Package org.biojava.nbio.structure.cath
Interface CathDatabase
- All Known Implementing Classes:
CathInstallation
public interface CathDatabase
General API for interacting with CATH.
- Author:
- Daniel Asarnow
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Method Summary
Modifier and TypeMethodDescriptionfilterByCathCode(String query) Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query.filterByDescription(String query) Return list of CATH descriptions whose descriptions (name field) starts with the query.filterByNodeName(String query) Return list of CATH domains whose node name (e.g.getByCategory(CathCategory category) Return list of CATH descriptions for node representatives at a CATH category (e.g.getCathNode(String nodeId) Return the CathNode for a node ID.Return the CATH release version.getDescriptionByCathId(String cathId) Return CATH description for CATH domain ID.getDescriptionByNodeId(String nodeId) Return CATH description for node representative by node ID.getDomainByCathId(String cathId) Return CATH domain for CATH domain ID.getDomainsByNodeId(String nodeId) Return all CATH domains for a particular CATH node.getDomainsForPdb(String pdbId) Return all CATH domains for a PDB ID.getFragmentsByPdbId(String pdbId) getTree(CathDomain domain) Return the CATH sub-tree for a particular domain.
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Method Details
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getCathVersion
Return the CATH release version.- Returns:
- CATH version
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getCathNode
Return the CathNode for a node ID.- Parameters:
nodeId-- Returns:
- CATH node
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getByCategory
Return list of CATH descriptions for node representatives at a CATH category (e.g. "T").- Parameters:
category-- Returns:
- CATH descriptions
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filterByCathCode
Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query. This is currently redundant with getDescriptionsByNodeId.- Parameters:
query-- Returns:
- CATH descriptions
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getTree
Return the CATH sub-tree for a particular domain.- Parameters:
domain-- Returns:
- CATH sub-tree
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filterByNodeName
Return list of CATH domains whose node name (e.g. Orthogonal Bundle) starts with the query.- Parameters:
query-- Returns:
- CATH domains
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filterByDescription
Return list of CATH descriptions whose descriptions (name field) starts with the query.- Parameters:
query-- Returns:
- CATH descriptions
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getDescriptionByNodeId
Return CATH description for node representative by node ID.- Parameters:
nodeId-- Returns:
- CATH description
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getDomainsForPdb
Return all CATH domains for a PDB ID.- Parameters:
pdbId-- Returns:
- CATH domains
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getDomainByCathId
Return CATH domain for CATH domain ID.- Parameters:
cathId-- Returns:
- CATH domain
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getDescriptionByCathId
Return CATH description for CATH domain ID.- Parameters:
cathId-- Returns:
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getDomainsByNodeId
Return all CATH domains for a particular CATH node.- Parameters:
nodeId-- Returns:
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getFragmentsByPdbId
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