diff options
Diffstat (limited to 'java/joelib2/io')
79 files changed, 0 insertions, 914 deletions
diff --git a/java/joelib2/io/AbstractReaderWriterPipe.class b/java/joelib2/io/AbstractReaderWriterPipe.class Binary files differdeleted file mode 100644 index ddbb542..0000000 --- a/java/joelib2/io/AbstractReaderWriterPipe.class +++ /dev/null diff --git a/java/joelib2/io/BasicIOType.class b/java/joelib2/io/BasicIOType.class Binary files differdeleted file mode 100644 index 402ff79..0000000 --- a/java/joelib2/io/BasicIOType.class +++ /dev/null diff --git a/java/joelib2/io/BasicIOTypeHolder.class b/java/joelib2/io/BasicIOTypeHolder.class Binary files differdeleted file mode 100644 index 6474a44..0000000 --- a/java/joelib2/io/BasicIOTypeHolder.class +++ /dev/null diff --git a/java/joelib2/io/BasicImageWriter.class b/java/joelib2/io/BasicImageWriter.class Binary files differdeleted file mode 100644 index ee6d78c..0000000 --- a/java/joelib2/io/BasicImageWriter.class +++ /dev/null diff --git a/java/joelib2/io/BasicMoleculeWriter.class b/java/joelib2/io/BasicMoleculeWriter.class Binary files differdeleted file mode 100644 index 25d8035..0000000 --- a/java/joelib2/io/BasicMoleculeWriter.class +++ /dev/null diff --git a/java/joelib2/io/BasicReader.class b/java/joelib2/io/BasicReader.class Binary files differdeleted file mode 100644 index 4691f9a..0000000 --- a/java/joelib2/io/BasicReader.class +++ /dev/null diff --git a/java/joelib2/io/IOType.class b/java/joelib2/io/IOType.class Binary files differdeleted file mode 100644 index a5246dc..0000000 --- a/java/joelib2/io/IOType.class +++ /dev/null diff --git a/java/joelib2/io/IOTypeHolder.class b/java/joelib2/io/IOTypeHolder.class Binary files differdeleted file mode 100644 index 0553057..0000000 --- a/java/joelib2/io/IOTypeHolder.class +++ /dev/null diff --git a/java/joelib2/io/ImageWriter.class b/java/joelib2/io/ImageWriter.class Binary files differdeleted file mode 100644 index 7b91751..0000000 --- a/java/joelib2/io/ImageWriter.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeCallback.class b/java/joelib2/io/MoleculeCallback.class Binary files differdeleted file mode 100644 index a83b750..0000000 --- a/java/joelib2/io/MoleculeCallback.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeFileExport.class b/java/joelib2/io/MoleculeFileExport.class Binary files differdeleted file mode 100644 index d0220b6..0000000 --- a/java/joelib2/io/MoleculeFileExport.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeFileHelper.class b/java/joelib2/io/MoleculeFileHelper.class Binary files differdeleted file mode 100644 index 79784b9..0000000 --- a/java/joelib2/io/MoleculeFileHelper.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeFileIO.class b/java/joelib2/io/MoleculeFileIO.class Binary files differdeleted file mode 100644 index 3f9ba6b..0000000 --- a/java/joelib2/io/MoleculeFileIO.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeFileImport.class b/java/joelib2/io/MoleculeFileImport.class Binary files differdeleted file mode 100644 index c03722f..0000000 --- a/java/joelib2/io/MoleculeFileImport.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeIOException.class b/java/joelib2/io/MoleculeIOException.class Binary files differdeleted file mode 100644 index 6602d55..0000000 --- a/java/joelib2/io/MoleculeIOException.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeReader.class b/java/joelib2/io/MoleculeReader.class Binary files differdeleted file mode 100644 index e9459b5..0000000 --- a/java/joelib2/io/MoleculeReader.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeReaderWriterPipe.class b/java/joelib2/io/MoleculeReaderWriterPipe.class Binary files differdeleted file mode 100644 index be071e6..0000000 --- a/java/joelib2/io/MoleculeReaderWriterPipe.class +++ /dev/null diff --git a/java/joelib2/io/MoleculeWriter.class b/java/joelib2/io/MoleculeWriter.class Binary files differdeleted file mode 100644 index 61ba8b2..0000000 --- a/java/joelib2/io/MoleculeWriter.class +++ /dev/null diff --git a/java/joelib2/io/PropertyWriter.class b/java/joelib2/io/PropertyWriter.class Binary files differdeleted file mode 100644 index 7fcf7f5..0000000 --- a/java/joelib2/io/PropertyWriter.class +++ /dev/null diff --git a/java/joelib2/io/types/Amber.class