org.biojava.bio.structure.io
public class PDBFileParser extends java.lang.Object
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; }
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
HELIX
Helix secondary structure assignment.
|
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 and Description |
---|
PDBFileParser() |
Modifier and Type | Method and Description |
---|---|
FileParsingParameters |
getFileParsingParameters() |
protected java.lang.String |
getTimeStamp()
Returns a time stamp.
|
void |
linkChains2Compound(Structure s)
|
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 |
setFileParsingParameters(FileParsingParameters params) |
public static final java.lang.String PDB_AUTHOR_ASSIGNMENT
public static final java.lang.String HELIX
public static final java.lang.String STRAND
public static final java.lang.String TURN
protected java.lang.String getTimeStamp()
public Structure parsePDBFile(java.io.InputStream inStream) throws java.io.IOException
inStream
- an InputStream objectjava.io.IOException
public Structure parsePDBFile(java.io.BufferedReader buf) throws java.io.IOException
buf
- a BufferedReader objectjava.io.IOException
- ...public void linkChains2Compound(Structure s)
s
- the structurepublic void setFileParsingParameters(FileParsingParameters params)
public FileParsingParameters getFileParsingParameters()