public class SimpleMMcifParser extends java.lang.Object implements MMcifParser
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.
Modifier and Type | Field and Description |
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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 |
Constructor and Description |
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SimpleMMcifParser() |
Modifier and Type | Method and 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 parser
|
void |
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) |
public static final java.lang.String LOOP_END
public static final java.lang.String LOOP_START
public static final java.lang.String FIELD_LINE
public static final java.lang.String STRING_LIMIT
public static java.util.logging.Logger logger
public void addMMcifConsumer(MMcifConsumer consumer)
MMcifParser
addMMcifConsumer
in interface MMcifParser
consumer
- a consumer object.public void clearConsumers()
MMcifParser
clearConsumers
in interface MMcifParser
public void removeMMcifConsumer(MMcifConsumer consumer)
MMcifParser
removeMMcifConsumer
in interface MMcifParser
public static void main(java.lang.String[] args)
public void parse(java.io.InputStream inStream) throws java.io.IOException
MMcifParser
parse
in interface MMcifParser
inStream
- InputStream to parse from.java.io.IOException
public void parse(java.io.BufferedReader buf) throws java.io.IOException
MMcifParser
parse
in interface MMcifParser
buf
- a BufferedReader.java.io.IOException
public void triggerGeneric(java.lang.String category, java.util.List<java.lang.String> loopFields, java.util.List<java.lang.String> lineData)
public void triggerNewEntity(Entity entity)
public void triggerNewEntityPolySeq(EntityPolySeq epolseq)
public void triggerNewChemComp(ChemComp cc)
public void triggerNewStructAsym(StructAsym sasym)
public void triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly pen)
public void triggerNewStructKeywords(StructKeywords kw)
public void triggerNewRefine(Refine r)
public void triggerDocumentStart()
public void triggerDocumentEnd()