b/java/joelib2/io/types/Amber.class Binary files differdeleted file mode 100644 index 9ce9ae3..0000000 --- a/java/joelib2/io/types/Amber.class +++ /dev/null diff --git a/java/joelib2/io/types/BMP.class b/java/joelib2/io/types/BMP.class Binary files differdeleted file mode 100644 index 464a0f6..0000000 --- a/java/joelib2/io/types/BMP.class +++ /dev/null diff --git a/java/joelib2/io/types/ChemicalMarkupLanguage.class b/java/joelib2/io/types/ChemicalMarkupLanguage.class Binary files differdeleted file mode 100644 index ec19323..0000000 --- a/java/joelib2/io/types/ChemicalMarkupLanguage.class +++ /dev/null diff --git a/java/joelib2/io/types/ClearTextFormat.class b/java/joelib2/io/types/ClearTextFormat.class Binary files differdeleted file mode 100644 index 46b4bd7..0000000 --- a/java/joelib2/io/types/ClearTextFormat.class +++ /dev/null diff --git a/java/joelib2/io/types/Flat.class b/java/joelib2/io/types/Flat.class Binary files differdeleted file mode 100644 index 4dfb41c..0000000 --- a/java/joelib2/io/types/Flat.class +++ /dev/null diff --git a/java/joelib2/io/types/GIF.class b/java/joelib2/io/types/GIF.class Binary files differdeleted file mode 100644 index c252f06..0000000 --- a/java/joelib2/io/types/GIF.class +++ /dev/null diff --git a/java/joelib2/io/types/Gaussian.class b/java/joelib2/io/types/Gaussian.class Binary files differdeleted file mode 100644 index 90e35b8..0000000 --- a/java/joelib2/io/types/Gaussian.class +++ /dev/null diff --git a/java/joelib2/io/types/Ghemical.class b/java/joelib2/io/types/Ghemical.class Binary files differdeleted file mode 100644 index c776727..0000000 --- a/java/joelib2/io/types/Ghemical.class +++ /dev/null diff --git a/java/joelib2/io/types/HIN.class b/java/joelib2/io/types/HIN.class Binary files differdeleted file mode 100644 index 4c02ecb..0000000 --- a/java/joelib2/io/types/HIN.class +++ /dev/null diff --git a/java/joelib2/io/types/JCAMP.class b/java/joelib2/io/types/JCAMP.class Binary files differdeleted file mode 100644 index 4be9b8d..0000000 --- a/java/joelib2/io/types/JCAMP.class +++ /dev/null diff --git a/java/joelib2/io/types/JPEG.class b/java/joelib2/io/types/JPEG.class Binary files differdeleted file mode 100644 index e53cd46..0000000 --- a/java/joelib2/io/types/JPEG.class +++ /dev/null diff --git a/java/joelib2/io/types/MDLSD.class b/java/joelib2/io/types/MDLSD.class Binary files differdeleted file mode 100644 index 466ce65..0000000 --- a/java/joelib2/io/types/MDLSD.class +++ /dev/null diff --git a/java/joelib2/io/types/Matlab.class b/java/joelib2/io/types/Matlab.class Binary files differdeleted file mode 100644 index 439e73c..0000000 --- a/java/joelib2/io/types/Matlab.class +++ /dev/null diff --git a/java/joelib2/io/types/MolconnZ.class b/java/joelib2/io/types/MolconnZ.class Binary files differdeleted file mode 100644 index 0757adf..0000000 --- a/java/joelib2/io/types/MolconnZ.class +++ /dev/null diff --git a/java/joelib2/io/types/Mopac.class b/java/joelib2/io/types/Mopac.class Binary files differdeleted file mode 100644 index d315e50..0000000 --- a/java/joelib2/io/types/Mopac.class +++ /dev/null diff --git a/java/joelib2/io/types/PDB.class b/java/joelib2/io/types/PDB.class Binary files differdeleted file mode 100644 index 2fb591f..0000000 --- a/java/joelib2/io/types/PDB.class +++ /dev/null diff --git a/java/joelib2/io/types/PDF.class b/java/joelib2/io/types/PDF.class Binary files differdeleted file mode 100644 index 0aef55a..0000000 --- a/java/joelib2/io/types/PDF.class +++ /dev/null diff --git a/java/joelib2/io/types/PNG.class b/java/joelib2/io/types/PNG.class Binary files differdeleted file mode 100644 index ad5cc88..0000000 --- a/java/joelib2/io/types/PNG.class +++ /dev/null diff --git a/java/joelib2/io/types/POVRay.class b/java/joelib2/io/types/POVRay.class Binary files differdeleted file mode 100644 index ac784fd..0000000 --- a/java/joelib2/io/types/POVRay.class +++ /dev/null diff --git a/java/joelib2/io/types/PPM.class b/java/joelib2/io/types/PPM.class Binary files differdeleted file mode 100644 index cb4abe4..0000000 --- a/java/joelib2/io/types/PPM.class +++ /dev/null diff --git a/java/joelib2/io/types/Smiles.class b/java/joelib2/io/types/Smiles.class Binary files differdeleted file mode 100644 index 31d2155..0000000 --- a/java/joelib2/io/types/Smiles.class +++ /dev/null diff --git a/java/joelib2/io/types/SybylMol2.class b/java/joelib2/io/types/SybylMol2.class Binary files differdeleted file mode 100644 index 626d238..0000000 --- a/java/joelib2/io/types/SybylMol2.class +++ /dev/null diff --git a/java/joelib2/io/types/Tinker.class b/java/joelib2/io/types/Tinker.class Binary files differdeleted file mode 100644 index 03ac641..0000000 --- a/java/joelib2/io/types/Tinker.class +++ /dev/null diff --git a/java/joelib2/io/types/Undefined.class b/java/joelib2/io/types/Undefined.class Binary files differdeleted file mode 100644 index 3d7df62..0000000 --- a/java/joelib2/io/types/Undefined.class +++ /dev/null diff --git a/java/joelib2/io/types/XYZ.class b/java/joelib2/io/types/XYZ.class Binary files differdeleted file mode 100644 index 8c4aa24..0000000 --- a/java/joelib2/io/types/XYZ.class +++ /dev/null diff --git a/java/joelib2/io/types/ZIP.class b/java/joelib2/io/types/ZIP.class Binary files differdeleted file mode 100644 index 42e2a72..0000000 --- a/java/joelib2/io/types/ZIP.class +++ /dev/null diff --git a/java/joelib2/io/types/chemrss/RSSHandler.class b/java/joelib2/io/types/chemrss/RSSHandler.class Binary files differdeleted file mode 100644 index 2cfd26f..0000000 --- a/java/joelib2/io/types/chemrss/RSSHandler.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/CDKConvention.class b/java/joelib2/io/types/cml/CDKConvention.class Binary files differdeleted file mode 100644 index 403adfc..0000000 --- a/java/joelib2/io/types/cml/CDKConvention.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/CDOAcceptedObjects.class b/java/joelib2/io/types/cml/CDOAcceptedObjects.class Binary files differdeleted file mode 100644 index e8e23d7..0000000 --- a/java/joelib2/io/types/cml/CDOAcceptedObjects.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/CDOInterface.class b/java/joelib2/io/types/cml/CDOInterface.class Binary files differdeleted file mode 100644 index cd30c77..0000000 --- a/java/joelib2/io/types/cml/CDOInterface.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/CMLCoreModule.class b/java/joelib2/io/types/cml/CMLCoreModule.class Binary files differdeleted file mode 100644 index 7c29f82..0000000 --- a/java/joelib2/io/types/cml/CMLCoreModule.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/CMLErrorHandler.class 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/dev/null diff --git a/java/joelib2/io/types/cml/MoleculeFileCDO.class b/java/joelib2/io/types/cml/MoleculeFileCDO.class Binary files differdeleted file mode 100644 index 7ba0a4b..0000000 --- a/java/joelib2/io/types/cml/MoleculeFileCDO.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/MoleculeHuge.class b/java/joelib2/io/types/cml/MoleculeHuge.class Binary files differdeleted file mode 100644 index 4c4dc88..0000000 --- a/java/joelib2/io/types/cml/MoleculeHuge.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/MoleculeLarge.class b/java/joelib2/io/types/cml/MoleculeLarge.class Binary files differdeleted file mode 100644 index 6bc2226..0000000 --- a/java/joelib2/io/types/cml/MoleculeLarge.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/ResultCMLProperties.class b/java/joelib2/io/types/cml/ResultCMLProperties.class Binary files differdeleted file mode 100644 index 99a9b69..0000000 --- a/java/joelib2/io/types/cml/ResultCMLProperties.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/XMLHandler.class b/java/joelib2/io/types/cml/XMLHandler.class Binary files differdeleted file mode 100644 index 02333b2..0000000 --- a/java/joelib2/io/types/cml/XMLHandler.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/XMLSpecialCharacter.class b/java/joelib2/io/types/cml/XMLSpecialCharacter.class Binary files differdeleted file mode 100644 index a03039e..0000000 --- a/java/joelib2/io/types/cml/XMLSpecialCharacter.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/data/cml1_0.dtd b/java/joelib2/io/types/cml/data/cml1_0.dtd deleted file mode 100644 index 6cafefe..0000000 --- a/java/joelib2/io/types/cml/data/cml1_0.dtd +++ /dev/null @@ -1,429 +0,0 @@ -<!-- Appendix A - CML DTD-1999-05-15 --> -<!-- Authors: - P.Murray-Rust - H.Rzepa -This DTD is fully described in Journal of Chemical Information - and Computer Science, Vol xxx, 1999, pp. xxx ---> - -<!