Package org.jmol.adapter.smarter

Class Resolver

  • public class Resolver
extends Object

    • Field Detail

      • readerSets

        private static final String[] readerSets

      • sptRecords

        private static final String[] sptRecords

      • m3dStartRecords

        private static final String[] m3dStartRecords

      • cubeFileStartRecords

        private static final String[] cubeFileStartRecords

      • mol2Records

        private static final String[] mol2Records

      • webmoFileStartRecords

        private static final String[] webmoFileStartRecords

      • moldenFileStartRecords

        private static final String[] moldenFileStartRecords

      • dcdFileStartRecords

        private static final String[] dcdFileStartRecords

      • tlsDataOnlyFileStartRecords

        private static final String[] tlsDataOnlyFileStartRecords

      • inputFileStartRecords

        private static final String[] inputFileStartRecords

      • magresFileStartRecords

        private static final String[] magresFileStartRecords

      • pymolStartRecords

        private static final String[] pymolStartRecords

      • janaStartRecords

        private static final String[] janaStartRecords

      • jsonStartRecords

        private static final String[] jsonStartRecords

      • jcampdxStartRecords

        private static final String[] jcampdxStartRecords

      • jmoldataStartRecords

        private static final String[] jmoldataStartRecords

      • pqrStartRecords

        private static final String[] pqrStartRecords

      • p2nStartRecords

        private static final String[] p2nStartRecords

      • cif2StartRecords

        private static final String[] cif2StartRecords

      • xmlStartRecords

        private static final String[] xmlStartRecords

      • cfiStartRecords

        private static final String[] cfiStartRecords

      • fileStartsWithRecords

        private static final String[][] fileStartsWithRecords

      • n

        private static int[] n

      • mmcifLineStartRecords

        private static final String[] mmcifLineStartRecords

      • cifLineStartRecords

        private static final String[] cifLineStartRecords

      • pdbLineStartRecords

        private static final String[] pdbLineStartRecords

      • cgdLineStartRecords

        private static final String[] cgdLineStartRecords

      • shelxLineStartRecords

        private static final String[] shelxLineStartRecords

      • ghemicalMMLineStartRecords

        private static final String[] ghemicalMMLineStartRecords

      • jaguarLineStartRecords

        private static final String[] jaguarLineStartRecords

      • mdlLineStartRecords

        private static final String[] mdlLineStartRecords

      • spartanSmolLineStartRecords

        private static final String[] spartanSmolLineStartRecords

      • csfLineStartRecords

        private static final String[] csfLineStartRecords

      • mdTopLineStartRecords

        private static final String[] mdTopLineStartRecords

      • hyperChemLineStartRecords

        private static final String[] hyperChemLineStartRecords

      • vaspOutcarLineStartRecords

        private static final String[] vaspOutcarLineStartRecords

      • lineStartsWithRecords

        private static final String[][] lineStartsWithRecords

      • bilbaoContainsRecords

        private static final String[] bilbaoContainsRecords

      • xmlContainsRecords

        private static final String[] xmlContainsRecords

      • gaussianContainsRecords

        private static final String[] gaussianContainsRecords

      • ampacContainsRecords

        private static final String[] ampacContainsRecords

      • mopacContainsRecords

        private static final String[] mopacContainsRecords

      • qchemContainsRecords

        private static final String[] qchemContainsRecords

      • gamessUKContainsRecords

        private static final String[] gamessUKContainsRecords

      • gamessUSContainsRecords

        private static final String[] gamessUSContainsRecords

      • spartanBinaryContainsRecords

        private static final String[] spartanBinaryContainsRecords

      • spartanContainsRecords

        private static final String[] spartanContainsRecords

      • adfContainsRecords

        private static final String[] adfContainsRecords

      • psiContainsRecords

        private static final String[] psiContainsRecords

      • nwchemContainsRecords

        private static final String[] nwchemContainsRecords

      • uicrcifContainsRecords

        private static final String[] uicrcifContainsRecords

      • dgridContainsRecords

        private static final String[] dgridContainsRecords

      • crystalContainsRecords

        private static final String[] crystalContainsRecords

      • dmolContainsRecords

        private static final String[] dmolContainsRecords

      • gulpContainsRecords

        private static final String[] gulpContainsRecords

      • espressoContainsRecords

        private static final String[] espressoContainsRecords

      • siestaContainsRecords

        private static final String[] siestaContainsRecords

      • xcrysDenContainsRecords

        private static final String[] xcrysDenContainsRecords

      • mopacArchiveContainsRecords

        private static final String[] mopacArchiveContainsRecords

      • abinitContainsRecords

        private static final String[] abinitContainsRecords

      • qcJsonContainsRecords

        private static final String[] qcJsonContainsRecords

      • gaussianFchkContainsRecords

        private static final String[] gaussianFchkContainsRecords

      • inputContainsRecords

        private static final String[] inputContainsRecords

      • aflowContainsRecords

        private static final String[] aflowContainsRecords

      • magCifContainsRecords

        private static final String[] magCifContainsRecords

      • headerContainsRecords

        private static final String[][] headerContainsRecords

    • Constructor Detail

      • Resolver

        public Resolver()

    • Method Detail

      • getReaderClassBase

        public static final String getReaderClassBase​(String type)

      • getFileType

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

      • getAtomCollectionReader

        static Object getAtomCollectionReader​(String fullName,
                                      String type,
                                      Object readerOrDocument,
                                      Map<String,​Object> htParams,
                                      int ptFile)
                               throws 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:
        Exception

      • getReader

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

      • getReaderFromType

        private static final String getReaderFromType​(String type)

      • DOMResolve

        public static Object DOMResolve​(Map<String,​Object> htParams)
                         throws 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:
        Exception

      • determineAtomSetCollectionReader

        private static String determineAtomSetCollectionReader​(Object readerOrDocument,
                                                       boolean returnLines)
                                                throws 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:
        Exception

      • checkFileStart

        private static String checkFileStart​(String leader)

      • checkSpecial1

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

      • checkAims

        private static boolean checkAims​(String[] lines)

      • checkAlchemy

        private static boolean checkAlchemy​(String line)

      • isInt

        private static boolean isInt​(String s)

      • isFloat

        private static boolean isFloat​(String s)

      • checkCube

        private static boolean checkCube​(String[] lines)

      • checkFoldingXyz

        private static boolean checkFoldingXyz​(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​(String[] lines,
                                   String leader)

      • checkMol

        private static int checkMol​(String[] lines)

      • checkMopacGraphf

        private static boolean checkMopacGraphf​(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​(String[] lines)

      • checkWien2k

        private static boolean checkWien2k​(String[] lines)

      • checkXyz

        private static int checkXyz​(String[] lines)

      • checkLineStarts

        private static String checkLineStarts​(String[] lines)

      • checkSpecial2

        private static final String checkSpecial2​(String[] lines)

      • checkFAH

        private static boolean checkFAH​(String[] lines)

      • checkCrystal

        private static boolean checkCrystal​(String[] lines)

      • checkGromacs

        private static boolean checkGromacs​(String[] lines)

      • checkCastepVaspSiesta

        private static String checkCastepVaspSiesta​(String[] lines)