Package org.biojava.bio.structure.io.mmcif

Class SimpleMMcifParser

java.lang.Object

org.biojava.bio.structure.io.mmcif.SimpleMMcifParser

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

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

Constructor Summary

Constructors

Constructor	Description
SimpleMMcifParser()

Method Summary

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 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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

LOOP_END

public static final java.lang.String LOOP_END

See Also:

Constant Field Values

LOOP_START

public static final java.lang.String LOOP_START

See Also:

Constant Field Values

FIELD_LINE

public static final java.lang.String FIELD_LINE

See Also:

Constant Field Values

STRING_LIMIT

public static final java.lang.String STRING_LIMIT

See Also:

Constant Field Values

logger

public static java.util.logging.Logger logger

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(java.lang.String[] args)

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 interface MMcifParser

Parameters:

inStream - InputStream to parse from.

Throws:

java.io.IOException

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 interface MMcifParser

Parameters:

buf - a BufferedReader.

Throws:

java.io.IOException

triggerGeneric

public void triggerGeneric(java.lang.String category,
                           java.util.List<java.lang.String> loopFields,
                           java.util.List<java.lang.String> lineData)

triggerNewEntity

public void triggerNewEntity(Entity entity)

triggerNewEntityPolySeq

public void triggerNewEntityPolySeq(EntityPolySeq epolseq)

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()