-- =======================================================--> -<!-- PARAMETER ENTITIES --> -<!-- =======================================================--> - -<!-- ======attributes found on almost all elements ==========--> - -<!ENTITY % title 'title CDATA #IMPLIED'> -<!ENTITY % id 'id CDATA #IMPLIED'> -<!ENTITY % convention 'convention CDATA "CML"'> -<!ENTITY % dictRef 'dictRef CDATA #IMPLIED'> - -<!-- ======linking information ==============================--> - -<!ENTITY % simpleLink 'href CDATA #REQUIRED'> - -<!-- ======quantifiers and constraints on some primitives ===--> - -<!ENTITY % count 'count CDATA "1"'> -<!ENTITY % size 'size CDATA #IMPLIED'> -<!ENTITY % rows 'rows CDATA #REQUIRED'> -<!ENTITY % columns 'columns CDATA #REQUIRED'> - -<!-- ======constraints on some numeric data primitives ===--> - -<!ENTITY % min 'min CDATA #IMPLIED'> -<!ENTITY % max 'max CDATA #IMPLIED'> -<!ENTITY % units 'units CDATA #IMPLIED'> -<!ENTITY % angleUnits 'units (degrees | radians) "degrees"'> -<!ENTITY % unitsRef 'unitsRef CDATA #IMPLIED'> - -<!-- values which may be useful in min and max attributes --> -<!ENTITY % integer.zero '0'> -<!ENTITY % integer.max '2147483647'> -<!ENTITY % integer.min '-2147483648'> -<!ENTITY % float.zero '0.0'> -<!ENTITY % float.max '8.98846567431158E307'> -<!ENTITY % float.min '4.9E-324'> - -<!-- ======= builtin values for any element ================--> -<!ENTITY % builtinId 'id'> - -<!-- ======= builtin values for atoms ======================--> -<!ENTITY % elementType 'elementType'> -<!ENTITY % atomId 'atomId'> - -<!ENTITY % x2 'x2'> -<!ENTITY % y2 'y2'> -<!ENTITY % x3 'x3'> -<!ENTITY % y3 'y3'> -<!ENTITY % z3 'z3'> -<!ENTITY % xy2 'xy2'> -<!ENTITY % xyz3 'xyz3'> -<!ENTITY % xFract 'xFract'> -<!ENTITY % yFract 'yFract'> -<!ENTITY % zFract 'zFract'> -<!ENTITY % xyzFract 'xyzFract'> -<!ENTITY % occupancy 'occupancy'> -<!ENTITY % isotope 'isotope'> -<!ENTITY % formalCharge 'formalCharge'> -<!ENTITY % nonHydrogenCount 'nonHydrogenCount'> -<!ENTITY % hydrogenCount 'hydrogenCount'> -<!ENTITY % atomParity 'atomParity'> - -<!ENTITY % residueType 'residueType'> -<!ENTITY % residueId 'residueId'> - -<!ENTITY % atomStringBuiltin ' - %elementType; | %atomId; | - %residueType; | %residueId; - ' -> -<!ENTITY % atomFloatBuiltin ' - %x2; | %y2; | - %x3; | %y3; | %z3; | - %xFract; | %yFract; | %zFract; | - %occupancy; | %isotope; | - %formalCharge; | %hydrogenCount; | %nonHydrogenCount; | - %atomParity; - ' -> -<!ENTITY % atomIntegerBuiltin ' - %isotope; | - %formalCharge; | %hydrogenCount; | %nonHydrogenCount; | - %atomParity; - ' -> -<!ENTITY % atomCoordinate2Builtin ' - %xy2; - ' -> -<!ENTITY % atomCoordinate3Builtin ' - %xyz3; | %xyzFract; - ' -> -<!-- ======= builtin values for bonds ======================--> -<!ENTITY % atomRef 'atomRef'> -<!ENTITY % builtinAtomRefs 'atomRefs'> -<!ENTITY % length 'length'> -<!ENTITY % order 'order'> -<!ENTITY % stereo 'stereo'> -<!ENTITY % atomRefs 'atomRefs CDATA #IMPLIED'> - -<!ENTITY % bondStringBuiltin ' - %atomRef; | %builtinAtomRefs; | - %order; | - %stereo; - ' -> -<!ENTITY % bondFloatBuiltin ' - %length; - ' -> -<!ENTITY % bondIntegerBuiltin '' -> -<!-- ======= builtin values for crystal ====================--> - -<!ENTITY % acell 'acell'> -<!ENTITY % bcell 'bcell'> -<!ENTITY % ccell 'ccell'> -<!ENTITY % alpha 'alpha'> -<!ENTITY % beta 'beta'> -<!ENTITY % gamma 'gamma'> -<!ENTITY % z 'z'> -<!ENTITY % spacegroup 'spacegroup'> - -<!ENTITY % crystalStringBuiltin ' - %spacegroup; - ' -> -<!ENTITY % crystalFloatBuiltin ' - %acell; | %bcell; | %ccell; | - %alpha; | %beta; | %gamma; | - %z; - ' -> -<!ENTITY % crystalIntegerBuiltin ' - %z; - ' -> -<!-- =======================================================--> -<!ENTITY % stringBuiltin ' - builtin ( - %builtinId; | - %atomStringBuiltin; | - %bondStringBuiltin; | - %crystalStringBuiltin; - ) #IMPLIED ' -> -<!ENTITY % floatBuiltin ' - builtin ( - %atomFloatBuiltin; | - %bondFloatBuiltin; | - %crystalFloatBuiltin; - ) #IMPLIED ' -> -<!ENTITY % integerBuiltin ' - builtin ( - %atomIntegerBuiltin; | - %crystalIntegerBuiltin; - ) #IMPLIED ' -> -<!ENTITY % coordinate2Builtin ' - builtin ( - %atomCoordinate2Builtin; - ) #IMPLIED ' -> -<!ENTITY % coordinate3Builtin ' - builtin ( - %atomCoordinate3Builtin; - ) #IMPLIED ' -> - -<!