SimpleMMcifParser (biojava 5.3.0 API)

java.lang.Object
- org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser

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

Field Summary

Fields
Modifier and Type	Field and 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)

Constructor Summary

Constructors
Constructor and Description

SimpleMMcifParser()

Constructors
Constructor and Description
`SimpleMMcifParser()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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(String[] args)`
`void`	`parse(BufferedReader buf)` Start the actual parsing.
`void`	`parse(InputStream inStream)` Start the actual parsing.
`void`	`removeMMcifConsumer(MMcifConsumer consumer)` remove a single consumer from the parser
`void`	`triggerDocumentEnd()`
`void`	`triggerDocumentStart()`
`void`	`triggerGeneric(String category, List<String> loopFields, List<String> lineData)`
`void`	`triggerNewAtomSites(AtomSites atomSites)`
`void`	`triggerNewChemComp(ChemComp cc)`
`void`	`triggerNewChemCompDescriptor(ChemCompDescriptor ccd)`
`void`	`triggerNewEntity(Entity entity)`
`void`	`triggerNewEntityPoly(EntityPoly entityPoly)`
`void`	`triggerNewEntityPolySeq(EntityPolySeq epolseq)`
`void`	`triggerNewEntitySrcGen(EntitySrcGen entitySrcGen)`
`void`	`triggerNewEntitySrcNat(EntitySrcNat entitySrcNat)`
`void`	`triggerNewEntitySrcSyn(EntitySrcSyn entitySrcSyn)`
`void`	`triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly pen)`
`void`	`triggerNewPdbxStructOper(PdbxStructOperList structOper)`
`void`	`triggerNewRefine(Refine r)`
`void`	`triggerNewStructAsym(StructAsym sasym)`
`void`	`triggerNewStructKeywords(StructKeywords kw)`
`void`	`triggerNewStructNcsOper(StructNcsOper sNcsOper)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - 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
  - COMMENT_CHAR
```
public static final String COMMENT_CHAR
```
    See Also:
    
    Constant Field Values
  - LOOP_START
```
public static final String LOOP_START
```
    See Also:
    
    Constant Field Values
  - FIELD_LINE
```
public static final String FIELD_LINE
```
    See Also:
    
    Constant Field Values
  - STRING_LIMIT
```
public static final String STRING_LIMIT
```
    Quoting character ; (multi-line quoting)
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SimpleMMcifParser
```
public SimpleMMcifParser()
```
- Method Detail
  - 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 interface MMcifParser
    
    Parameters:
    
    consumer - a consumer object.
  - clearConsumers
```
public void clearConsumers()
```
    Description copied from interface: MMcifParser
    
    Remove all consumers from the parser.
    
    Specified by:
    
    clearConsumers in interface MMcifParser
  - removeMMcifConsumer
```
public void removeMMcifConsumer(MMcifConsumer consumer)
```
    Description copied from interface: MMcifParser
    
    remove a single consumer from the parser
    
    Specified by:
    
    removeMMcifConsumer in interface MMcifParser
  - main
```
public static void main(String[] args)
```
  - 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 interface MMcifParser
    
    Parameters:
    
    inStream - InputStream to parse from.
    
    Throws:
    
    IOException
  - 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 interface MMcifParser
    
    Parameters:
    
    buf - a BufferedReader.
    
    Throws:
    
    IOException
  - triggerNewPdbxStructOper
```
public void triggerNewPdbxStructOper(PdbxStructOperList structOper)
```
  - triggerNewStructNcsOper
```
public void triggerNewStructNcsOper(StructNcsOper sNcsOper)
```
  - triggerNewAtomSites
```
public void triggerNewAtomSites(AtomSites atomSites)
```
  - triggerGeneric
```
public void triggerGeneric(String category,
                           List<String> loopFields,
                           List<String> lineData)
```
  - triggerNewEntity
```
public void triggerNewEntity(Entity entity)
```
  - triggerNewEntityPoly
```
public void triggerNewEntityPoly(EntityPoly entityPoly)
```
  - triggerNewEntityPolySeq
```
public void triggerNewEntityPolySeq(EntityPolySeq epolseq)
```
  - triggerNewEntitySrcGen
```
public void triggerNewEntitySrcGen(EntitySrcGen entitySrcGen)
```
  - triggerNewEntitySrcNat
```
public void triggerNewEntitySrcNat(EntitySrcNat entitySrcNat)
```
  - triggerNewEntitySrcSyn
```
public void triggerNewEntitySrcSyn(EntitySrcSyn entitySrcSyn)
```
  - triggerNewChemComp
```
public void triggerNewChemComp(ChemComp cc)
```
  - triggerNewStructAsym
```
public void triggerNewStructAsym(StructAsym sasym)
```
  - triggerNewPdbxEntityNonPoly
```
public void triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly pen)
```
  - triggerNewStructKeywords
```
public void triggerNewStructKeywords(StructKeywords kw)
```
  - triggerNewRefine
```
public void triggerNewRefine(Refine r)
```
  - triggerDocumentStart
```
public void triggerDocumentStart()
```
  - triggerDocumentEnd
```
public void triggerDocumentEnd()
```
  - triggerNewChemCompDescriptor
```
public void triggerNewChemCompDescriptor(ChemCompDescriptor ccd)
```

Class SimpleMMcifParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MMCIF_TOP_HEADER

COMMENT_CHAR

LOOP_START

FIELD_LINE

STRING_LIMIT

Constructor Detail

SimpleMMcifParser

Method Detail

addMMcifConsumer

clearConsumers

removeMMcifConsumer

main

parse

parse

triggerNewPdbxStructOper

triggerNewStructNcsOper

triggerNewAtomSites

triggerGeneric

triggerNewEntity

triggerNewEntityPoly

triggerNewEntityPolySeq

triggerNewEntitySrcGen

triggerNewEntitySrcNat

triggerNewEntitySrcSyn

triggerNewChemComp

triggerNewStructAsym

triggerNewPdbxEntityNonPoly

triggerNewStructKeywords

triggerNewRefine

triggerDocumentStart

triggerDocumentEnd

triggerNewChemCompDescriptor