Package org.biojava.nbio.structure.ecod
Interface EcodDatabase
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- All Known Implementing Classes:
EcodInstallation
public interface EcodDatabase
General API for interacting with ECOD.- Author:
- Spencer Bliven
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.util.List<EcodDomain>
filterByHierarchy(java.lang.String hierarchy)
Get a list of domains within a particular level of the hierarchyjava.util.List<EcodDomain>
getAllDomains()
Get all ECOD domainsEcodDomain
getDomainsById(java.lang.String ecodId)
Get a particular ECOD domain by the domain ID (e.g.java.util.List<EcodDomain>
getDomainsForPdb(java.lang.String pdbId)
Get a list of all ECOD domains for a particular PDB IDjava.lang.String
getVersion()
Return the release version.
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Method Detail
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getVersion
java.lang.String getVersion() throws java.io.IOException
Return the release version.- Returns:
- version
- Throws:
java.io.IOException
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getDomainsById
EcodDomain getDomainsById(java.lang.String ecodId) throws java.io.IOException
Get a particular ECOD domain by the domain ID (e.g. "e4hhbA1")- Parameters:
ecodId
-- Returns:
- Throws:
java.io.IOException
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getDomainsForPdb
java.util.List<EcodDomain> getDomainsForPdb(java.lang.String pdbId) throws java.io.IOException
Get a list of all ECOD domains for a particular PDB ID- Parameters:
pdbId
-- Returns:
- the list of domains, or null if no matching domains were found
- Throws:
java.io.IOException
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filterByHierarchy
java.util.List<EcodDomain> filterByHierarchy(java.lang.String hierarchy) throws java.io.IOException
Get a list of domains within a particular level of the hierarchy- Parameters:
hierarchy
- A dot-separated list giving the X-group, H-group, and/or T-group (e.g. "1.1" for all members of the RIFT-related H-group)- Returns:
- Throws:
java.io.IOException
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getAllDomains
java.util.List<EcodDomain> getAllDomains() throws java.io.IOException
Get all ECOD domains- Returns:
- Throws:
java.io.IOException
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