-- =======================================================--> -<!-- ELEMENTS for widely used data primitives --> -<!-- =======================================================--> - -<!ELEMENT string (#PCDATA)> -<!ATTLIST string - %title; - %id; - %stringBuiltin; - %dictRef; - %convention; -> -<!ELEMENT link (#PCDATA)> -<!ATTLIST link - %title; - %id; - %simpleLink; - %convention; -> -<!ELEMENT float (#PCDATA)> -<!ATTLIST float - %title; - %id; - %floatBuiltin; - %min; - %max; - %units; - %unitsRef; - %dictRef; - %convention; -> -<!ELEMENT integer (#PCDATA)> -<!ATTLIST integer - %title; - %id; - %integerBuiltin; - %min; - %max; - %units; - %unitsRef; - %dictRef; - %convention; -> -<!ELEMENT stringArray (#PCDATA)> -<!ATTLIST stringArray - %title; - %id; - %stringBuiltin; - %size; - %min; - %max; - delimiter CDATA #IMPLIED - %dictRef; - %convention; -> -<!ELEMENT floatArray (#PCDATA)> -<!ATTLIST floatArray - %title; - %id; - %floatBuiltin; - %size; - %min; - %max; - %units; - %unitsRef; - %dictRef; - %convention; -> -<!ELEMENT integerArray (#PCDATA)> -<!ATTLIST integerArray - %title; - %id; - %integerBuiltin; - %size; - %min; - %max; - %units; - %unitsRef; - %dictRef; - %convention; -> -<!ELEMENT floatMatrix (#PCDATA)> -<!ATTLIST floatMatrix - %title; - %id; - %rows; - %delimiter; - %columns; - %min; - %max; - %units; - %unitsRef; - %dictRef; - %convention; -> - -<!ELEMENT coordinate2 (#PCDATA)> -<!ATTLIST coordinate2 - %title; - %id; - %coordinate2Builtin; - %unitsRef; - %dictRef; - %convention; -> - -<!ELEMENT coordinate3 (#PCDATA)> -<!ATTLIST coordinate3 - %title; - %id; - %coordinate3Builtin; - %unitsRef; - %dictRef; - %convention; -> -<!ELEMENT angle (#PCDATA)> -<!ATTLIST angle - %title; - %id; - %atomRefs; - %angleUnits; - %min; - %max; - %dictRef; - %convention; -> - -<!ELEMENT torsion (#PCDATA)> -<!ATTLIST torsion - %title; - %id; - %atomRefs; - %angleUnits; - %min; - %max; - %dictRef; - %convention; -> - -<!ELEMENT list ANY> -<!ATTLIST list - %title; - %id; -> - -<!-- =======================================================--> -<!-- ELEMENTS for chemical and crystallographic concepts --> -<!-- =======================================================--> -<!-- NOTE - for elements which have element-specific values for the - builtin attribute, those values are already listed as - entities ---> -<!-- =======================================================--> - -<!ELEMENT molecule ANY> -<!ATTLIST molecule - %title; - %id; - %count; - %dictRef; - %convention; -> - -<!-- ========================================================--> -<!ELEMENT formula ANY> -<!ATTLIST formula - %title; - %id; - %count; - %dictRef; - %convention; -> - -<!-- ========================================================--> -<!ELEMENT atom ANY> -<!ATTLIST atom - %title; - %id; - %count; - %dictRef; - %convention; -> - -<!-- .......................................................--> -<!ELEMENT atomArray ANY> -<!ATTLIST atomArray - %title; - %id; - %dictRef; - %convention; -> - -<!-- ========================================================--> -<!ELEMENT bond ANY> -<!ATTLIST bond - %id; - %atomRefs; - %dictRef; - %convention; -> - -<!-- ========================================================--> -<!ELEMENT bondArray ANY> -<!ATTLIST bondArray - %id; - %dictRef; - %convention; -> -<!-- ========================================================--> -<!ELEMENT electron ANY> -<!ATTLIST electron - %id; - %count; - %dictRef; - %convention; -> -<!-- ========================================================--> -<!ELEMENT reaction ANY> -<!ATTLIST reaction - %id; - %dictRef; - %convention; -> -<!-- ======================================================= --> -<!ELEMENT crystal ANY> -<!ATTLIST crystal - %title; - %id; - %dictRef; - %convention; -> -<!-- ======================================================= --> -<!ELEMENT sequence ANY> -<!ATTLIST sequence - %title; - %id; - %dictRef; - %convention; -> - -<!-- ======================================================= --> -<!ELEMENT feature ANY> -<!ATTLIST feature - %title; - %id; - %dictRef; - %convention; -> diff --git a/java/joelib2/io/types/cml/data/cml1_0_1.dtd b/java/joelib2/io/types/cml/data/cml1_0_1.dtd deleted file mode 100644 index 706b1ab..0000000 --- a/java/joelib2/io/types/cml/data/cml1_0_1.dtd +++ /dev/null @@ -1,485 +0,0 @@ -<!