package Basic.ChemicalMarkupLanguage;
import org.web3d.x3d.jsail.Core.*;
import org.web3d.x3d.jsail.EnvironmentalEffects.*;
import org.web3d.x3d.jsail.fields.*;
import org.web3d.x3d.jsail.Geometry3D.*;
import org.web3d.x3d.jsail.Grouping.*;
import org.web3d.x3d.jsail.Lighting.*;
import org.web3d.x3d.jsail.Navigation.*;
import org.web3d.x3d.jsail.Rendering.*;
import org.web3d.x3d.jsail.Shape.*;
import org.web3d.x3d.jsail.Text.*;
// Javadoc metadata annotations follow, see below for X3DJSAIL Java source code.
/**
* <p> Autogenerated version of Oxytocin.x3d scene produced from Oxytocin.xml Chemical Markup Language (CML) version 1.0 source file. </p>
<p> Related links: Catalog page <a href="../../../ChemicalMarkupLanguage/OxytocinIndex.html" target="_blank">Oxytocin</a>, source <a href="../../../ChemicalMarkupLanguage/Oxytocin.java">Oxytocin.java</a>, <a href="https://www.web3d.org/x3d/content/examples/X3dResources.html" target="_blank">X3D Resources</a>, <a href="https://www.web3d.org/x3d/content/examples/X3dSceneAuthoringHints.html" target="_blank">X3D Scene Authoring Hints</a>, and <a href="https://www.web3d.org/x3d/content/X3dTooltips.html" target="_blank">X3D Tooltips</a>. </p>
<table style="color:black; border:0px solid; border-spacing:10px 0px;">
<caption>Scene Meta Information</caption>
<tr style="background-color:silver; border-color:silver;">
<td style="text-align:center; padding:10px 0px;"><i>meta tags</i></td>
<td style="text-align:left; padding:10px 0px;"> Document Metadata </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> title </i> </td>
<td> <a href="../../../ChemicalMarkupLanguage/Oxytocin.x3d">Oxytocin.x3d</a> </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> description </i> </td>
<td> Autogenerated version of Oxytocin.x3d scene produced from Oxytocin.xml Chemical Markup Language (CML) version 1.0 source file. </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> creator </i> </td>
<td> Nicholas F. Polys </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> translator </i> </td>
<td> Don Brutzman </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> created </i> </td>
<td> 24 November 2005 </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> translated </i> </td>
<td> 2 JAN 2025 </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> modified </i> </td>
<td> 2 JAN 2025 </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> reference </i> </td>
<td> <a href="../../../ChemicalMarkupLanguage/Oxytocin.xml">Oxytocin.xml</a> </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> reference </i> </td>
<td> CML sources <a href="https://www.xml-cml.org" target="_blank">https://www.xml-cml.org</a> </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> reference </i> </td>
<td> Wikipedia <a href="https://en.wikipedia.org/wiki/Chemical_Markup_Language" target="_blank">https://en.wikipedia.org/wiki/Chemical_Markup_Language</a> </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> reference </i> </td>
<td> JUMBO Chemical Format Conversion Tool </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> reference </i> </td>
<td> <a href="https://webbook.nist.gov/chemistry" target="_blank">https://webbook.nist.gov/chemistry</a> </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> reference </i> </td>
<td> <a href="../../../ChemicalMarkupLanguage/Polys.StylesheetTransformationsInteractiveVisualization.Web3d2003Symposium.pdf">Polys.StylesheetTransformationsInteractiveVisualization.Web3d2003Symposium.pdf</a> </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> reference </i> </td>
<td> Originally Published in Proceedings of Web3D 2003, ACM Press </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> generator </i> </td>
<td> CmlToX3d.xslt </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> identifier </i> </td>
<td> <a href="https://www.web3d.org/x3d/content/examples/Basic/ChemicalMarkupLanguage/Oxytocin.x3d" target="_blank">https://www.web3d.org/x3d/content/examples/Basic/ChemicalMarkupLanguage/Oxytocin.x3d</a> </td>
</tr>
<tr>
<td style="text-align:right; vertical-align: text-top;"> <i> license </i> </td>
<td> <a href="../../../ChemicalMarkupLanguage/../license.html">../license.html</a> </td>
</tr>
<tr style="background-color:silver; border-color:silver;">
<td style="text-align:center;" colspan="2"> </td>
</tr>
</table>
<p>
This program uses the
<a href="https://www.web3d.org/specifications/java/X3DJSAIL.html" target="_blank">X3D Java Scene Access Interface Library (X3DJSAIL)</a>.
