Package org.biojava.nbio.structure.rcsb
Class RCSBLigandsFactory
java.lang.Object
org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
Fetches information from RCSB's RESTful Web Service
Interface. A factory for
RCSBLigands from ligandInfo XML files. The factory methods
will return null if the data was not found (rather than throwing an exception); client code should test for this.
This is for consistency: if the factory could not read some part (corresponding to a field in a class in
rcsb.descriptions) of the XML file, either because it was blank or contained an error that could not be
safely ignored, that field will simply be null. This holds even for numerical values. On some parse errors, the error
will additionally be printed to standard error.
Example usage:
RCSBLigands ligands = RCSBLigandsFactory.getFromPdbIds("1w0p");
List<RCSBLigand> list = ligands.getLigands();
System.out.println(list.get(0).getFormula()); // prints "CA 2"
System.out.println(list.get(1).getFormula()); // prints "C11 H19 N O9"
- Since:
- 3.0.6
- Author:
- dmyerstu
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic RCSBLigandgetFromHeteroAtomId(InputStream stream) static RCSBLigandgetFromHeteroAtomId(String heteroAtomId) static List<RCSBLigand>getFromHeteroAtomIds(InputStream stream) static List<RCSBLigand>getFromHeteroAtomIds(String... heteroAtomIds) static List<RCSBLigand>getFromHeteroAtomIds(List<String> heteroAtomIds) static RCSBLigandsgetFromPdbId(InputStream stream) static RCSBLigandsgetFromPdbId(String pdbId) static List<RCSBLigands>getFromPdbIds(InputStream stream) static RCSBLigandsgetFromPdbIds(String pdbId) static List<RCSBLigands>getFromPdbIds(String... pdbIds) static List<RCSBLigands>getFromPdbIds(List<String> pdbIds)
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Constructor Details
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RCSBLigandsFactory
public RCSBLigandsFactory()
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Method Details
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getFromHeteroAtomId
- Returns:
- A list of
RCSBLigandsfrom the XML file loaded asstream. Prefer callinggetFromHeteroAtomId(String)if you want data directly from RCSB's RESTful service. - See Also:
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getFromHeteroAtomId
- Returns:
- An
RCSBLigandsfrom the XML file at"http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid". This is the preferred factory method, unless a different URL or input source is required. - See Also:
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getFromHeteroAtomIds
- Returns:
- A list of
RCSBLigandsfrom the XML file loaded asstream. Prefer callinggetFromHeteroAtomId(String)if you want data directly from RCSB's RESTful service. - See Also:
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getFromHeteroAtomIds
- Returns:
- An
RCSBLigandsfrom the XML file at"http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid". This is the preferred factory method, unless a different URL or input source is required. - See Also:
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getFromHeteroAtomIds
- Returns:
- An
RCSBLigandsfrom the XML file at"http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid". This is the preferred factory method, unless a different URL or input source is required. - See Also:
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getFromPdbId
- Returns:
- An
RCSBLigandsfrom the XML file loaded asstream. Prefer callinggetFromPdbId(String)if you want data directly from RCSB's RESTful service. - See Also:
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getFromPdbId
- Returns:
- An
RCSBLigandsfrom the XML file at"http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId". This is the preferred factory method, unless a different URL or input source is required. - See Also:
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getFromPdbIds
- Returns:
- An
RCSBLigandsfrom the XML file loaded asstream. Prefer callinggetFromPdbId(String)if you want data directly from RCSB's RESTful service. - See Also:
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getFromPdbIds
- Returns:
- An
RCSBLigandsfrom the XML file at"http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId". This is the preferred factory method, unless a different URL or input source is required. - See Also:
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getFromPdbIds
- Returns:
- An
RCSBLigandsfrom the XML file at"http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId". This is the preferred factory method, unless a different URL or input source is required. - See Also:
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getFromPdbIds
- Returns:
- An
RCSBLigandsfrom the XML file at"http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId". This is the preferred factory method, unless a different URL or input source is required. - See Also:
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