LocalProteinDomainParser (biojava 5.2.0 API)

java.lang.Object
- org.biojava.nbio.structure.domain.LocalProteinDomainParser

```
public class LocalProteinDomainParser
extends Object
```
Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures. Since domains in proteins are difficult to define, results detected by automated algorithms have to be taken with a grain of salt. see
```
J Mol Biol. 2004 Jun 4;339(3):647-78.

Toward consistent assignment of structural domains in proteins.

Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN.
```
This implementation is based on a Java port of the PDP algorithm, as described in:
Since:

3.0.2

Author:

Andreas Prlic

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static List<Domain>`	`suggestDomains(Atom[] ca)`	Suggest domains for a set of Calpha atoms
`static List<Domain>`	`suggestDomains(Structure s)`	Suggest domains for a protein structure

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Method Detail
  - suggestDomains
```
public static List<Domain> suggestDomains(Structure s)
                                   throws StructureException
```
    Suggest domains for a protein structure
    
    Parameters:
    
    s - the protein structure
    
    Returns:
    
    a list of possible domains
    
    Throws:
    
    StructureException
  - suggestDomains
```
public static List<Domain> suggestDomains(Atom[] ca)
                                   throws StructureException
```
    Suggest domains for a set of Calpha atoms
    
    Parameters:
    
    ca - an array of Calpha atoms
    
    Returns:
    
    a list of possible domains
    
    Throws:
    
    StructureException