Package org.jmol.adapter.smarter

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:

    • cdxMagic

      private static byte[] cdxMagic

    • 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)

    • bytesMatch

      private static boolean bytesMatch(byte[] a, byte[] b)

    • 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)