From 3cd136861c68b8c24cc653c903c620d55be4b294 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 2 Apr 2012 09:18:14 +0200
Subject: Remove PC descriptor

---
 java/joelib2/io/types/cml/CDKConvention.class      | Bin 2674 -> 0 bytes
 java/joelib2/io/types/cml/CDOAcceptedObjects.class | Bin 536 -> 0 bytes
 java/joelib2/io/types/cml/CDOInterface.class       | Bin 433 -> 0 bytes
 java/joelib2/io/types/cml/CMLCoreModule.class      | Bin 23204 -> 0 bytes
 java/joelib2/io/types/cml/CMLErrorHandler.class    | Bin 1389 -> 0 bytes
 java/joelib2/io/types/cml/CMLHandler.class         | Bin 3679 -> 0 bytes
 java/joelib2/io/types/cml/CMLIDCreator.class       | Bin 2398 -> 0 bytes
 java/joelib2/io/types/cml/CMLMoleculeWriter.class  | Bin 164 -> 0 bytes
 .../io/types/cml/CMLMoleculeWriterBase.class       | Bin 11186 -> 0 bytes
 java/joelib2/io/types/cml/CMLPropertyWriter.class  | Bin 8771 -> 0 bytes
 java/joelib2/io/types/cml/CMLReactionModule.class  | Bin 2307 -> 0 bytes
 java/joelib2/io/types/cml/CMLResolver.class        | Bin 2214 -> 0 bytes
 .../io/types/cml/CMLSequentialSAXReader.class      | Bin 2837 -> 0 bytes
 java/joelib2/io/types/cml/CMLStack.class           | Bin 803 -> 0 bytes
 java/joelib2/io/types/cml/CMLSymmetryWriter.class  | Bin 4132 -> 0 bytes
 .../joelib2/io/types/cml/CMLWriterProperties.class | Bin 392 -> 0 bytes
 .../joelib2/io/types/cml/ConventionInterface.class | Bin 136 -> 0 bytes
 java/joelib2/io/types/cml/ModuleInterface.class    | Bin 577 -> 0 bytes
 java/joelib2/io/types/cml/MoleculeArray.class      | Bin 5902 -> 0 bytes
 .../io/types/cml/MoleculeAttributeArray.class      | Bin 5093 -> 0 bytes
 java/joelib2/io/types/cml/MoleculeFileCDO.class    | Bin 11310 -> 0 bytes
 java/joelib2/io/types/cml/MoleculeHuge.class       | Bin 3569 -> 0 bytes
 java/joelib2/io/types/cml/MoleculeLarge.class      | Bin 4281 -> 0 bytes
 .../joelib2/io/types/cml/ResultCMLProperties.class | Bin 375 -> 0 bytes
 java/joelib2/io/types/cml/XMLHandler.class         | Bin 890 -> 0 bytes
 .../joelib2/io/types/cml/XMLSpecialCharacter.class | Bin 842 -> 0 bytes
 java/joelib2/io/types/cml/data/cml1_0.dtd          | 429 ------------------
 java/joelib2/io/types/cml/data/cml1_0_1.dtd        | 485 ---------------------
 java/joelib2/io/types/cml/elements/ArrayCML.class  | Bin 4129 -> 0 bytes
 .../joelib2/io/types/cml/elements/ElementCML.class | Bin 248 -> 0 bytes
 java/joelib2/io/types/cml/elements/Elements.class  | Bin 1743 -> 0 bytes
 java/joelib2/io/types/cml/elements/MatrixCML.class | Bin 3944 -> 0 bytes
 java/joelib2/io/types/cml/elements/ScalarCML.class | Bin 4362 -> 0 bytes
 33 files changed, 914 deletions(-)
 delete mode 100644 java/joelib2/io/types/cml/CDKConvention.class
 delete mode 100644 java/joelib2/io/types/cml/CDOAcceptedObjects.class
 delete mode 100644 java/joelib2/io/types/cml/CDOInterface.class
 delete mode 100644 java/joelib2/io/types/cml/CMLCoreModule.class
 delete mode 100644 java/joelib2/io/types/cml/CMLErrorHandler.class
 delete mode 100644 java/joelib2/io/types/cml/CMLHandler.class
 delete mode 100644 java/joelib2/io/types/cml/CMLIDCreator.class
 delete mode 100644 java/joelib2/io/types/cml/CMLMoleculeWriter.class
 delete mode 100644 java/joelib2/io/types/cml/CMLMoleculeWriterBase.class
 delete mode 100644 java/joelib2/io/types/cml/CMLPropertyWriter.class
 delete mode 100644 java/joelib2/io/types/cml/CMLReactionModule.class
 delete mode 100644 java/joelib2/io/types/cml/CMLResolver.class
 delete mode 100644 java/joelib2/io/types/cml/CMLSequentialSAXReader.class
 delete mode 100644 java/joelib2/io/types/cml/CMLStack.class
 delete mode 100644 java/joelib2/io/types/cml/CMLSymmetryWriter.class
 delete mode 100644 java/joelib2/io/types/cml/CMLWriterProperties.class
 delete mode 100644 java/joelib2/io/types/cml/ConventionInterface.class
 delete mode 100644 java/joelib2/io/types/cml/ModuleInterface.class
 delete mode 100644 java/joelib2/io/types/cml/MoleculeArray.class
 delete mode 100644 java/joelib2/io/types/cml/MoleculeAttributeArray.class
