<!-- Appendix A - CML DTD-1999-05-15 -->
<!-- Authors:P.Murray-RustH.RzepaThis DTD is fully described in Journal of Chemical Informationand Computer Science, Vol xxx, 1999, pp. xxx-->
<!-- =======================================================-->
<!-- PARAMETER ENTITIES -->
<!-- =======================================================-->
<!-- ======attributes found on almost all elements ==========-->
<!ENTITY % title "titleCDATA#IMPLIED">
<!ENTITY % id "idCDATA#IMPLIED">
<!ENTITY % convention "conventionCDATA"CML"">
<!ENTITY % dictRef "dictRefCDATA#IMPLIED">
<!-- ======linking information ==============================-->
<!ENTITY % simpleLink "hrefCDATA#REQUIRED">
<!-- ======quantifiers and constraints on some primitives ===-->
<!ENTITY % count "countCDATA"1"">
<!ENTITY % size "sizeCDATA#IMPLIED">
<!ENTITY % rows "rowsCDATA#REQUIRED">
<!ENTITY % columns "columnsCDATA#REQUIRED">
<!-- ======constraints on some numeric data primitives ===-->
<!ENTITY % min "minCDATA#IMPLIED">
<!ENTITY % max "maxCDATA#IMPLIED">
<!ENTITY % units "unitsCDATA#IMPLIED">
<!ENTITY % angleUnits "units(degrees | radians) "degrees"">
<!ENTITY % unitsRef "unitsRefCDATA#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 "atomRefsCDATA#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; %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 -->
<!-- =======================================================-->
<!-- NOTEfor elements which have element-specific values for thebuiltin 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; >
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