-- CML V1.01 DTD --> -<!-- Amendments and errata from V1. (1999-05-15) --> -<!-- Authors: - P.Murray-Rust - H.Rzepa -This DTD is fully described in P. Murray-Rust and H. S. Rzepa, Journal of Chem -ical Information - and Computer Science, 1999, 39, 928. ---> -<!-- Changes (2001-04-06): -1. atomRefs has been added as an attribute for string, - float, integer and their *Arrays -2. some elements and attributes have been annotated as - belonging to a subset "CoreCML" for simple small molecules -3. multiple dictRef on molecule removed -4. delimiter attribute added to floatArray, integerArray, floatMatrix -5. generic PE's created for many attributes for ease of maintenance - no new attributes created -6. dictRef added to a very small number of elements - this is now - almost universal ---> - -<!-- elements and attributes fall into 2 categories: - coreCML - a subset of CML for easy implementation for small molecules - fullCML - the full DTD (includes coreCML) ---> -<!-- % fullCML can be overridden -by prepending the statement: -<!ENTITY % fullCML "IGNORE"> -at this stage (or transmitting it in from the parser controls if -implemented) --> - -<!ENTITY % coreCML "INCLUDE"> -<!ENTITY % fullCML "INCLUDE"> - -<!-- =======================================================--> -<!-- PARAMETER ENTITIES --> -<!-- =======================================================--> - -<!-- ======attributes found on almost all elements ==========--> - -<!ENTITY % title 'title CDATA #IMPLIED'> -<!ENTITY % id 'id CDATA #IMPLIED'> -<!ENTITY % convention 'convention CDATA "CML"'> -<!ENTITY % dictRef 'dictRef CDATA #IMPLIED'> - -<!-- a very common combination (on most elements) --> -<!ENTITY % tit_id_conv '%title; %id; %convention;'> -<!ENTITY % tit_id_conv_dict '%tit_id_conv; %dictRef;'> - -<!-- ======linking information ==============================--> - -<!ENTITY % simpleLink 'href CDATA #REQUIRED'> - -<!-- ======quantifiers and constraints on some primitives ===--> - -<!ENTITY % count 'count CDATA "1"'> -<![ %fullCML; [ -<!ENTITY % size 'size CDATA #IMPLIED'> -<!ENTITY % rows 'rows CDATA #REQUIRED'> -<!ENTITY % columns 'columns CDATA #REQUIRED'> -]]> -<!ENTITY % size ''> -<!ENTITY % rows ''> -<!ENTITY % columns ''> - -<!-- ====== delimiter in Array elements ===--> -<!ENTITY % delimiter 'delimiter CDATA #IMPLIED'> - -<!-- ======constraints on some numeric data primitives ===--> - -<!ENTITY % units 'units CDATA #IMPLIED'> - -<![%fullCML;[ -<!ENTITY % min 'min CDATA #IMPLIED'> -<!ENTITY % max 'max CDATA #IMPLIED'> -<!ENTITY % angleUnits 'units (degrees | radians) "degrees"'> -<!ENTITY % unitsRef 'unitsRef CDATA #IMPLIED'> -]]> -<!ENTITY % min ''> -<!ENTITY % max ''> -<!ENTITY % angleUnits ''> -<!ENTITY % unitsRef ''> - -<!-- for CoreCML degrees are mandatory --> -<!ENTITY % angleUnits 'units CDATA #FIXED "degrees"'> - -<!-- values which may be useful in min and max attributes --> -<!ENTITY % integer.zero '0'> -<!ENTITY % integer.max '2147483647'> -<!ENTITY % integer.min '-2147483648'> -<!ENTITY % float.zero '0.0'> -<!ENTITY % float.max '8.98846567431158E307'> -<!ENTITY % float.min '4.9E-324'> - -<!-- ======= builtin values for any element ================--> -<!ENTITY % builtinId 'id'> - -<!-- ======= builtin values for atoms ======================--> -<!ENTITY % elementType 'elementType'> - -<![%fullCML;[ -<!ENTITY % atomId ' | atomId '> -]]> -<!ENTITY % atomId ''> - -<!ENTITY % x2 'x2'> -<!ENTITY % y2 'y2'> -<!ENTITY % x3 'x3'> -<!ENTITY % y3 'y3'> -<!ENTITY % z3 'z3'> -<!ENTITY % xy2 'xy2'> -<!ENTITY % xyz3 'xyz3'> -<!ENTITY % xFract 'xFract'> -<!ENTITY % yFract 'yFract'> -<!ENTITY % zFract 'zFract'> -<!ENTITY % xyzFract 'xyzFract'> -<!ENTITY % occupancy 'occupancy'> -<!ENTITY % isotope 'isotope'> -<!ENTITY % formalCharge 'formalCharge'> -<!ENTITY % nonHydrogenCount 'nonHydrogenCount'> -<!ENTITY % hydrogenCount 'hydrogenCount'> -<!ENTITY % atomParity 'atomParity'> - -<![%fullCML;[ -<!ENTITY % residueType ' | residueType'> -<!ENTITY % residueId ' | residueId'> -]]> -<!ENTITY % residueType ''> -<!ENTITY % residueId ''> - -<!ENTITY % atomStringBuiltin ' - %elementType; %atomId; - %residueType; %residueId; - ' -> -<!ENTITY % atomFloatBuiltin ' - %x2; | %y2; | - %x3; | %y3; | %z3; | - %xFract; | %yFract; | %zFract; | - %occupancy; | %isotope; | - %formalCharge; | %hydrogenCount; | %nonHydrogenCount; | - %atomParity; - ' -> -<!ENTITY % atomIntegerBuiltin ' - %isotope; | - %formalCharge; | %hydrogenCount; | %nonHydrogenCount; | - %atomParity; - ' -> -<!ENTITY % atomCoordinate2Builtin ' - %xy2; - ' -> -<!ENTITY % atomCoordinate3Builtin ' - %xyz3; | %xyzFract; - ' -> -<!