 delete mode 100644 java/joelib2/io/types/cml/MoleculeFileCDO.class
 delete mode 100644 java/joelib2/io/types/cml/MoleculeHuge.class
 delete mode 100644 java/joelib2/io/types/cml/MoleculeLarge.class
 delete mode 100644 java/joelib2/io/types/cml/ResultCMLProperties.class
 delete mode 100644 java/joelib2/io/types/cml/XMLHandler.class
 delete mode 100644 java/joelib2/io/types/cml/XMLSpecialCharacter.class
 delete mode 100644 java/joelib2/io/types/cml/data/cml1_0.dtd
 delete mode 100644 java/joelib2/io/types/cml/data/cml1_0_1.dtd
 delete mode 100644 java/joelib2/io/types/cml/elements/ArrayCML.class
 delete mode 100644 java/joelib2/io/types/cml/elements/ElementCML.class
 delete mode 100644 java/joelib2/io/types/cml/elements/Elements.class
 delete mode 100644 java/joelib2/io/types/cml/elements/MatrixCML.class
 delete mode 100644 java/joelib2/io/types/cml/elements/ScalarCML.class

(limited to 'java/joelib2/io/types/cml')

diff --git a/java/joelib2/io/types/cml/CDKConvention.class b/java/joelib2/io/types/cml/CDKConvention.class
deleted file mode 100644
index 403adfc..0000000
Binary files a/java/joelib2/io/types/cml/CDKConvention.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CDOAcceptedObjects.class b/java/joelib2/io/types/cml/CDOAcceptedObjects.class
deleted file mode 100644
index e8e23d7..0000000
Binary files a/java/joelib2/io/types/cml/CDOAcceptedObjects.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CDOInterface.class b/java/joelib2/io/types/cml/CDOInterface.class
deleted file mode 100644
index cd30c77..0000000
Binary files a/java/joelib2/io/types/cml/CDOInterface.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLCoreModule.class b/java/joelib2/io/types/cml/CMLCoreModule.class
deleted file mode 100644
index 7c29f82..0000000
Binary files a/java/joelib2/io/types/cml/CMLCoreModule.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLErrorHandler.class b/java/joelib2/io/types/cml/CMLErrorHandler.class
deleted file mode 100644
index 65e5e2a..0000000
Binary files a/java/joelib2/io/types/cml/CMLErrorHandler.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLHandler.class b/java/joelib2/io/types/cml/CMLHandler.class
deleted file mode 100644
index dc179b7..0000000
Binary files a/java/joelib2/io/types/cml/CMLHandler.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLIDCreator.class b/java/joelib2/io/types/cml/CMLIDCreator.class
deleted file mode 100644
index c4d7421..0000000
Binary files a/java/joelib2/io/types/cml/CMLIDCreator.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLMoleculeWriter.class b/java/joelib2/io/types/cml/CMLMoleculeWriter.class
deleted file mode 100644
index 772fb97..0000000
Binary files a/java/joelib2/io/types/cml/CMLMoleculeWriter.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLMoleculeWriterBase.class b/java/joelib2/io/types/cml/CMLMoleculeWriterBase.class
deleted file mode 100644
index b065968..0000000
Binary files a/java/joelib2/io/types/cml/CMLMoleculeWriterBase.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLPropertyWriter.class b/java/joelib2/io/types/cml/CMLPropertyWriter.class
deleted file mode 100644
index 4ce4b96..0000000
Binary files a/java/joelib2/io/types/cml/CMLPropertyWriter.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLReactionModule.class b/java/joelib2/io/types/cml/CMLReactionModule.class
deleted file mode 100644
index 84c8fb4..0000000
Binary files a/java/joelib2/io/types/cml/CMLReactionModule.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLResolver.class b/java/joelib2/io/types/cml/CMLResolver.class
deleted file mode 100644
index bd6714e..0000000
Binary files a/java/joelib2/io/types/cml/CMLResolver.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLSequentialSAXReader.class b/java/joelib2/io/types/cml/CMLSequentialSAXReader.class
deleted file mode 100644
index 8b1d387..0000000
Binary files a/java/joelib2/io/types/cml/CMLSequentialSAXReader.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLStack.class b/java/joelib2/io/types/cml/CMLStack.class
deleted file mode 100644
index 97eaed1..0000000