It has been produced using the
<a href="https://www.web3d.org/x3d/stylesheets/X3dToJava.xslt" target="_blank">X3dToJava.xslt</a>
stylesheet
(<a href="https://sourceforge.net/p/x3d/code/HEAD/tree/www.web3d.org/x3d/stylesheets/X3dToJava.xslt" target="_blank">version control</a>)
which is used to create Java source code from an original <code>.x3d</code> model.
</p>
* @author Nicholas F. Polys
*/
public class Oxytocin
{
/** Default constructor to create this object. */
public Oxytocin ()
{
initialize();
}
/** Create and initialize the X3D model for this object. */
public final void initialize()
{
try { // catch-all
x3dModel = new X3D().setProfile(X3D.PROFILE_IMMERSIVE).setVersion(X3D.VERSION_4_0)
.setHead(new head()
.addMeta(new meta().setName(meta.NAME_TITLE ).setContent("Oxytocin.x3d"))
.addMeta(new meta().setName(meta.NAME_DESCRIPTION).setContent("Autogenerated version of Oxytocin.x3d scene produced from Oxytocin.xml Chemical Markup Language (CML) version 1.0 source file."))
.addMeta(new meta().setName(meta.NAME_CREATOR ).setContent("Nicholas F. Polys"))
.addMeta(new meta().setName(meta.NAME_TRANSLATOR ).setContent("Don Brutzman"))
.addMeta(new meta().setName(meta.NAME_CREATED ).setContent("24 November 2005"))
.addMeta(new meta().setName(meta.NAME_TRANSLATED ).setContent("2 JAN 2025"))
.addMeta(new meta().setName(meta.NAME_MODIFIED ).setContent("2 JAN 2025"))
.addMeta(new meta().setName(meta.NAME_REFERENCE ).setContent("Oxytocin.xml"))
.addMeta(new meta().setName(meta.NAME_REFERENCE ).setContent("CML sources https://www.xml-cml.org"))
.addMeta(new meta().setName(meta.NAME_REFERENCE ).setContent("Wikipedia https://en.wikipedia.org/wiki/Chemical_Markup_Language"))
.addMeta(new meta().setName(meta.NAME_REFERENCE ).setContent("JUMBO Chemical Format Conversion Tool"))
.addMeta(new meta().setName(meta.NAME_REFERENCE ).setContent("https://webbook.nist.gov/chemistry"))
.addMeta(new meta().setName(meta.NAME_REFERENCE ).setContent("Polys.StylesheetTransformationsInteractiveVisualization.Web3d2003Symposium.pdf"))
.addMeta(new meta().setName(meta.NAME_REFERENCE ).setContent("Originally Published in Proceedings of Web3D 2003, ACM Press"))
.addMeta(new meta().setName(meta.NAME_GENERATOR ).setContent("CmlToX3d.xslt"))
.addMeta(new meta().setName(meta.NAME_IDENTIFIER ).setContent("https://www.web3d.org/x3d/content/examples/Basic/ChemicalMarkupLanguage/Oxytocin.x3d"))
.addMeta(new meta().setName(meta.NAME_LICENSE ).setContent("../license.html")))
.setScene(new Scene()
.addChild(new ProtoDeclare("Carbon").setName("Carbon")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoC")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoC_mat").setDiffuseColor(0.0,0.0,0.0).setShininess(.8).setSpecularColor(.29,.3,.29)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(.77)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"C"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Hydrogen").setName("Hydrogen")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoH")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoH_mat").setAmbientIntensity(.0933).setDiffuseColor(.38,.38,.42).setShininess(0.5).setSpecularColor(.53,.53,.53)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(.32)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"H"})
.setFontStyle(new FontStyle().setSize(.4))))))))
.addChild(new ProtoDeclare("Nitrogen").setName("Nitrogen")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoN")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoN_mat").setDiffuseColor(0.0,0.0,.72).setEmissiveColor(0.0,0.0,.13).setSpecularColor(.5,.5,.5)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(.75)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"N"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Oxygen").setName("Oxygen")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoO")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoO_mat").setAmbientIntensity(.487).setDiffuseColor(.54,.05,.25).setShininess(.2).setSpecularColor(.81,.77,.75)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(.73)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"O"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Fluorine").setName("Fluorine")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoF")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoF_mat").setDiffuseColor(1.0,.48,.79).setEmissiveColor(.09,.04,.07)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(.72)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"F"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Silicon").setName("Silicon")