Package org.jmol.adapter.smarter
Class Resolver
- java.lang.Object
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- org.jmol.adapter.smarter.Resolver
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public class Resolver extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description private static java.lang.String[]
abinitContainsRecords
private static java.lang.String[]
adfContainsRecords
private static java.lang.String[]
aflowContainsRecords
private static java.lang.String[]
ampacContainsRecords
private static java.lang.String[]
bilbaoContainsRecords
private static java.lang.String[]
cfiStartRecords
private static java.lang.String[]
cgdLineStartRecords
private static java.lang.String[]
cif2StartRecords
private static java.lang.String[]
cifLineStartRecords
private static java.lang.String
classBase
private static java.lang.String
CML_NAMESPACE_URI
private static java.lang.String[]
crystalContainsRecords
private static java.lang.String[]
csfLineStartRecords
private static java.lang.String[]
cubeFileStartRecords
private static java.lang.String[]
dcdFileStartRecords
private static java.lang.String[]
dgridContainsRecords
private static java.lang.String[]
dmolContainsRecords
private static java.lang.String[]
espressoContainsRecords
private static java.lang.String[][]
fileStartsWithRecords
private static java.lang.String[]
gamessUKContainsRecords
private static java.lang.String[]
gamessUSContainsRecords
private static java.lang.String[]
gaussianContainsRecords
private static java.lang.String[]
gaussianFchkContainsRecords
private static java.lang.String[]
ghemicalMMLineStartRecords
private static java.lang.String[]
gulpContainsRecords
private static java.lang.String[][]
headerContainsRecords
private static java.lang.String[]
hyperChemLineStartRecords
private static java.lang.String[]
inputContainsRecords
private static java.lang.String[]
inputFileStartRecords
private static java.lang.String[]
jaguarLineStartRecords
private static java.lang.String[]
janaStartRecords
private static java.lang.String[]
jcampdxStartRecords
private static java.lang.String[]
jmoldataStartRecords
private static java.lang.String[]
jsonStartRecords
private static int
LEADER_CHAR_MAX
private static java.lang.String[][]
lineStartsWithRecords
private static java.lang.String[]
m3dStartRecords
private static java.lang.String[]
magCifContainsRecords
private static java.lang.String[]
magresFileStartRecords
private static java.lang.String[]
mdlLineStartRecords
private static java.lang.String[]
mdTopLineStartRecords
private static java.lang.String[]
mmcifLineStartRecords
private static java.lang.String[]
mol2Records
private static java.lang.String[]
moldenFileStartRecords
private static java.lang.String[]
mopacArchiveContainsRecords
private static java.lang.String[]
mopacContainsRecords
private static int[]
n
private static java.lang.String[]
nwchemContainsRecords
private static java.lang.String[]
p2nStartRecords
private static java.lang.String[]
pdbLineStartRecords
private static java.lang.String[]
pqrStartRecords
private static java.lang.String[]
psiContainsRecords
private static java.lang.String[]
pymolStartRecords
private static java.lang.String[]
qchemContainsRecords
private static java.lang.String[]
qcJsonContainsRecords
private static java.lang.String[]
readerSets
private static java.lang.String[]
shelxLineStartRecords
private static java.lang.String[]
siestaContainsRecords
private static java.lang.String[]
spartanBinaryContainsRecords
private static java.lang.String[]
spartanContainsRecords
private static java.lang.String[]
spartanSmolLineStartRecords
private static java.lang.String[]
sptRecords
private static java.lang.String[]
tlsDataOnlyFileStartRecords
private static java.lang.String[]
uicrcifContainsRecords
private static java.lang.String[]
vaspOutcarLineStartRecords
private static java.lang.String[]
webmoFileStartRecords
private static java.lang.String[]
xcrysDenContainsRecords
private static java.lang.String[]
xmlContainsRecords
private static java.lang.String[]
xmlStartRecords
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Constructor Summary
Constructors Constructor Description Resolver()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description private static boolean
checkAims(java.lang.String[] lines)
private static boolean
checkAlchemy(java.lang.String line)
private static java.lang.String
checkCastepVaspSiesta(java.lang.String[] lines)
private static boolean
checkCrystal(java.lang.String[] lines)
private static boolean
checkCube(java.lang.String[] lines)
private static boolean
checkFAH(java.lang.String[] lines)
private static java.lang.String
checkFileStart(java.lang.String leader)
private static boolean
checkFoldingXyz(java.lang.String[] lines)
private static boolean
checkGenNBO(java.lang.String[] lines, java.lang.String leader)
private static boolean
checkGromacs(java.lang.String[] lines)
private static java.lang.String
checkHeaderContains(java.lang.String header)
private static java.lang.String
checkLineStarts(java.lang.String[] lines)
private static int
checkMol(java.lang.String[] lines)
private static boolean
checkMopacGraphf(java.lang.String[] lines)
private static boolean
checkOdyssey(java.lang.String[] lines)
private static java.lang.String
checkSpecial1(int nLines, java.lang.String[] lines, java.lang.String leader)
private static java.lang.String
checkSpecial2(java.lang.String[] lines)
private static boolean
checkWien2k(java.lang.String[] lines)
private static int
checkXyz(java.lang.String[] lines)
private static java.lang.String
determineAtomSetCollectionReader(java.lang.Object readerOrDocument, boolean returnLines)
the main resolver method.static java.lang.Object
DOMResolve(java.util.Map<java.lang.String,java.lang.Object> htParams)
a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.(package private) 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)
the main method for reading files.static java.lang.String
getBinaryType(java.io.InputStream inputStream)
static java.lang.String
getFileType(java.io.BufferedReader br)
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issuesstatic 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.static java.lang.String
getReaderClassBase(java.lang.String type)
private static java.lang.String
getReaderFromType(java.lang.String type)
private static java.lang.String
getXmlType(java.lang.String header)
private static boolean
isFloat(java.lang.String s)
private static boolean
isInt(java.lang.String s)
private static java.lang.String
split(java.lang.String a, int n)
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Field Detail
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classBase
private static final java.lang.String classBase
