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java.lang.Objectorg.biojava.bio.structure.io.PDBFileParser
public class PDBFileParser
A PDB file parser.
Q: How can I get a Structure object from a PDB file?
A:
String filename = "path/to/pdbfile.ent" ; PDBFileReader pdbreader = new PDBFileReader(); try{ Structure struc = pdbreader.getStructure(filename); System.out.println(struc); } catch (Exception e) { e.printStackTrace(); }
Field Summary | |
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static java.lang.String |
idCode
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Constructor Summary | |
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PDBFileParser()
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Method Summary | |
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java.lang.Character |
convert_3code_1code(java.lang.String code3)
convert three character amino acid codes into single character e.g. |
protected java.lang.String |
getTimeStamp()
Returns a time stamp. |
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. |
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 java.lang.String idCode
Constructor Detail |
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public PDBFileParser()
Method Detail |
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protected java.lang.String getTimeStamp()
public java.lang.Character convert_3code_1code(java.lang.String code3) throws IllegalSymbolException
code3
- a three character amino acid representation String
IllegalSymbolException
public Structure parsePDBFile(java.io.InputStream inStream) throws java.io.IOException
inStream
- an InputStream object
java.io.IOException
public Structure parsePDBFile(java.io.BufferedReader buf) throws java.io.IOException
buf
- a BufferedReader object
java.io.IOException
- ...
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