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, 429 insertions, 0 deletions
diff --git a/java/joelib2/io/types/cml/data/cml1_0.dtd b/java/joelib2/io/types/cml/data/cml1_0.dtd new file mode 100644 index 0000000..6cafefe --- /dev/null +++ b/java/joelib2/io/types/cml/data/cml1_0.dtd @@ -0,0 +1,429 @@ +<!-- 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; +> |