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