Class SimpleMMcifParser

  • All Implemented Interfaces:
    MMcifParser

    public class SimpleMMcifParser
    extends java.lang.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 Detail

      • MMCIF_TOP_HEADER

        public static final java.lang.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
      • STRING_LIMIT

        public static final java.lang.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
      • 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
      • triggerNewPdbxStructOper

        public void triggerNewPdbxStructOper​(PdbxStructOperList structOper)
      • triggerNewStructNcsOper

        public void triggerNewStructNcsOper​(StructNcsOper sNcsOper)
      • triggerNewAtomSites

        public void triggerNewAtomSites​(AtomSites atomSites)
      • 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)
      • 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)