Package org.jmol.adapter.smarter

Class Resolver

  • public class Resolver
extends java.lang.Object

    • Field Detail

      • readerSets

        private static final java.lang.String[] readerSets

      • CML_NAMESPACE_URI

        private static final java.lang.String CML_NAMESPACE_URI
        See Also:
        Constant Field Values

      • sptRecords

        private static final java.lang.String[] sptRecords

      • m3dStartRecords

        private static final java.lang.String[] m3dStartRecords

      • cubeFileStartRecords

        private static final java.lang.String[] cubeFileStartRecords

      • mol2Records

        private static final java.lang.String[] mol2Records

      • webmoFileStartRecords

        private static final java.lang.String[] webmoFileStartRecords

      • moldenFileStartRecords

        private static final java.lang.String[] moldenFileStartRecords

      • dcdFileStartRecords

        private static final java.lang.String[] dcdFileStartRecords

      • tlsDataOnlyFileStartRecords

        private static final java.lang.String[] tlsDataOnlyFileStartRecords

      • inputFileStartRecords

        private static final java.lang.String[] inputFileStartRecords

      • magresFileStartRecords

        private static final java.lang.String[] magresFileStartRecords

      • pymolStartRecords

        private static final java.lang.String[] pymolStartRecords

      • janaStartRecords

        private static final java.lang.String[] janaStartRecords

      • jsonStartRecords

        private static final java.lang.String[] jsonStartRecords

      • jcampdxStartRecords

        private static final java.lang.String[] jcampdxStartRecords

      • jmoldataStartRecords

        private static final java.lang.String[] jmoldataStartRecords

      • pqrStartRecords

        private static final java.lang.String[] pqrStartRecords

      • p2nStartRecords

        private static final java.lang.String[] p2nStartRecords

      • xmlStartRecords

        private static final java.lang.String[] xmlStartRecords

      • fileStartsWithRecords

        private static final java.lang.String[][] fileStartsWithRecords

      • mmcifLineStartRecords

        private static final java.lang.String[] mmcifLineStartRecords

      • cifLineStartRecords

        private static final java.lang.String[] cifLineStartRecords

      • pdbLineStartRecords

        private static final java.lang.String[] pdbLineStartRecords

      • cgdLineStartRecords

        private static final java.lang.String[] cgdLineStartRecords

      • shelxLineStartRecords

        private static final java.lang.String[] shelxLineStartRecords

      • ghemicalMMLineStartRecords

        private static final java.lang.String[] ghemicalMMLineStartRecords

      • jaguarLineStartRecords

        private static final java.lang.String[] jaguarLineStartRecords

      • mdlLineStartRecords

        private static final java.lang.String[] mdlLineStartRecords

      • spartanSmolLineStartRecords

        private static final java.lang.String[] spartanSmolLineStartRecords

      • csfLineStartRecords

        private static final java.lang.String[] csfLineStartRecords

      • mdTopLineStartRecords

        private static final java.lang.String[] mdTopLineStartRecords

      • hyperChemLineStartRecords

        private static final java.lang.String[] hyperChemLineStartRecords

      • vaspOutcarLineStartRecords

        private static final java.lang.String[] vaspOutcarLineStartRecords

      • lineStartsWithRecords

        private static final java.lang.String[][] lineStartsWithRecords

      • bilbaoContainsRecords

        private static final java.lang.String[] bilbaoContainsRecords

      • xmlContainsRecords

        private static final java.lang.String[] xmlContainsRecords

      • gaussianContainsRecords

        private static final java.lang.String[] gaussianContainsRecords

      • ampacContainsRecords

        private static final java.lang.String[] ampacContainsRecords

      • mopacContainsRecords

        private static final java.lang.String[] mopacContainsRecords

      • qchemContainsRecords

        private static final java.lang.String[] qchemContainsRecords

      • gamessUKContainsRecords

        private static final java.lang.String[] gamessUKContainsRecords

      • gamessUSContainsRecords

        private static final java.lang.String[] gamessUSContainsRecords

      • spartanBinaryContainsRecords

        private static final java.lang.String[] spartanBinaryContainsRecords

      • spartanContainsRecords

        private static final java.lang.String[] spartanContainsRecords

      • adfContainsRecords

        private static final java.lang.String[] adfContainsRecords

      • psiContainsRecords

        private static final java.lang.String[] psiContainsRecords

      • nwchemContainsRecords

        private static final java.lang.String[] nwchemContainsRecords

      • uicrcifContainsRecords

        private static final java.lang.String[] uicrcifContainsRecords

      • dgridContainsRecords

        private static final java.lang.String[] dgridContainsRecords

      • crystalContainsRecords

        private static final java.lang.String[] crystalContainsRecords

      • dmolContainsRecords

        private static final java.lang.String[] dmolContainsRecords

      • gulpContainsRecords

        private static final java.lang.String[] gulpContainsRecords

      • espressoContainsRecords

        private static final java.lang.String[] espressoContainsRecords

      • siestaContainsRecords

        private static final java.lang.String[] siestaContainsRecords

      • xcrysDenContainsRecords

        private static final java.lang.String[] xcrysDenContainsRecords

      • mopacArchiveContainsRecords

        private static final java.lang.String[] mopacArchiveContainsRecords

      • abinitContainsRecords

        private static final java.lang.String[] abinitContainsRecords

      • gaussianFchkContainsRecords

        private static final java.lang.String[] gaussianFchkContainsRecords

      • inputContainsRecords

        private static final java.lang.String[] inputContainsRecords

      • aflowContainsRecords

        private static final java.lang.String[] aflowContainsRecords

      • headerContainsRecords

        private static final java.lang.String[][] headerContainsRecords

    • Constructor Detail

      • Resolver

        public Resolver()

