Package org.biojava.nbio.structure.rcsb
Class PdbIdLists
- java.lang.Object
-
- org.biojava.nbio.structure.rcsb.PdbIdLists
-
public class PdbIdLists extends Object
Utility classes for retrieving lists of PDB IDs.- Since:
- 4.2.0
- Author:
- Andreas Prlic
-
-
Field Summary
Fields Modifier and Type Field Description static String
SERVICELOCATION
-
Constructor Summary
Constructors Constructor Description PdbIdLists()
-
Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static InputStream
doPOST(URL url, String data)
do a POST to a URL and return the response stream for further processing elsewhere.static Set<String>
getAllViruses()
Get the PDB IDs of all virus structures in the current PDBstatic Set<String>
getCurrentPDBIds()
get the list of current PDB IDsstatic Set<String>
getGagPolyproteins()
get all PDB IDs of gag-polyproteinsstatic Set<String>
getNMRStructures()
get list of all current NMR structuresstatic Set<String>
getNucleotides()
static Set<String>
getRibosomes()
static Set<String>
getTransmembraneProteins()
get all Transmembrane proteinsstatic void
main(String[] args)
static Set<String>
postQuery(String xml)
post am XML query (PDB XML query format) to the RESTful RCSB web service
-
-
-
Field Detail
-
SERVICELOCATION
public static final String SERVICELOCATION
- See Also:
- Constant Field Values
-
-
Constructor Detail
-
PdbIdLists
public PdbIdLists()
-
-
Method Detail
-
getCurrentPDBIds
public static Set<String> getCurrentPDBIds() throws IOException
get the list of current PDB IDs- Returns:
- list of current PDB IDs
- Throws:
IOException
-
getAllViruses
public static Set<String> getAllViruses() throws IOException
Get the PDB IDs of all virus structures in the current PDB- Returns:
- list of all virus structures
- Throws:
IOException
-
getNMRStructures
public static Set<String> getNMRStructures() throws IOException
get list of all current NMR structures- Returns:
- list of NMR structures
- Throws:
IOException
-
getGagPolyproteins
public static Set<String> getGagPolyproteins() throws IOException
get all PDB IDs of gag-polyproteins- Returns:
- list of PDB IDs
- Throws:
IOException
-
getTransmembraneProteins
public static Set<String> getTransmembraneProteins() throws IOException
get all Transmembrane proteins- Returns:
- list of PDB IDs
- Throws:
IOException
-
getNucleotides
public static Set<String> getNucleotides() throws IOException
- Throws:
IOException
-
getRibosomes
public static Set<String> getRibosomes() throws IOException
- Throws:
IOException
-
postQuery
public static Set<String> postQuery(String xml) throws IOException
post am XML query (PDB XML query format) to the RESTful RCSB web service- Parameters:
xml
-- Returns:
- a list of PDB ids.
- Throws:
IOException
-
doPOST
public static InputStream doPOST(URL url, String data) throws IOException
do a POST to a URL and return the response stream for further processing elsewhere.- Parameters:
url
-- Returns:
- Throws:
IOException
-
-