Interface PDPProvider
-
- All Known Implementing Classes:
RemotePDPProvider
public interface PDPProvider
Decomposes a structure into representative PDP domains. Implementations will probably want to also implementDomainProvider
, which provides a very similar set of methods for general structure domain decomposition.- Since:
- 3.0.2
- Author:
- Andreas Prlic
-
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description Structure
getDomain(String pdpDomainName, AtomCache cache)
Get the structure for a particular PDP domainPDPDomain
getPDPDomain(String pdpDomainName)
Get a StructureIdentifier representing the specified PDP domain.SortedSet<String>
getPDPDomainNamesForPDB(String pdbId)
Get a list of all PDP domains for a given PDB entry
-
-
-
Method Detail
-
getPDPDomainNamesForPDB
SortedSet<String> getPDPDomainNamesForPDB(String pdbId) throws IOException
Get a list of all PDP domains for a given PDB entry- Parameters:
pdbId
- PDB ID- Returns:
- Set of domain names, e.g. "PDP:4HHBAa"
- Throws:
IOException
-
getDomain
Structure getDomain(String pdpDomainName, AtomCache cache) throws IOException, StructureException
Get the structure for a particular PDP domain- Parameters:
pdpDomainName
- PDP identifier, e.g. "PDP:4HHBAa"cache
- AtomCache, responsible for fetching and storing the coordinates- Returns:
- Structure representing the PDP domain
- Throws:
IOException
- For IO errors, e.g. when parsing PDP informationStructureException
- For errors creating the structure
-
getPDPDomain
PDPDomain getPDPDomain(String pdpDomainName) throws IOException
Get a StructureIdentifier representing the specified PDP domain.- Parameters:
pdpDomainName
- PDP domain name- Returns:
- a PDPDomain representing this domain name
- Throws:
IOException
-
-