Class 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
    • 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
      • 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()