<!-- 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;
			%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;
			%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; 
>