- See Also:
- Constant Field Values
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readerSets
private static final java.lang.String[] readerSets
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CML_NAMESPACE_URI
private static final java.lang.String CML_NAMESPACE_URI
- See Also:
- Constant Field Values
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LEADER_CHAR_MAX
private static final int LEADER_CHAR_MAX
- See Also:
- Constant Field Values
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sptRecords
private static final java.lang.String[] sptRecords
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m3dStartRecords
private static final java.lang.String[] m3dStartRecords
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cubeFileStartRecords
private static final java.lang.String[] cubeFileStartRecords
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mol2Records
private static final java.lang.String[] mol2Records
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webmoFileStartRecords
private static final java.lang.String[] webmoFileStartRecords
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moldenFileStartRecords
private static final java.lang.String[] moldenFileStartRecords
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dcdFileStartRecords
private static final java.lang.String[] dcdFileStartRecords
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tlsDataOnlyFileStartRecords
private static final java.lang.String[] tlsDataOnlyFileStartRecords
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inputFileStartRecords
private static final java.lang.String[] inputFileStartRecords
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magresFileStartRecords
private static final java.lang.String[] magresFileStartRecords
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pymolStartRecords
private static final java.lang.String[] pymolStartRecords
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janaStartRecords
private static final java.lang.String[] janaStartRecords
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jsonStartRecords
private static final java.lang.String[] jsonStartRecords
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jcampdxStartRecords
private static final java.lang.String[] jcampdxStartRecords
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jmoldataStartRecords
private static final java.lang.String[] jmoldataStartRecords
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pqrStartRecords
private static final java.lang.String[] pqrStartRecords
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p2nStartRecords
private static final java.lang.String[] p2nStartRecords
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cif2StartRecords
private static final java.lang.String[] cif2StartRecords
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xmlStartRecords
private static final java.lang.String[] xmlStartRecords
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cfiStartRecords
private static final java.lang.String[] cfiStartRecords
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fileStartsWithRecords
private static final java.lang.String[][] fileStartsWithRecords
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n
private static int[] n
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mmcifLineStartRecords
private static final java.lang.String[] mmcifLineStartRecords
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cifLineStartRecords
private static final java.lang.String[] cifLineStartRecords
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pdbLineStartRecords
private static final java.lang.String[] pdbLineStartRecords
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cgdLineStartRecords
private static final java.lang.String[] cgdLineStartRecords
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shelxLineStartRecords
private static final java.lang.String[] shelxLineStartRecords
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ghemicalMMLineStartRecords
private static final java.lang.String[] ghemicalMMLineStartRecords
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jaguarLineStartRecords
private static final java.lang.String[] jaguarLineStartRecords
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mdlLineStartRecords
private static final java.lang.String[] mdlLineStartRecords
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spartanSmolLineStartRecords
private static final java.lang.String[] spartanSmolLineStartRecords
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csfLineStartRecords
private static final java.lang.String[] csfLineStartRecords
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mdTopLineStartRecords
private static final java.lang.String[] mdTopLineStartRecords
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hyperChemLineStartRecords
private static final java.lang.String[] hyperChemLineStartRecords
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vaspOutcarLineStartRecords
private static final java.lang.String[] vaspOutcarLineStartRecords
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lineStartsWithRecords
private static final java.lang.String[][] lineStartsWithRecords
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bilbaoContainsRecords
private static final java.lang.String[] bilbaoContainsRecords
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xmlContainsRecords
private static final java.lang.String[] xmlContainsRecords
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gaussianContainsRecords
private static final java.lang.String[] gaussianContainsRecords
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ampacContainsRecords
private static final java.lang.String[] ampacContainsRecords
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mopacContainsRecords
private static final java.lang.String[] mopacContainsRecords
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qchemContainsRecords
private static final java.lang.String[] qchemContainsRecords
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gamessUKContainsRecords
private static final java.lang.String[] gamessUKContainsRecords
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gamessUSContainsRecords
private static final java.lang.String[] gamessUSContainsRecords
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spartanBinaryContainsRecords
private static final java.lang.String[] spartanBinaryContainsRecords
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spartanContainsRecords
private static final java.lang.String[] spartanContainsRecords
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adfContainsRecords
private static final java.lang.String[] adfContainsRecords