    • Method Detail

      • getReaderClassBase

        public static final java.lang.String getReaderClassBase​(java.lang.String type)

      • getFileType

        static java.lang.String getFileType​(java.io.BufferedReader br)
        From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
        Parameters:
        br -
        Returns:
        String file type

      • getAtomCollectionReader

        static java.lang.Object getAtomCollectionReader​(java.lang.String fullName,
                                                java.lang.String type,
                                                java.lang.Object readerOrDocument,
                                                java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                int ptFile)
                                         throws java.lang.Exception
        the main method for reading files. Called from SmarterJmolAdapter when reading a file, reading a set of files, or reading a ZIP file
        Parameters:
        fullName -
        type -
        readerOrDocument -
        htParams -
        ptFile -
        Returns:
        an AtomSetCollection or a String error
        Throws:
        java.lang.Exception

      • getReader

        public static java.lang.Object getReader​(java.lang.String readerName,
                                         java.util.Map<java.lang.String,​java.lang.Object> htParams)
        Get a reader based on its name.
        Parameters:
        readerName -
        htParams -
        Returns:
        AtomSetCollectionReader or error message

      • getReaderFromType

        private static final java.lang.String getReaderFromType​(java.lang.String type)

      • split

        private static java.lang.String split​(java.lang.String a,
                                      int n)

      • DOMResolve

        public static java.lang.Object DOMResolve​(java.util.Map<java.lang.String,​java.lang.Object> htParams)
                                   throws java.lang.Exception
        a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page. -- Egon Willighagen
        Parameters:
        htParams -
        Returns:
        an AtomSetCollection or a String error
        Throws:
        java.lang.Exception

      • determineAtomSetCollectionReader

        private static java.lang.String determineAtomSetCollectionReader​(java.lang.Object readerOrDocument,
                                                                 boolean returnLines)
                                                          throws java.lang.Exception
        the main resolver method. One of the great advantages of Jmol is that it can smartly determine a file type from its contents. In cases where this is not possible, one can force a file type using a prefix to a filename. For example: load mol2::xxxx.whatever This is only necessary for a few file types, where only numbers are involved -- molecular dynamics coordinate files, for instance (mdcrd).
        Parameters:
        readerOrDocument -
        returnLines -
        Returns:
        readerName or a few lines, if requested, or null
        Throws:
        java.lang.Exception

      • getBinaryType

        public static java.lang.String getBinaryType​(java.io.InputStream inputStream)

      • checkFileStart

        private static java.lang.String checkFileStart​(java.lang.String leader)

      • checkSpecial1

        private static final java.lang.String checkSpecial1​(int nLines,
                                                    java.lang.String[] lines,
                                                    java.lang.String leader)

      • checkAims

        private static boolean checkAims​(java.lang.String[] lines)

      • checkAlchemy

        private static boolean checkAlchemy​(java.lang.String line)

      • checkCube

        private static boolean checkCube​(java.lang.String[] lines)

      • checkFoldingXyz

        private static boolean checkFoldingXyz​(java.lang.String[] lines)
        Parameters:
        lines - First lines of the files.
        Returns:
        Indicates if the file may be a Folding@Home file.

      • checkGenNBO

        private static boolean checkGenNBO​(java.lang.String[] lines,
                                   java.lang.String leader)

      • checkMol

        private static int checkMol​(java.lang.String[] lines)

      • checkMopacGraphf

        private static boolean checkMopacGraphf​(java.lang.String[] lines)
        Parameters:
        lines - First lines of the files.
        Returns:
        Indicates if the file is a Mopac GRAPHF output file.

      • checkOdyssey

        private static boolean checkOdyssey​(java.lang.String[] lines)

      • checkWien2k

        private static boolean checkWien2k​(java.lang.String[] lines)

      • checkXyz

        private static int checkXyz​(java.lang.String[] lines)

      • checkLineStarts

        private static java.lang.String checkLineStarts​(java.lang.String[] lines)

      • checkHeaderContains

        private static java.lang.String checkHeaderContains​(java.lang.String header)
                                             throws java.lang.Exception
        Throws:
        java.lang.Exception

      • getXmlType

        private static java.lang.String getXmlType​(java.lang.String header)
                                    throws java.lang.Exception
        Throws:
        java.lang.Exception

      • checkSpecial2

        private static final java.lang.String checkSpecial2​(java.lang.String[] lines)

      • checkCrystal

        private static boolean checkCrystal​(java.lang.String[] lines)

      • checkGromacs

        private static boolean checkGromacs​(java.lang.String[] lines)

      • checkCastepVasp

        private static java.lang.String checkCastepVasp​(java.lang.String[] lines)