Class SimpleMMcifParser
- java.lang.Object
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- org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
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- All Implemented Interfaces:
MMcifParser
public class SimpleMMcifParser extends java.lang.Object implements MMcifParser
A simple mmCif file parser- Since:
- 1.7
Usage:
String file = "path/to/mmcif/file"; StructureIOFile pdbreader = new MMCIFFileReader(); try { Structure s = pdbreader.getStructure(file); System.out.println(s); // you can convert it to a PDB file... System.out.println(s.toPDB()); } catch (IOException e) { e.printStackTrace(); }
For more documentation see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure. - Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
FIELD_LINE
static java.util.logging.Logger
logger
static java.lang.String
LOOP_END
static java.lang.String
LOOP_START
static java.lang.String
STRING_LIMIT
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Constructor Summary
Constructors Constructor Description SimpleMMcifParser()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addMMcifConsumer(MMcifConsumer consumer)
Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.void
clearConsumers()
Remove all consumers from the parser.static void
main(java.lang.String[] args)
void
parse(java.io.BufferedReader buf)
Start the actual parsing.void
parse(java.io.InputStream inStream)
Start the actual parsing.void
removeMMcifConsumer(MMcifConsumer consumer)
remove a single consumer from the parservoid
triggerDocumentEnd()
void
triggerDocumentStart()
void
triggerGeneric(java.lang.String category, java.util.List<java.lang.String> loopFields, java.util.List<java.lang.String> lineData)
void
triggerNewChemComp(ChemComp cc)
void
triggerNewEntity(Entity entity)
void
triggerNewEntityPolySeq(EntityPolySeq epolseq)
void
triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly pen)
void
triggerNewRefine(Refine r)
void
triggerNewStructAsym(StructAsym sasym)
void
triggerNewStructKeywords(StructKeywords kw)
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Field Detail
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LOOP_END
public static final java.lang.String LOOP_END
- See Also:
- Constant Field Values
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LOOP_START
public static final java.lang.String LOOP_START
- See Also:
- Constant Field Values
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FIELD_LINE
public static final java.lang.String FIELD_LINE
- See Also:
- Constant Field Values
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STRING_LIMIT
public static final java.lang.String STRING_LIMIT
- See Also:
- Constant Field Values
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logger
public static java.util.logging.Logger logger
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Method Detail
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addMMcifConsumer
public void addMMcifConsumer(MMcifConsumer consumer)
Description copied from interface:MMcifParser
Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.- Specified by:
addMMcifConsumer
in interfaceMMcifParser
- Parameters:
consumer
- a consumer object.
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clearConsumers
public void clearConsumers()
Description copied from interface:MMcifParser
Remove all consumers from the parser.- Specified by:
clearConsumers
in interfaceMMcifParser
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removeMMcifConsumer
public void removeMMcifConsumer(MMcifConsumer consumer)
Description copied from interface:MMcifParser
remove a single consumer from the parser- Specified by:
removeMMcifConsumer
in interfaceMMcifParser
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main
public static void main(java.lang.String[] args)
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parse
public void parse(java.io.InputStream inStream) throws java.io.IOException
Description copied from interface:MMcifParser
Start the actual parsing. The parser will trigger events that are defined by the MMcifConsumer class.- Specified by:
parse
in interfaceMMcifParser
- Parameters:
inStream
- InputStream to parse from.- Throws:
java.io.IOException
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parse
public void parse(java.io.BufferedReader buf) throws java.io.IOException
Description copied from interface:MMcifParser
Start the actual parsing. The parser will trigger events that are defined by the MMcifConsumer class.- Specified by:
parse
in interfaceMMcifParser
- Parameters:
buf
- a BufferedReader.- Throws:
java.io.IOException
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triggerGeneric
public void triggerGeneric(java.lang.String category, java.util.List<java.lang.String> loopFields, java.util.List<java.lang.String> lineData)
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triggerNewEntity
public void triggerNewEntity(Entity entity)
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triggerNewEntityPolySeq
public void triggerNewEntityPolySeq(EntityPolySeq epolseq)
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triggerNewChemComp
public void triggerNewChemComp(ChemComp cc)
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triggerNewStructAsym
public void triggerNewStructAsym(StructAsym sasym)
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triggerNewPdbxEntityNonPoly
public void triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly pen)
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triggerNewStructKeywords
public void triggerNewStructKeywords(StructKeywords kw)
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triggerNewRefine
public void triggerNewRefine(Refine r)
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triggerDocumentStart
public void triggerDocumentStart()
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triggerDocumentEnd
public void triggerDocumentEnd()
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