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psiContainsRecords
private static final java.lang.String[] psiContainsRecords
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nwchemContainsRecords
private static final java.lang.String[] nwchemContainsRecords
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uicrcifContainsRecords
private static final java.lang.String[] uicrcifContainsRecords
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dgridContainsRecords
private static final java.lang.String[] dgridContainsRecords
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crystalContainsRecords
private static final java.lang.String[] crystalContainsRecords
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dmolContainsRecords
private static final java.lang.String[] dmolContainsRecords
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gulpContainsRecords
private static final java.lang.String[] gulpContainsRecords
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espressoContainsRecords
private static final java.lang.String[] espressoContainsRecords
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siestaContainsRecords
private static final java.lang.String[] siestaContainsRecords
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xcrysDenContainsRecords
private static final java.lang.String[] xcrysDenContainsRecords
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mopacArchiveContainsRecords
private static final java.lang.String[] mopacArchiveContainsRecords
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abinitContainsRecords
private static final java.lang.String[] abinitContainsRecords
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qcJsonContainsRecords
private static final java.lang.String[] qcJsonContainsRecords
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gaussianFchkContainsRecords
private static final java.lang.String[] gaussianFchkContainsRecords
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inputContainsRecords
private static final java.lang.String[] inputContainsRecords
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aflowContainsRecords
private static final java.lang.String[] aflowContainsRecords
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magCifContainsRecords
private static final java.lang.String[] magCifContainsRecords
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headerContainsRecords
private static final java.lang.String[][] headerContainsRecords
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Method Detail
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getReaderClassBase
public static final java.lang.String getReaderClassBase(java.lang.String type)
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getFileType
public 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
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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
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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
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getReaderFromType
private static final java.lang.String getReaderFromType(java.lang.String type)
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split
private static java.lang.String split(java.lang.String a, int n)
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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
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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
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getBinaryType
public static java.lang.String getBinaryType(java.io.InputStream inputStream)
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checkFileStart
private static java.lang.String checkFileStart(java.lang.String leader)
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checkSpecial1
private static final java.lang.String checkSpecial1(int nLines, java.lang.String[] lines, java.lang.String leader)
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checkAims
private static boolean checkAims(java.lang.String[] lines)
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checkAlchemy
private static boolean checkAlchemy(java.lang.String line)
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isInt
private static boolean isInt(java.lang.String s)
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isFloat
private static boolean isFloat(java.lang.String s)
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checkCube
private static boolean checkCube(java.lang.String[] lines)
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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.
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checkGenNBO
private static boolean checkGenNBO(java.lang.String[] lines, java.lang.String leader)
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checkMol
private static int checkMol(java.lang.String[] lines)
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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.
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checkOdyssey
private static boolean checkOdyssey(java.lang.String[] lines)
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checkWien2k
private static boolean checkWien2k(java.lang.String[] lines)
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checkXyz
private static int checkXyz(java.lang.String[] lines)
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checkLineStarts
private static java.lang.String checkLineStarts(java.lang.String[] lines)
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checkHeaderContains
private static java.lang.String checkHeaderContains(java.lang.String header) throws java.lang.Exception
- Throws:
java.lang.Exception
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getXmlType
private static java.lang.String getXmlType(java.lang.String header) throws java.lang.Exception
- Throws:
java.lang.Exception
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checkSpecial2
private static final java.lang.String checkSpecial2(java.lang.String[] lines)
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checkFAH
private static boolean checkFAH(java.lang.String[] lines)
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checkCrystal
private static boolean checkCrystal(java.lang.String[] lines)
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checkGromacs
private static boolean checkGromacs(java.lang.String[] lines)
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checkCastepVaspSiesta
private static java.lang.String checkCastepVaspSiesta(java.lang.String[] lines)
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