-- ======= builtin values for bonds ======================--> -<!ENTITY % atomRef 'atomRef'> -<!ENTITY % builtinAtomRefs 'atomRefs'> -<!ENTITY % length 'length'> -<!ENTITY % order 'order'> -<!ENTITY % stereo 'stereo'> -<!ENTITY % atomRefs 'atomRefs CDATA #IMPLIED'> - -<!ENTITY % bondStringBuiltin ' - %atomRef; | %builtinAtomRefs; | - %order; | - %stereo; - ' -> -<!ENTITY % bondFloatBuiltin ' - %length; - ' -> -<!ENTITY % bondIntegerBuiltin '' -> -<!-- ======= builtin values for crystal ====================--> - -<!ENTITY % acell 'acell'> -<!ENTITY % bcell 'bcell'> -<!ENTITY % ccell 'ccell'> -<!ENTITY % alpha 'alpha'> -<!ENTITY % beta 'beta'> -<!ENTITY % gamma 'gamma'> -<!ENTITY % z 'z'> -<!ENTITY % spacegroup 'spacegroup'> - -<!ENTITY % crystalStringBuiltin ' - %spacegroup; - ' -> -<!ENTITY % crystalFloatBuiltin ' - %acell; | %bcell; | %ccell; | - %alpha; | %beta; | %gamma; | - %z; - ' -> -<!ENTITY % crystalIntegerBuiltin ' - %z; - ' -> -<!-- =======================================================--> -<!ENTITY % stringBuiltin ' - builtin ( - %builtinId; | - %atomStringBuiltin; | - %bondStringBuiltin; | - %crystalStringBuiltin; - ) #IMPLIED ' -> -<!ENTITY % floatBuiltin ' - builtin ( - %atomFloatBuiltin; | - %bondFloatBuiltin; | - %crystalFloatBuiltin; - ) #IMPLIED ' -> -<!ENTITY % integerBuiltin ' - builtin ( - %atomIntegerBuiltin; | - %crystalIntegerBuiltin; - ) #IMPLIED ' -> -<!ENTITY % coordinate2Builtin ' - builtin ( - %atomCoordinate2Builtin; - ) #IMPLIED ' -> -<!ENTITY % coordinate3Builtin ' - builtin ( - %atomCoordinate3Builtin; - ) #IMPLIED ' -> - -<!-- =======================================================--> -<!-- ELEMENTS for widely used data primitives --> -<!-- =======================================================--> - -<!-- CML-DTD V1.01 addition - certain children of atom or bond may refer to atoms (particularly - builtin="atomParity" and builtin="stereo"). For these - we need the attribute 'atomRefs' ---> -<!ENTITY % scalar.content '(#PCDATA)'> -<!ENTITY % array.content '(#PCDATA)'> -<!ENTITY % matrix.content '(#PCDATA)'> -<!ENTITY % angle.content '(#PCDATA)'> -<!ENTITY % coordinate.content '(#PCDATA)'> - -<!ENTITY % array.atts - '%size; - %delimiter; -'> - -<!ELEMENT string %scalar.content;> -<!ATTLIST string - %tit_id_conv_dict; - %stringBuiltin; - %atomRefs; -> -<!-- link is for implementing XLink - only used in fullCML --> -<![ %fullCML; [ -<!ELEMENT link %scalar.content;> -<!ATTLIST link - %tit_id_conv; - %simpleLink; -> -]]> - -<!ELEMENT float %scalar.content;> -<!ATTLIST float - %tit_id_conv_dict; - %floatBuiltin; - %min; - %max; - %units; - %unitsRef; - %atomRefs; -> -<!ELEMENT integer %scalar.content;> -<!ATTLIST integer - %tit_id_conv_dict; - %integerBuiltin; - %min; - %max; - %units; - %unitsRef; - %atomRefs; -> -<!ELEMENT stringArray %array.content;> -<!ATTLIST stringArray - %tit_id_conv_dict; - %stringBuiltin; - %array.atts; - %min; - %max; -> -<!ELEMENT floatArray %array.content;> -<!ATTLIST floatArray - %tit_id_conv_dict; - %floatBuiltin; - %array.atts; - %units; - %unitsRef; - %min; - %max; -> -<!ELEMENT integerArray %array.content;> -<!ATTLIST integerArray - %tit_id_conv_dict; - %integerBuiltin; - %array.atts; - %min; - %max; - %units; - %unitsRef; -> -<!ELEMENT floatMatrix %matrix.content;> -<!ATTLIST floatMatrix - %tit_id_conv_dict; - %rows; - %columns; - %min; - %max; - %units; - %unitsRef; - %delimiter; -> - -<!ELEMENT coordinate2 %coordinate.content;> -<!ATTLIST coordinate2 - %tit_id_conv_dict; - %coordinate2Builtin; - %unitsRef; -> - -<!ELEMENT coordinate3 %coordinate.content;> -<!ATTLIST coordinate3 - %tit_id_conv_dict; - %coordinate3Builtin; - %unitsRef; -> -<!ELEMENT angle %angle.content;> -<!ATTLIST angle - %tit_id_conv_dict; - %atomRefs; - %angleUnits; - %min; - %max; -> - -<!ELEMENT torsion %angle.content;> -<!ATTLIST torsion - %tit_id_conv_dict; - %atomRefs; - %angleUnits; - %min; - %max; -> - -<!ELEMENT list ANY> -<!ATTLIST list - %tit_id_conv_dict; -> - -<!