Class Resolver

java.lang.Object
org.jmol.adapter.smarter.Resolver

public class Resolver extends Object
  • Field Details

    • classBase

      private static final String classBase
      See Also:
    • readerSets

      private static final String[] readerSets
    • CML_NAMESPACE_URI

      private static final String CML_NAMESPACE_URI
      See Also:
    • LEADER_CHAR_MAX

      private static final int LEADER_CHAR_MAX
      See Also:
    • 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
    • orcaInputLineStartRecords

      private static final String[] orcaInputLineStartRecords
    • 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
    • optimadeContainsRecords

      private static final String[] optimadeContainsRecords
    • jsonArrayContainsRecords

      private static final String[] jsonArrayContainsRecords
    • orcaContainsRecords

      private static final String[] orcaContainsRecords
    • 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
    • jsonContainsRecords

      private static final String[][] jsonContainsRecords
  • Constructor Details

    • Resolver

      public Resolver()
  • Method Details

    • getReaderClassBase

      public static final String getReaderClassBase(String type)
    • getFileType

      public 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)
    • split

      private static String split(String a, int n)
    • 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, Map<String,Object> htParams) 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 -
      htParams -
      Returns:
      readerName or a few lines, if requested, or null
      Throws:
      Exception
    • getBinaryType

      public static String getBinaryType(InputStream inputStream)
    • checkFileStart

      private static String checkFileStart(String leader)
    • checkSpecial1

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

      private static boolean checkXSF(String[] lines)
    • 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)
    • checkHeaderContains

      private static String checkHeaderContains(String header) throws Exception
      Throws:
      Exception
    • checkJSONContains

      private static String checkJSONContains(String header) throws Exception
      Throws:
      Exception
    • checkHeaderRecords

      private static String checkHeaderRecords(String header, String[] recordTags) throws Exception
      Throws:
      Exception
    • getXmlType

      private static String getXmlType(String header) throws Exception
      Throws:
      Exception
    • 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)