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoSi")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoSi_mat").setDiffuseColor(.8,.8,.8)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(1.18)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"Si"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Phosphorus").setName("Phosphorus")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoP")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoP_mat").setAmbientIntensity(.11).setDiffuseColor(.9,.41,0.0).setEmissiveColor(.1,.04,0.0).setShininess(0.8).setSpecularColor(.1,.1,.1)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(1.1)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"P"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Sulphur").setName("Sulphur")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoS")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoS_mat").setAmbientIntensity(.0467).setDiffuseColor(.25,.39,.25).setEmissiveColor(.05,.08,.05).setShininess(0.6).setSpecularColor(.11,.12,.08)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(1.3)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"S"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Chlorine").setName("Chlorine")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoCl")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoCl_mat").setDiffuseColor(.28,.7,0.0).setEmissiveColor(.06,.15,0.0).setShininess(0.8).setSpecularColor(.5,.5,.5)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(1.01)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"Cl"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Bromine").setName("Bromine")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoBr")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoBr_mat").setAmbientIntensity(.0833).setDiffuseColor(.5,.3,.19).setEmissiveColor(.12,.13,.08).setShininess(0.17).setSpecularColor(.08,.08,.05)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(1.14)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"Br"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("Iodine").setName("Iodine")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("atoI")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("atoI_mat").setDiffuseColor(.56,.37,.74).setEmissiveColor(.15,.1,.2).setShininess(.09).setSpecularColor(.12,.12,.12)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(1.33)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"I"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("unknown").setName("unknown")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("position").setType(field.TYPE_SFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new SFVec3f(0.0,0.0,0.0)))
.addField(new field().setName("materialTransparency").setType(field.TYPE_SFFLOAT).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(.6)))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Transform("ato_")
.setIS(new IS()
.addConnect(new connect().setNodeField("translation").setProtoField("position")))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material("ato__mat").setDiffuseColor(1.0,1.0,1.0).setEmissiveColor(.15,.1,.2).setShininess(.09).setSpecularColor(.12,.12,.12)
.setIS(new IS()
.addConnect(new connect().setNodeField("transparency").setProtoField("materialTransparency")))))
.setGeometry(new Sphere().setRadius(1.001)))
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(0.9,0.9,0.9)))
.setGeometry(new Text().setString(new String[] {"?"})
.setFontStyle(new FontStyle().setSize(.8))))))))
.addChild(new ProtoDeclare("line").setName("line")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("bond_set").setType(field.TYPE_MFVEC3F).setAccessType(field.ACCESSTYPE_INPUTOUTPUT).setValue(new MFVec3f(new MFVec3f(new double[] {-1.0,0.0,0.0,1.0,0.0,0.0})))))
.setProtoBody(new ProtoBody()
.addChild(new Group()
.addChild(new Shape()
.setAppearance(new Appearance()
.setMaterial(new Material().setDiffuseColor(1.0,1.0,1.0).setEmissiveColor(1.0,1.0,1.0)))
.setGeometry(new IndexedLineSet().setCoordIndex(new int[] {0,1,-1})
.setCoord(new Coordinate("bondo")
.setIS(new IS()
.addConnect(new connect().setNodeField("point").setProtoField("bond_set")))))))))
.addChild(new ProtoDeclare("title_text").setName("title_text")
.setProtoInterface(new ProtoInterface()
.addField(new field().setName("txt").setType(field.TYPE_MFSTRING).setAccessType(field.ACCESSTYPE_INPUTOUTPUT)))
.setProtoBody(new ProtoBody()
.addChild(new Transform()
.addChild(new Group()
.addChild(new Transform()
.addChild(new Shape()
.setAppearance(new Appearance()
