diff options
Diffstat (limited to 'java/joelib2/io/types/cml/data/cml1_0.dtd')
| -rw-r--r-- | java/joelib2/io/types/cml/data/cml1_0.dtd | 429 |
1 files changed, 0 insertions, 429 deletions
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; -> |