PDBFileParser (BioJava-1.7.1 API)

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

```
public class PDBFileParser
extends java.lang.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:
- setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms
- setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed. If true the assignment can be accessed through AminoAcid.getSecStruc();
- setAlignSeqRes(boolean) - should the AminoAcid sequences from the SEQRES and ATOM records of a PDB file be aligned? (default:yes)
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

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ATOM_CA_THRESHOLD` the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
`static java.lang.String`	`HELIX` Helix secondary structure assignment.
`static int`	`MAX_ATOMS` the maximum number of atoms we will add to a structure this protects from memory overflows in the few really big protein structures.
`boolean`	`parseCAOnly` Set the flag to only read in Ca atoms - this is useful for parsing large structures like 1htq.
`static java.lang.String`	`PDB_AUTHOR_ASSIGNMENT` Secondary strucuture assigned by the PDB author/
`static java.lang.String`	`STRAND` Strand secondary structure assignment.
`static java.lang.String`	`TURN` Turn secondary structure assignment.

Constructor Summary

Constructors
Constructor and Description

PDBFileParser()

Constructors
Constructor and Description
`PDBFileParser()`

Method Summary

Methods
Modifier and Type	Method and Description
`protected java.lang.String`	`getTimeStamp()` Returns a time stamp.
`boolean`	`isAlignSeqRes()` Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
`boolean`	`isParseCAOnly()` the flag if only the C-alpha atoms of the structure should be parsed.
`boolean`	`isParseSecStruc()` is secondary structure assignment being parsed from the file? default is null
`void`	`linkChains2Compound(Structure s)` After the parsing of a PDB file the `Chain` and `Compound` objects need to be linked to each other.
`Structure`	`parsePDBFile(java.io.BufferedReader buf)` parse a PDB file and return a datastructure implementing PDBStructure interface.
`Structure`	`parsePDBFile(java.io.InputStream inStream)` parse a PDB file and return a datastructure implementing PDBStructure interface.
`void`	`setAlignSeqRes(boolean alignSeqRes)` define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
`void`	`setParseCAOnly(boolean parseCAOnly)` the flag if only the C-alpha atoms of the structure should be parsed.
`void`	`setParseSecStruc(boolean parseSecStruc)` a flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e.

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

- Field Detail
  - PDB_AUTHOR_ASSIGNMENT
```
public static final java.lang.String PDB_AUTHOR_ASSIGNMENT
```
    Secondary strucuture assigned by the PDB author/
    
    See Also:
    Constant Field Values
  - HELIX
```
public static final java.lang.String HELIX
```
    Helix secondary structure assignment.
    
    See Also:
    Constant Field Values
  - STRAND
```
public static final java.lang.String STRAND
```
    Strand secondary structure assignment.
    
    See Also:
    Constant Field Values
  - TURN
```
public static final java.lang.String TURN
```
    Turn secondary structure assignment.
    
    See Also:
    Constant Field Values
  - ATOM_CA_THRESHOLD
```
public static final int ATOM_CA_THRESHOLD
```
    the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file. If this limit is exceeded also the SEQRES groups will be ignored.
    
    See Also:
    Constant Field Values
  - MAX_ATOMS
```
public static final int MAX_ATOMS
```
    the maximum number of atoms we will add to a structure this protects from memory overflows in the few really big protein structures.
    
    See Also:
    Constant Field Values
  - parseCAOnly
```
public boolean parseCAOnly
```
    Set the flag to only read in Ca atoms - this is useful for parsing large structures like 1htq.
- Constructor Detail
  - PDBFileParser
```
public PDBFileParser()
```
- Method Detail
  - isParseCAOnly
```
public boolean isParseCAOnly()
```
    the flag if only the C-alpha atoms of the structure should be parsed.
    
    Returns:
    the flag
  - setParseCAOnly
```
public void setParseCAOnly(boolean parseCAOnly)
```
    the flag if only the C-alpha atoms of the structure should be parsed.
    
    Parameters:
    parseCAOnly - boolean flag to enable or disable C-alpha only parsing
  - isAlignSeqRes
```
public boolean isAlignSeqRes()
```
    Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
    
    Returns:
    flag if SEQRES - ATOM amino acids alignment is enabled
  - setAlignSeqRes
```
public void setAlignSeqRes(boolean alignSeqRes)
```
    define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
    
    Parameters:
    alignSeqRes -
  - isParseSecStruc
```
public boolean isParseSecStruc()
```
    is secondary structure assignment being parsed from the file? default is null
    
    Returns:
    boolean if HELIX STRAND and TURN fields are being parsed
  - setParseSecStruc
```
public void setParseSecStruc(boolean parseSecStruc)
```
    a flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e. do NOT parse.
    
    Parameters:
    parseSecStruc - if HELIX STRAND and TURN fields are being parsed
  - getTimeStamp
```
protected java.lang.String getTimeStamp()
```
    Returns a time stamp.
    
    Returns:
    a String representing the time stamp value
  - parsePDBFile
```
public Structure parsePDBFile(java.io.InputStream inStream)
                       throws java.io.IOException
```
    parse a PDB file and return a datastructure implementing PDBStructure interface.
    
    Parameters:
    inStream - an InputStream object
    
    Returns:
    a Structure object
    
    Throws:
    
    java.io.IOException
  - parsePDBFile
```
public Structure parsePDBFile(java.io.BufferedReader buf)
                       throws java.io.IOException
```
    parse a PDB file and return a datastructure implementing PDBStructure interface.
    
    Parameters:
    buf - a BufferedReader object
    
    Returns:
    the Structure object
    
    Throws:
    
    java.io.IOException - ...
  - linkChains2Compound
```
public void linkChains2Compound(Structure s)
```
    After the parsing of a PDB file the Chain and Compound objects need to be linked to each other.
    
    Parameters:
    s - the structure

Class PDBFileParser

Parsing

Example

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

PDB_AUTHOR_ASSIGNMENT

HELIX

STRAND

TURN

ATOM_CA_THRESHOLD

MAX_ATOMS

parseCAOnly

Constructor Detail

PDBFileParser

Method Detail

isParseCAOnly

setParseCAOnly

isAlignSeqRes

setAlignSeqRes

isParseSecStruc

setParseSecStruc

getTimeStamp

parsePDBFile

parsePDBFile

linkChains2Compound