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.addChild(new ProtoInstance("line", "b21").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-8.7071,0.3568,0.0,-9.7662,-0.7804,0.0})))))
.addChild(new ProtoInstance("line", "b22").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-8.7271,0.3568,0.0,-9.2288,1.8507,0.0})))))
.addChild(new ProtoInstance("line", "b22_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-8.687100000000001,0.3568,0.0,-9.1888,1.8507,0.0})))))
.addChild(new ProtoInstance("line", "b23").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-6.7226,-1.4382,0.0,-7.7483,-2.5753,0.0})))))
.addChild(new ProtoInstance("line", "b24").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {2.3078,4.4929,0.0,3.6902,5.1841,0.0})))))
.addChild(new ProtoInstance("line", "b25").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {2.3078,4.4929,0.0,1.3936,5.7416,0.0})))))
.addChild(new ProtoInstance("line", "b26").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {2.2855,-3.5118,0.0,3.6568,-4.2253,0.0})))))
.addChild(new ProtoInstance("line", "b27").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-9.7662,-0.7804,0.0,-11.2825,-0.4459,0.0})))))
.addChild(new ProtoInstance("line", "b28").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-7.7483,-2.5753,0.0,-7.2243,-4.0693,0.0})))))
.addChild(new ProtoInstance("line", "b29").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-7.7483,-2.5753,0.0,-8.7963,-2.4081,0.0})))))
.addChild(new ProtoInstance("line", "b30").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {3.6902,5.1841,0.0,5.2064,5.4405,0.0})))))
.addChild(new ProtoInstance("line", "b31").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {1.3936,5.7416,0.0,2.0291,7.1797,0.0})))))
.addChild(new ProtoInstance("line", "b32").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {3.6568,-4.2253,0.0,5.1841,-4.4818,0.0})))))
.addChild(new ProtoInstance("line", "b33").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-11.2825,-0.4459,0.0,-12.3304,-1.6054,0.0})))))
.addChild(new ProtoInstance("line", "b34").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {5.2064,5.4405,0.0,6.7561,5.1841,0.0})))))
.addChild(new ProtoInstance("line", "b35").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {5.186400000000001,5.4405,0.0,5.2199,6.9791,0.0})))))
.addChild(new ProtoInstance("line", "b35_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {5.2264,5.4405,0.0,5.259899999999999,6.9791,0.0})))))
.addChild(new ProtoInstance("line", "b36").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {2.0291,7.1797,0.0,1.126,8.4507,0.0})))))
.addChild(new ProtoInstance("line", "b37").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {2.0091,7.1797,0.0,3.5587,7.3135,0.0})))))
.addChild(new ProtoInstance("line", "b37_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {2.0491,7.1797,0.0,3.5987,7.3135,0.0})))))
.addChild(new ProtoInstance("line", "b38").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {5.1841,-4.4818,0.0,6.7226,-4.2253,0.0})))))
.addChild(new ProtoInstance("line", "b39").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {5.1841,-4.4818,0.0,5.1841,-6.0203,0.0})))))
.addChild(new ProtoInstance("line", "b40").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-12.3304,-1.6054,0.0,-13.8466,-1.2709,0.0})))))
.addChild(new ProtoInstance("line", "b41").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-12.350399999999999,-1.6054,0.0,-11.8822,-3.0659,0.0})))))
.addChild(new ProtoInstance("line", "b41_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-12.3104,-1.6054,0.0,-11.8422,-3.0659,0.0})))))
.addChild(new ProtoInstance("line", "b42").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {6.7561,5.1841,0.0,8.1385,4.4706,0.0})))))
.addChild(new ProtoInstance("line", "b43").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {6.7561,5.1841,0.0,7.2243,6.6781,0.0})))))
.addChild(new ProtoInstance("line", "b44").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {6.7226,-4.2253,0.0,8.1051,-3.5341,0.0})))))
.addChild(new ProtoInstance("line", "b45").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {6.7026,-4.2253,0.0,7.182,-5.7193,0.0})))))
.addChild(new ProtoInstance("line", "b45_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {6.7425999999999995,-4.2253,0.0,7.2219999999999995,-5.7193,0.0})))))
.addChild(new ProtoInstance("line", "b46").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {8.1385,4.4706,0.0,9.2422,3.3669,0.0})))))
.addChild(new ProtoInstance("line", "b47").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {7.2243,6.6781,0.0,8.7406,6.9791,0.0})))))
