Class SimpleMMcifParser
- java.lang.Object
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- org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
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- All Implemented Interfaces:
MMcifParser
public class SimpleMMcifParser extends Object implements MMcifParser
A simple mmCif file parser Usage:String file = "path/to/mmcif/file"; StructureIOFile pdbreader = new MMCIFFileReader(); Structure s = pdbreader.getStructure(file); System.out.println(s); // you can convert it to a PDB file... System.out.println(s.toPDB());
For more documentation see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure.- Since:
- 1.7
- Author:
- Andreas Prlic, Jose Duarte
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Field Summary
Fields Modifier and Type Field Description static String
COMMENT_CHAR
static String
FIELD_LINE
static String
LOOP_START
static String
MMCIF_TOP_HEADER
The header appearing at the beginning of a mmCIF file.static String
STRING_LIMIT
Quoting character ; (multi-line quoting)
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Constructor Summary
Constructors Constructor Description SimpleMMcifParser()
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Method Summary
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Field Detail
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MMCIF_TOP_HEADER
public static final String MMCIF_TOP_HEADER
The header appearing at the beginning of a mmCIF file. A "block code" can be added to it of no more than 32 chars. See http://www.iucr.org/__data/assets/pdf_file/0019/22618/cifguide.pdf- See Also:
- Constant Field Values
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COMMENT_CHAR
public static final String COMMENT_CHAR
- See Also:
- Constant Field Values
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LOOP_START
public static final String LOOP_START
- See Also:
- Constant Field Values
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FIELD_LINE
public static final String FIELD_LINE
- See Also:
- Constant Field Values
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STRING_LIMIT
public static final String STRING_LIMIT
Quoting character ; (multi-line quoting)- See Also:
- Constant Field Values
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Constructor Detail
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SimpleMMcifParser
public SimpleMMcifParser()
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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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parse
public void parse(InputStream inStream) throws 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:
IOException
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parse
public void parse(BufferedReader buf) throws 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:
IOException
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triggerNewPdbxStructOper
public void triggerNewPdbxStructOper(PdbxStructOperList structOper)
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triggerNewStructNcsOper
public void triggerNewStructNcsOper(StructNcsOper sNcsOper)
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triggerNewAtomSites
public void triggerNewAtomSites(AtomSites atomSites)
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triggerGeneric
public void triggerGeneric(String category, List<String> loopFields, List<String> lineData)
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triggerNewEntity
public void triggerNewEntity(Entity entity)
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triggerNewEntityPoly
public void triggerNewEntityPoly(EntityPoly entityPoly)
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triggerNewEntityPolySeq
public void triggerNewEntityPolySeq(EntityPolySeq epolseq)
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triggerNewEntitySrcGen
public void triggerNewEntitySrcGen(EntitySrcGen entitySrcGen)
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triggerNewEntitySrcNat
public void triggerNewEntitySrcNat(EntitySrcNat entitySrcNat)
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triggerNewEntitySrcSyn
public void triggerNewEntitySrcSyn(EntitySrcSyn entitySrcSyn)
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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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triggerNewChemCompDescriptor
public void triggerNewChemCompDescriptor(ChemCompDescriptor ccd)
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