path: root/java/joelib2/io/types/cml/data/cml1_0_1.dtd

<!-- 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;
>
]]>