Package org.biojava.bio.structure.io
Class PDBFileReader
- java.lang.Object
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- org.biojava.bio.structure.io.PDBFileReader
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- All Implemented Interfaces:
StructureIO
,StructureIOFile
public class PDBFileReader extends java.lang.Object implements StructureIOFile
The wrapper class for parsing a PDB file.
Several flags can be set for this class
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setParseCAOnly(boolean)
- parse only the Atom records for C-alpha atoms (default:false) -
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 throughAminoAcid
.getSecStruc(); (default:false) -
setAlignSeqRes(boolean)
- should the AminoAcid sequences from the SEQRES and ATOM records of a PDB file be aligned? (default:true) -
setAutoFetch(boolean)
- if the PDB file can not be found locally, should it be fetched from the EBI - ftp server? (default:false)
Example
Q: How can I get a Structure object from a PDB file?
A:
public
Access PDB files from a directory, take care of compressed PDB filesStructure
loadStructure(String pathToPDBFile){PDBFileReader
pdbreader = newPDBFileReader
();Structure
structure = null; try{ structure = pdbreader.getStructure(pathToPDBFile); System.out.println(structure); } catch (IOException e) { e.printStackTrace(); } return structure; }public
Structure
loadStructureById() { String path = "/path/to/PDB/directory/";PDBFileReader
pdbreader = newPDBFileReader
(); pdbreader.setPath(path);Structure
structure = null; try { structure = pdbreader.getStructureById("5pti"); } catch (IOException e){ e.printStackTrace(); } return structure; }- Author:
- Andreas Prlic
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Constructor Summary
Constructors Constructor Description PDBFileReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addExtension(java.lang.String s)
define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.void
clearExtensions()
clear the supported file extensionsjava.lang.String
getPath()
Returns the path value.Structure
getStructure(java.io.File filename)
opens filename, parses it and returns a Structure objectStructure
getStructure(java.lang.String filename)
opens filename, parses it and returns aStructure object .Structure
getStructureById(java.lang.String pdbId)
load a structure from local file system and return a PDBStructure objectboolean
isAlignSeqRes()
get the flag if the SEQRES and ATOM amino acids are going to be alignedboolean
isAutoFetch()
should the parser to fetch missing PDB files from the EBI FTP server automatically? default is falseboolean
isParseCAOnly()
return the flag if only the CA atoms should be parsedboolean
isParseSecStruc()
static void
main(java.lang.String[] args)
void
setAlignSeqRes(boolean alignSeqRes)
set the flag if the SEQRES and ATOM amino acids should be aligned and linkedvoid
setAutoFetch(boolean autoFetch)
tell the parser to fetch missing PDB files from the EBI FTP server automatically.void
setParseCAOnly(boolean parseCAOnly)
only the CA atoms should be parsed from the PDB filevoid
setParseSecStruc(boolean parseSecStruc)
void
setPath(java.lang.String p)
directory where to find PDB files
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Method Detail
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main
public static void main(java.lang.String[] args)
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isParseCAOnly
public boolean isParseCAOnly()
return the flag if only the CA atoms should be parsed- Returns:
- flag if CA only should be read
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setParseCAOnly
public void setParseCAOnly(boolean parseCAOnly)
only the CA atoms should be parsed from the PDB file- Parameters:
parseCAOnly
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isAlignSeqRes
public boolean isAlignSeqRes()
get the flag if the SEQRES and ATOM amino acids are going to be aligned- Returns:
- flag
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setAlignSeqRes
public void setAlignSeqRes(boolean alignSeqRes)
set the flag if the SEQRES and ATOM amino acids should be aligned and linked- Parameters:
alignSeqRes
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-
isAutoFetch
public boolean isAutoFetch()
should the parser to fetch missing PDB files from the EBI FTP server automatically? default is false- Specified by:
isAutoFetch
in interfaceStructureIOFile
- Returns:
- flag
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setAutoFetch
public void setAutoFetch(boolean autoFetch)
tell the parser to fetch missing PDB files from the EBI FTP server automatically. default is false. If true, new PDB files will be automatically stored in the Path and gzip compressed.- Specified by:
setAutoFetch
in interfaceStructureIOFile
- Parameters:
autoFetch
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isParseSecStruc
public boolean isParseSecStruc()
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setParseSecStruc
public void setParseSecStruc(boolean parseSecStruc)
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setPath
public void setPath(java.lang.String p)
directory where to find PDB files- Specified by:
setPath
in interfaceStructureIOFile
- Parameters:
p
- a String specifying the path value
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getPath
public java.lang.String getPath()
Returns the path value.- Specified by:
getPath
in interfaceStructureIOFile
- Returns:
- a String representing the path value
- See Also:
setPath(java.lang.String)
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addExtension
public void addExtension(java.lang.String s)
define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.- Specified by:
addExtension
in interfaceStructureIOFile
- Parameters:
s
- a String ...
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clearExtensions
public void clearExtensions()
clear the supported file extensions- Specified by:
clearExtensions
in interfaceStructureIOFile
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getStructureById
public Structure getStructureById(java.lang.String pdbId) throws java.io.IOException
load a structure from local file system and return a PDBStructure object- Specified by:
getStructureById
in interfaceStructureIO
- Parameters:
pdbId
- a String specifying the id value (PDB code)- Returns:
- the Structure object
- Throws:
java.io.IOException
- ...
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getStructure
public Structure getStructure(java.lang.String filename) throws java.io.IOException
opens filename, parses it and returns aStructure object .- Specified by:
getStructure
in interfaceStructureIOFile
- Parameters:
filename
- a String- Returns:
- the Structure object
- Throws:
java.io.IOException
- ...
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getStructure
public Structure getStructure(java.io.File filename) throws java.io.IOException
opens filename, parses it and returns a Structure object- Specified by:
getStructure
in interfaceStructureIOFile
- Parameters:
filename
- a File object- Returns:
- the Structure object
- Throws:
java.io.IOException
- ...
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