Binary files a/java/joelib2/io/types/cml/CMLStack.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLSymmetryWriter.class b/java/joelib2/io/types/cml/CMLSymmetryWriter.class
deleted file mode 100644
index 60297d4..0000000
Binary files a/java/joelib2/io/types/cml/CMLSymmetryWriter.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/CMLWriterProperties.class b/java/joelib2/io/types/cml/CMLWriterProperties.class
deleted file mode 100644
index 1198763..0000000
Binary files a/java/joelib2/io/types/cml/CMLWriterProperties.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/ConventionInterface.class b/java/joelib2/io/types/cml/ConventionInterface.class
deleted file mode 100644
index 997260b..0000000
Binary files a/java/joelib2/io/types/cml/ConventionInterface.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/ModuleInterface.class b/java/joelib2/io/types/cml/ModuleInterface.class
deleted file mode 100644
index 71c9681..0000000
Binary files a/java/joelib2/io/types/cml/ModuleInterface.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/MoleculeArray.class b/java/joelib2/io/types/cml/MoleculeArray.class
deleted file mode 100644
index ebaa789..0000000
Binary files a/java/joelib2/io/types/cml/MoleculeArray.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/MoleculeAttributeArray.class b/java/joelib2/io/types/cml/MoleculeAttributeArray.class
deleted file mode 100644
index 7d3f8db..0000000
Binary files a/java/joelib2/io/types/cml/MoleculeAttributeArray.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/MoleculeFileCDO.class b/java/joelib2/io/types/cml/MoleculeFileCDO.class
deleted file mode 100644
index 7ba0a4b..0000000
Binary files a/java/joelib2/io/types/cml/MoleculeFileCDO.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/MoleculeHuge.class b/java/joelib2/io/types/cml/MoleculeHuge.class
deleted file mode 100644
index 4c4dc88..0000000
Binary files a/java/joelib2/io/types/cml/MoleculeHuge.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/MoleculeLarge.class b/java/joelib2/io/types/cml/MoleculeLarge.class
deleted file mode 100644
index 6bc2226..0000000
Binary files a/java/joelib2/io/types/cml/MoleculeLarge.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/ResultCMLProperties.class b/java/joelib2/io/types/cml/ResultCMLProperties.class
deleted file mode 100644
index 99a9b69..0000000
Binary files a/java/joelib2/io/types/cml/ResultCMLProperties.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/XMLHandler.class b/java/joelib2/io/types/cml/XMLHandler.class
deleted file mode 100644
index 02333b2..0000000
Binary files a/java/joelib2/io/types/cml/XMLHandler.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/XMLSpecialCharacter.class b/java/joelib2/io/types/cml/XMLSpecialCharacter.class
deleted file mode 100644
index a03039e..0000000
Binary files a/java/joelib2/io/types/cml/XMLSpecialCharacter.class and /dev/null differ
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
deleted file mode 100644
index 3daf3ae..0000000
Binary files a/java/joelib2/io/types/cml/elements/ArrayCML.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/elements/ElementCML.class b/java/joelib2/io/types/cml/elements/ElementCML.class
deleted file mode 100644
index 6e298ff..0000000
Binary files a/java/joelib2/io/types/cml/elements/ElementCML.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/elements/Elements.class b/java/joelib2/io/types/cml/elements/Elements.class
deleted file mode 100644
index d9eb6fe..0000000
Binary files a/java/joelib2/io/types/cml/elements/Elements.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/elements/MatrixCML.class b/java/joelib2/io/types/cml/elements/MatrixCML.class
deleted file mode 100644
index 13cfcb2..0000000
Binary files a/java/joelib2/io/types/cml/elements/MatrixCML.class and /dev/null differ
diff --git a/java/joelib2/io/types/cml/elements/ScalarCML.class b/java/joelib2/io/types/cml/elements/ScalarCML.class
deleted file mode 100644
index b1165a8..0000000
Binary files a/java/joelib2/io/types/cml/elements/ScalarCML.class and /dev/null differ
-- 
cgit v1.2.3