org.jmol.adapter.smarter
public class Resolver extends Object
Constructor and Description |
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Resolver() |
Modifier and Type | Method and Description |
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private static boolean |
checkAims(String[] lines) |
private static boolean |
checkAlchemy(String line) |
private static boolean |
checkCastep(String[] lines) |
private static boolean |
checkCrystal(String[] lines) |
private static boolean |
checkCube(String[] lines) |
private static boolean |
checkFoldingXyz(String[] lines) |
private static boolean |
checkGenNBO(String[] lines) |
private static boolean |
checkGromacs(String[] lines) |
private static String |
checkHeaderContains(String header) |
private static String |
checkLineStarts(String[] lines) |
private static boolean |
checkMol(String[] lines) |
private static boolean |
checkMopacGraphf(String[] lines) |
private static boolean |
checkOdyssey(String[] lines) |
private static String |
checkSpecial(int nLines,
String[] lines,
boolean isEnd) |
(package private) static StringBuffer |
checkSpecialData(InputStream is,
String[] zipDirectory)
called by SmarterJmolAdapter to see if we have a Spartan directory and, if so,
open it and get all the data into the correct order.
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(package private) static String[] |
checkSpecialInZip(String[] zipDirectory)
called by SmarterJmolAdapter to see if we can automatically assign a file
from the zip file.
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private static String |
checkType(String[][] typeTags,
String type) |
private static boolean |
checkWien2k(String[] lines) |
private static boolean |
checkXyz(String[] lines) |
private static String |
determineAtomSetCollectionReader(BufferedReader bufferedReader,
boolean returnLines)
the main resolver method.
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(package private) static Object |
DOMResolve(Object DOMNode,
Map<String,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.
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(package private) static Object |
getAtomCollectionReader(String fullName,
String type,
BufferedReader bufferedReader,
Map<String,Object> htParams,
int ptFile)
the main method for reading files.
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(package private) static String |
getFileType(BufferedReader br)
From SmarterJmolAdapter.getFileTypeName(Object atomSetCollectionOrReader)
just return the file type with no exception issues
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static String |
getReaderClassBase(String type) |
private static String |
getReaderFromType(String type) |
private static String[] |
getSpartanDirs(String outputFileData)
read the output file from the Spartan directory and decide from that what
files need to be read and in what order - usually M0001 or a set of Profiles.
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private static String[] |
getSpartanFileList(String name,
String[] dirNums)
returns the list of files to read for every Spartan spardir.
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private static String |
getXmlType(netscape.javascript.JSObject DOMNode) |
private static String |
getXmlType(String header) |
(package private) static String[] |
specialLoad(String name,
String type)
Special loading for file directories.
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private static final String classBase
private static final String[] readerSets
private static final String CML_NAMESPACE_URI
private static final int SPECIAL_JME
private static final int SPECIAL_MOPACGRAPHF
private static final int SPECIAL_ODYSSEY
private static final int SPECIAL_MOL
private static final int SPECIAL_XYZ
private static final int SPECIAL_FOLDINGXYZ
private static final int SPECIAL_CUBE
private static final int SPECIAL_ALCHEMY
private static final int SPECIAL_WIEN
private static final int SPECIAL_CASTEP
private static final int SPECIAL_AIMS
private static final int SPECIAL_CRYSTAL
private static final int SPECIAL_GROMACS
private static final int SPECIAL_GENNBO
public static final int SPECIAL_ARGUS_XML
public static final int SPECIAL_CML_XML
public static final int SPECIAL_CHEM3D_XML
public static final int SPECIAL_MOLPRO_XML
public static final int SPECIAL_ODYSSEY_XML
public static final int SPECIAL_XSD_XML
public static final int SPECIAL_VASP_XML
public static final int SPECIAL_QE_XML
public static final int SPECIAL_ARGUS_DOM
public static final int SPECIAL_CML_DOM
public static final int SPECIAL_CHEM3D_DOM
public static final int SPECIAL_MOLPRO_DOM
public static final int SPECIAL_ODYSSEY_DOM
public static final int SPECIAL_XSD_DOM
public static final int SPECIAL_VASP_DOM
public static final String[][] specialTags
private static final int LEADER_CHAR_MAX
private static final String[] cubeFileStartRecords
private static final String[] mol2Records
private static final String[] webmoFileStartRecords
private static final String[] moldenFileStartRecords
private static final String[] dcdFileStartRecords
private static final String[][] fileStartsWithRecords
private static final String[] pqrLineStartRecords
private static final String[] p2nLineStartRecords
private static final String[] pdbLineStartRecords
private static final String[] shelxLineStartRecords
private static final String[] cifLineStartRecords
private static final String[] ghemicalMMLineStartRecords
private static final String[] jaguarLineStartRecords
private static final String[] mdlLineStartRecords
private static final String[] spartanSmolLineStartRecords
private static final String[] csfLineStartRecords
private static final String[] mdTopLineStartRecords
private static final String[] hyperChemLineStartRecords
private static final String[] vaspOutcarLineStartRecords
private static final String[][] lineStartsWithRecords
private static final String[] sptContainsRecords
private static final String[] xmlContainsRecords
private static final String[] gaussianContainsRecords
private static final String[] ampacContainsRecords
private static final String[] mopacContainsRecords
private static final String[] qchemContainsRecords
private static final String[] gamessUKContainsRecords
private static final String[] gamessUSContainsRecords
private static final String[] spartanBinaryContainsRecords
private static final String[] spartanContainsRecords
private static final String[] adfContainsRecords
private static final String[] dgridContainsRecords
private static final String[] dmolContainsRecords
private static final String[] gulpContainsRecords
private static final String[] psiContainsRecords
private static final String[] nwchemContainsRecords
private static final String[] uicrcifContainsRecords
private static final String[] crystalContainsRecords
private static final String[] espressoContainsRecords
private static final String[] siestaContainsRecords
private static final String[][] headerContainsRecords
static String getFileType(BufferedReader br)
br
- static String[] specialLoad(String name, String type)
name
- type
- static String[] checkSpecialInZip(String[] zipDirectory)
zipDirectory
- static StringBuffer checkSpecialData(InputStream is, String[] zipDirectory)
is
- zipDirectory
- static Object getAtomCollectionReader(String fullName, String type, BufferedReader bufferedReader, Map<String,Object> htParams, int ptFile) throws Exception
fullName
- type
- bufferedReader
- htParams
- ptFile
- Exception
static Object DOMResolve(Object DOMNode, Map<String,Object> htParams) throws Exception
DOMNode
- htParams
- Exception
private static String[] getSpartanFileList(String name, String[] dirNums)
name
- dirNums
- private static String[] getSpartanDirs(String outputFileData)
outputFileData
- private static String getXmlType(netscape.javascript.JSObject DOMNode)
private static String determineAtomSetCollectionReader(BufferedReader bufferedReader, boolean returnLines) throws Exception
bufferedReader
- returnLines
- Exception
private static String checkHeaderContains(String header) throws Exception
Exception
private static boolean checkAims(String[] lines)
private static boolean checkAlchemy(String line)
private static boolean checkCastep(String[] lines)
private static boolean checkCrystal(String[] lines)
private static boolean checkCube(String[] lines)
private static boolean checkFoldingXyz(String[] lines)
lines
- First lines of the files.private static boolean checkGenNBO(String[] lines)
private static boolean checkGromacs(String[] lines)
private static boolean checkMol(String[] lines)
private static boolean checkMopacGraphf(String[] lines)
lines
- First lines of the files.private static boolean checkOdyssey(String[] lines)
private static boolean checkWien2k(String[] lines)
private static boolean checkXyz(String[] lines)