PDBFileParser (biojava 6.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.io.PDBFileParser

```
public class PDBFileParser
extends Object
```
This class implements the actual PDB file parsing. Do not access it directly, but via the PDBFileReader class.
Parsing
During the PDBfile parsing several Flags can be set. See the setFileParsingParameters(FileParsingParameters) methods.
To provide excessive memory usage for large PDB files, there is the ATOM_CA_THRESHOLD. If more Atoms than this threshold are being parsed in a PDB file, the parser will automatically switch to a C-alpha only representation.
The result of the parsing of the PDB file is a new Structure object.
For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure
Example

Q: How can I get a Structure object from a PDB file?
A:
```
 public Structure loadStructure(String pathToPDBFile){
        // The PDBFileParser is wrapped by the PDBFileReader
        PDBFileReader pdbreader = new PDBFileReader();

        Structure structure = null;
        try{
                structure = pdbreader.getStructure(pathToPDBFile);
                System.out.println(structure);
        } catch (IOException e) {
                e.printStackTrace();
        }
        return structure;
 }
 
```
Since:

1.4

Author:

Andreas Prlic, Jules Jacobsen, Jose Duarte

Constructor Summary

Constructors
Constructor Description

PDBFileParser()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`FileParsingParameters`	`getFileParsingParameters()`
`Structure`	`parsePDBFile(BufferedReader buf)`	Parse a PDB file and return a datastructure implementing PDBStructure interface.
`Structure`	`parsePDBFile(InputStream inStream)`	Parse a PDB file and return a datastructure implementing PDBStructure interface.
`void`	`setFileParsingParameters(FileParsingParameters params)`

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

- Constructor Detail
  - PDBFileParser
```
public PDBFileParser()
```
- Method Detail
  - parsePDBFile
```
public Structure parsePDBFile(InputStream inStream)
                       throws IOException
```
    Parse a PDB file and return a datastructure implementing PDBStructure interface.
    
    Parameters:
    
    inStream - an InputStream object
    
    Returns:
    
    a Structure object
    
    Throws:
    
    IOException
  - parsePDBFile
```
public Structure parsePDBFile(BufferedReader buf)
                       throws IOException
```
    Parse a PDB file and return a datastructure implementing PDBStructure interface.
    
    Parameters:
    
    buf - a BufferedReader object
    
    Returns:
    
    the Structure object
    
    Throws:
    
    IOException - ...
  - setFileParsingParameters
```
public void setFileParsingParameters(FileParsingParameters params)
```
  - getFileParsingParameters
```
public FileParsingParameters getFileParsingParameters()
```