBs that have SNPs in the database. (coming from LS-SNP)

Returns:

Throws:

RemoteException

getSpaceGroupForStructure

String getSpaceGroupForStructure(String structureId)
                                 throws RemoteException

Finds the symmetry.space_group_name_H_M field for a structure (see mmCIF dictionary for more info)

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

A space group (see mmCIF dictionary for more info)

Throws:

RemoteException

getStructureGenomicsPdbIds

String[] getStructureGenomicsPdbIds()
                                    throws RemoteException

Finds info for structural genomics structures

Returns:

An array of strings where each string contains the target_id, database_name, and database_id separated by tabs.

Throws:

RemoteException

getSwissProtIds

String[] getSwissProtIds()
                         throws RemoteException

Returns the mapping from PDB and chain ID to UniProtKB entries.

Returns:

the mapping from PDB and chain ID to UniProtKB codes.

Throws:

RemoteException

isStructureIdObsolete

int isStructureIdObsolete(String structureId)
                          throws RemoteException

Determines if the given structure is obsolete

Parameters:

structureId - A PDB Structure Identifier (aka PDB ID)

Returns:

1 if obsolete, 0 if not

Throws:

RemoteException

keywordQuery

String[] keywordQuery(String keywordExpression,
                      boolean exactMatch,
                      boolean restrictToAuthors)
                      throws RemoteException

Runs a keyword query, like what would happen if you entered a search phrase in the search box at the top of the RCSB PDB web site.

Parameters:

keywordExpression - A search phrase - uses lucene syntax

exactMatch - determines if lucene should do an exact word match or not

restrictToAuthors - if true then only the author fields will be searched

Returns:

An array of PDB IDs

Throws:

RemoteException

pubmedAbstractQuery

String[] pubmedAbstractQuery(String keywordExpression)
                             throws RemoteException

Runs a keyword query, like what would happen if you entered a search phrase in the search box on the Pubmed Abstract page (e.g., http://www.pdb.org/pdb/explore/pubmed.do?structureId=4HHB)

Parameters:

keywordExpression - A search phrase - uses lucene syntax

Returns:

An array of PDB IDs

Throws:

RemoteException