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java.lang.Objectorg.biojava.bio.structure.io.PDBFileParser
public class PDBFileParser
This class implements the actual PDB file parsing. Do not access it directly, but via the PDBFileReader class.
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.
Q: How can I get a Structure object from a PDB file?
A:
publicStructure
loadStructure(String pathToPDBFile){ // The PDBFileParser is wrapped by the PDBFileReaderPDBFileReader
pdbreader = newPDBFileReader
();Structure
structure = null; try{ structure = pdbreader.getStructure(pathToPDBFile); System.out.println(structure); } catch (IOException e) { e.printStackTrace(); } return structure; }
Field Summary | |
---|---|
static String |
HELIX
Helix secondary structure assignment. |
static String |
PDB_AUTHOR_ASSIGNMENT
Secondary strucuture assigned by the PDB author/ |
static String |
STRAND
Strand secondary structure assignment. |
static String |
TURN
Turn secondary structure assignment. |
Constructor Summary | |
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PDBFileParser()
|
Method Summary | |
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FileParsingParameters |
getFileParsingParameters()
|
protected String |
getTimeStamp()
Returns a time stamp. |
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(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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String PDB_AUTHOR_ASSIGNMENT
public static final String HELIX
public static final String STRAND
public static final String TURN
Constructor Detail |
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public PDBFileParser()
Method Detail |
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protected String getTimeStamp()
public Structure parsePDBFile(InputStream inStream) throws IOException
inStream
- an InputStream object
IOException
public Structure parsePDBFile(BufferedReader buf) throws IOException
buf
- a BufferedReader object
IOException
- ...public void linkChains2Compound(Structure s)
Chain
and Compound
objects need to be linked to each other.
s
- the structurepublic void setFileParsingParameters(FileParsingParameters params)
public FileParsingParameters getFileParsingParameters()
|
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