-- =======================================================--> -<!-- ELEMENTS for chemical and crystallographic concepts --> -<!-- =======================================================--> -<!-- NOTE - for elements which have element-specific values for the - builtin attribute, those values are already listed as - entities ---> -<!-- =======================================================--> -<![%fullCML;[ -<!ENTITY % molecule.content 'ANY'> -]]> -<!ENTITY % molecule.content '(atomArray, bondArray)'> - -<!ELEMENT molecule %molecule.content;> -<!ATTLIST molecule - %tit_id_conv_dict; - %count; -> - -<!-- ========================================================--> -<!ELEMENT formula ANY> -<!ATTLIST formula - %tit_id_conv_dict; - %count; -> - -<!-- ========================================================--> -<![%fullCML;[ -<!ENTITY % atom.content 'ANY'> -]]> -<!ENTITY % atom.content '(string | float | integer)*'> -<!ELEMENT atom %atom.content;> -<!ATTLIST atom - %tit_id_conv_dict; - %count; -> - -<!-- .......................................................--> -<![%fullCML;[ -<!ENTITY % atomArray.content 'ANY'> -]]> -<!ENTITY % atomArray.content ' - (atom+ | (stringArray | floatArray | integerArray)*) - ' -> -<!ELEMENT atomArray %atomArray.content;> -<!ATTLIST atomArray - %tit_id_conv; -> - -<!-- ========================================================--> -<![%fullCML;[ -<!ENTITY % bond.content 'ANY'> -]]> -<!ENTITY % bond.content '(string | float | integer)*'> -<!ELEMENT bond %bond.content;> -<!ATTLIST bond - %tit_id_conv_dict; - %atomRefs; -> - -<!-- ========================================================--> -<![%fullCML;[ -<!ENTITY % bondArray.content 'ANY'> -]]> -<!ENTITY % bondArray.content ' - (bond+ | (stringArray | floatArray | integerArray)*) - ' -> -<!ELEMENT bondArray %bondArray.content;> -<!ATTLIST bondArray - %tit_id_conv; -> -<!-- ========================================================--> -<![ %fullCML; [ -<!ELEMENT electron ANY> -<!ATTLIST electron - %tit_id_conv_dict; - %count; -> -]]> -<!-- ========================================================--> -<![ %fullCML; [ -<!ELEMENT reaction ANY> -<!ATTLIST reaction - %tit_id_conv_dict; -> -]]> - -<!-- ======================================================= --> - -<![%fullCML;[ -<!ENTITY % crystal.content 'ANY'> -]]> -<!ENTITY % crystal.content '(string | float | integer)*'> -<!ELEMENT crystal %crystal.content;> -<!ATTLIST crystal - %tit_id_conv_dict; -> - -<!-- ======================================================= --> -<![ %fullCML; [ -<!ELEMENT sequence ANY> -<!ATTLIST sequence - %tit_id_conv_dict; -> -]]> - -<!-- ======================================================= --> -<![ %fullCML; [ -<!ELEMENT feature ANY> -<!ATTLIST feature - %tit_id_conv_dict; -> -]]> - diff --git a/java/joelib2/io/types/cml/elements/ArrayCML.class b/java/joelib2/io/types/cml/elements/ArrayCML.class Binary files differdeleted file mode 100644 index 3daf3ae..0000000 --- a/java/joelib2/io/types/cml/elements/ArrayCML.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/elements/ElementCML.class b/java/joelib2/io/types/cml/elements/ElementCML.class Binary files differdeleted file mode 100644 index 6e298ff..0000000 --- a/java/joelib2/io/types/cml/elements/ElementCML.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/elements/Elements.class b/java/joelib2/io/types/cml/elements/Elements.class Binary files differdeleted file mode 100644 index d9eb6fe..0000000 --- a/java/joelib2/io/types/cml/elements/Elements.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/elements/MatrixCML.class b/java/joelib2/io/types/cml/elements/MatrixCML.class Binary files differdeleted file mode 100644 index 13cfcb2..0000000 --- a/java/joelib2/io/types/cml/elements/MatrixCML.class +++ /dev/null diff --git a/java/joelib2/io/types/cml/elements/ScalarCML.class b/java/joelib2/io/types/cml/elements/ScalarCML.class Binary files differdeleted file mode 100644 index b1165a8..0000000 --- a/java/joelib2/io/types/cml/elements/ScalarCML.class +++ /dev/null |