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java.lang.Objectorg.biojava.bio.structure.io.MMCIFFileReader
public class MMCIFFileReader
How to parse an mmCif file:
public static void main(String[] args){ String filename = "/path/to/something.cif.gz" ; StructureIOFile reader = new MMCIFFileReader(); try{ Structure struc = reader.getStructure(filename); System.out.println(struc); } catch (Exception e) { e.printStackTrace(); } }
Constructor Summary | |
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MMCIFFileReader()
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Method Summary | |
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void |
addExtension(String ext)
add a known File extension. |
void |
clearExtensions()
clear all file extensions |
String |
getPath()
get the directory path to the files |
Structure |
getStructure(File filename)
Opens filename, parses it and returns a Structure object. |
Structure |
getStructure(String filename)
Opens filename, parses it and returns a Structure object . |
Structure |
getStructureById(String pdbId)
Get a structure by PDB code. |
boolean |
isAutoFetch()
Fetch files automatically from FTP server. |
static void |
main(String[] args)
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void |
setAutoFetch(boolean autoFetch)
Tell the parser to fetch missing PDB files from the FTP server automatically. |
void |
setPath(String path)
Set path to file / connection string to db. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MMCIFFileReader()
Method Detail |
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public static void main(String[] args)
public void addExtension(String ext)
StructureIOFile
addExtension
in interface StructureIOFile
ext
- a String ...public void clearExtensions()
StructureIOFile
clearExtensions
in interface StructureIOFile
public Structure getStructure(String filename) throws IOException
getStructure
in interface StructureIOFile
filename
- a String
IOException
- ...public Structure getStructure(File filename) throws IOException
getStructure
in interface StructureIOFile
filename
- a File object
IOException
- ...public void setPath(String path)
StructureIOFile
setPath
in interface StructureIOFile
path
- a String specifying the path valuepublic String getPath()
StructureIOFile
getPath
in interface StructureIOFile
public Structure getStructureById(String pdbId) throws IOException
getStructureById
in interface StructureIO
pdbId
- a 4 letter PDB code.
IOException
- ...public boolean isAutoFetch()
StructureIOFile
isAutoFetch
in interface StructureIOFile
public void setAutoFetch(boolean autoFetch)
StructureIOFile
setAutoFetch
in interface StructureIOFile
autoFetch
- flag.
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