olog - Arginine

xholonWorkbook.xml

<?xml version="1.0" encoding="UTF-8"?>
<!--Xholon Workbook http://www.primordion.com/Xholon/gwt/ MIT License, Copyright (C) Ken Webb, Mon Nov 27 2017 12:22:21 GMT-0500 (EST)-->
<XholonWorkbook>

<Notes><![CDATA[
Xholon
------
Title: olog - Arginine
Description: 
Url: http://www.primordion.com/Xholon/gwt/
InternalName: 7f27a443315d60457a5e8ec17e46699d
Keywords: 

My Notes
--------
November 27, 2017

In this workbook, I implement olog(1) in reference[1] (page 2), "a simple olog about an amino acid called arginine"

For this model, it's cumbersome using class inheritance to represent "is" and composite structure to represent "has".
Instead, the olog objects (types of things) should all be regular IXholon nodes, and the olog arrows should be regular Xholon JavaScript ports.
Ideally, I would specify the model using text such as the following:

<Xholon_String>
D an amino acide found in dairy
A arginine
E an electrically charged side chain
X an amino acid
R a side chain
N an amino group
C a carboxylic acid
A is D
A has E
A is X
D is X
X has N
X has R
X has C
E is R
</Xholon_String>

References
----------
(1) Spivak and Kent (2012) "Ologs: A Categorical Framework for Knowledge Representation"

]]></Notes> 

<_-.XholonClass>
  <PhysicalSystem/>
  
  <AminoAcid>
    <Arginine/>
  </AminoAcid>
  
  <!-- A -> X  "arginine is an amino acid" -->
  <X>
    <A/>
  </X>
  
  <!-- E -> R  "an electrically charged side chain is a side chain" -->
  <R>
    <E/>
  </R>
  
</_-.XholonClass>

<xholonClassDetails>
  <!--<Block>
    <port name="height" connector="Height"/>
  </Block>-->
</xholonClassDetails>

<PhysicalSystem>
  
  <A roleName="arginine">
    <E roleName="an electrically charged side chain"/>
  </A>
  
</PhysicalSystem>

<Blockbehavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
  var a = 123;
  var b = 456;
  var c = a * b;
  if (console) {
    console.log(c);
  }
]]></Blockbehavior>

<Heightbehavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
  var myHeight, testing;
  var beh = {
    postConfigure: function() {
      testing = Math.floor(Math.random() * 10);
      myHeight = this.cnode.parent();
    },
    act: function() {
      myHeight.println(this.toString());
    },
    toString: function() {
      return "testing:" + testing;
    }
  }
]]></Heightbehavior>

<Brickbehavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
  $wnd.xh.Brickbehavior = function Brickbehavior() {}

  $wnd.xh.Brickbehavior.prototype.postConfigure = function() {
    this.brick = this.cnode.parent();
    this.iam = " red brick";
  };

  $wnd.xh.Brickbehavior.prototype.act = function() {
    this.brick.println("I am a" + this.iam);
  };
]]></Brickbehavior>

<Brickbehavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
  console.log("I'm another brick behavior");
]]></Brickbehavior>

<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
<svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
  <g>
    <title>Block</title>
    <rect id="PhysicalSystem/Block" fill="#98FB98" height="50" width="50" x="25" y="0"/>
    <g>
      <title>Height</title>
      <rect id="PhysicalSystem/Block/Height" fill="#6AB06A" height="50" width="10" x="80" y="0"/>
    </g>
  </g>
</svg>
]]></Attribute_String><Attribute_String roleName="setup">${MODELNAME_DEFAULT},${SVGURI_DEFAULT}</Attribute_String></SvgClient>

</XholonWorkbook>