PDPProvider (biojava 5.4.0 API)

All Known Implementing Classes:

RemotePDPProvider
```
public interface PDPProvider
```
Decomposes a structure into representative PDP domains. Implementations will probably want to also implement DomainProvider, 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(java.lang.String pdpDomainName, AtomCache cache)`	Get the structure for a particular PDP domain
`PDPDomain`	`getPDPDomain(java.lang.String pdpDomainName)`	Get a StructureIdentifier representing the specified PDP domain.
`java.util.SortedSet<java.lang.String>`	`getPDPDomainNamesForPDB(java.lang.String pdbId)`	Get a list of all PDP domains for a given PDB entry

- Method Detail
  - getPDPDomainNamesForPDB
```
java.util.SortedSet<java.lang.String> getPDPDomainNamesForPDB(java.lang.String pdbId)
                                                       throws java.io.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:
    
    java.io.IOException
  - getDomain
```
Structure getDomain(java.lang.String pdpDomainName,
                    AtomCache cache)
             throws java.io.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:
    
    java.io.IOException - For IO errors, e.g. when parsing PDP information
    
    StructureException - For errors creating the structure
  - getPDPDomain
```
PDPDomain getPDPDomain(java.lang.String pdpDomainName)
                throws java.io.IOException
```
    Get a StructureIdentifier representing the specified PDP domain.
    
    Parameters:
    
    pdpDomainName - PDP domain name
    
    Returns:
    
    a PDPDomain representing this domain name
    
    Throws:
    
    java.io.IOException