From 3cd136861c68b8c24cc653c903c620d55be4b294 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 2 Apr 2012 09:18:14 +0200
Subject: Remove PC descriptor

---
 java/joelib2/io/types/cml/data/cml1_0_1.dtd | 485 ----------------------------
 1 file changed, 485 deletions(-)
 delete mode 100644 java/joelib2/io/types/cml/data/cml1_0_1.dtd

(limited to 'java/joelib2/io/types/cml/data/cml1_0_1.dtd')

diff --git a/java/joelib2/io/types/cml/data/cml1_0_1.dtd b/java/joelib2/io/types/cml/data/cml1_0_1.dtd
deleted file mode 100644
index 706b1ab..0000000
--- a/java/joelib2/io/types/cml/data/cml1_0_1.dtd
+++ /dev/null
@@ -1,485 +0,0 @@
-<!-- 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;
->
-]]>
-
-- 
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