.addChild(new ProtoInstance("line", "b48").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {8.1051,-3.5341,0.0,9.2088,-2.4304,0.0})))))
.addChild(new ProtoInstance("line", "b49").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2422,3.3669,0.0,9.9335,1.9845,0.0})))))
.addChild(new ProtoInstance("line", "b50").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2222,3.3669,0.0,10.4597,4.3034,0.0})))))
.addChild(new ProtoInstance("line", "b50_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2622,3.3669,0.0,10.499699999999999,4.3034,0.0})))))
.addChild(new ProtoInstance("line", "b51").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {8.7406,6.9791,0.0,9.2422,8.4507,0.0})))))
.addChild(new ProtoInstance("line", "b52").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2088,-2.4304,0.0,10.4797,-3.3446,0.0})))))
.addChild(new ProtoInstance("line", "b53").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2088,-2.4304,0.0,9.9335,-1.0591,0.0})))))
.addChild(new ProtoInstance("line", "b54").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.9335,1.9845,0.0,10.1787,0.4682,0.0})))))
.addChild(new ProtoInstance("line", "b55").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.9335,1.9845,0.0,11.4274,2.4862,0.0})))))
.addChild(new ProtoInstance("line", "b56").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2422,8.4507,0.0,10.7585,8.774,0.0})))))
.addChild(new ProtoInstance("line", "b57").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2222,8.4507,0.0,8.1966,9.6324,0.0})))))
.addChild(new ProtoInstance("line", "b57_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.2622,8.4507,0.0,8.2366,9.6324,0.0})))))
.addChild(new ProtoInstance("line", "b58").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {10.4797,-3.3446,0.0,10.3237,-4.8943,0.0})))))
.addChild(new ProtoInstance("line", "b59").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.9135,-1.0591,0.0,11.4074,-1.5274,0.0})))))
.addChild(new ProtoInstance("line", "b59_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.9535,-1.0591,0.0,11.4474,-1.5274,0.0})))))
.addChild(new ProtoInstance("line", "b60").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {11.4274,2.4862,0.0,12.5534,1.427,0.0})))))
.addChild(new ProtoInstance("line", "b61").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {11.4274,2.4862,0.0,11.7507,4.0024,0.0})))))
.addChild(new ProtoInstance("line", "b62").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {10.3237,-4.8943,0.0,8.8855,-5.5297,0.0})))))
.addChild(new ProtoInstance("line", "b63").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {10.303700000000001,-4.8943,0.0,11.5412,-5.8085,0.0})))))
.addChild(new ProtoInstance("line", "b63_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {10.3437,-4.8943,0.0,11.581199999999999,-5.8085,0.0})))))
.addChild(new ProtoInstance("line", "b64").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {12.5534,1.427,0.0,14.0473,1.9064,0.0})))))
.addChild(new ProtoInstance("line", "b65").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {8.8655,-5.5297,0.0,8.6983,-7.0794,0.0})))))
.addChild(new ProtoInstance("line", "b65_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {8.9055,-5.5297,0.0,8.738299999999999,-7.0794,0.0})))))
.addChild(new ProtoInstance("line", "b66").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {11.5612,-5.8085,0.0,11.3939,-7.347,0.0})))))
.addChild(new ProtoInstance("line", "b67").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {8.7183,-7.0794,0.0,9.9892,-7.9824,0.0})))))
.addChild(new ProtoInstance("line", "b68").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.9892,-7.9824,0.0,9.7885,-9.5321,0.0})))))
.addChild(new ProtoInstance("line", "b69").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {-3.9355,3.5341,0.0,-2.5753,4.3034,0.0})))))
.addChild(new ProtoInstance("line", "b70").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {9.9335,-1.0591,0.0,10.1787,0.4682,0.0})))))
.addChild(new ProtoInstance("line", "b71").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {11.3739,-7.347,0.0,9.9692,-7.9824,0.0})))))
.addChild(new ProtoInstance("line", "b71_2").setContainerField("children")
.addFieldValue(new fieldValue().setName("bond_set").setValue(new MFVec3f(new MFVec3f(new double[] {11.4139,-7.347,0.0,10.0092,-7.9824,0.0})))))));
}
catch (Exception ex)
{
System.err.println ("*** Further hints on X3DJSAIL errors and exceptions at");
System.err.println ("*** https://www.web3d.org/specifications/java/X3DJSAIL.html");
throw (ex);
}
}
// end of initialize() method
/** The initialized model object, created within initialize() method. */
private X3D x3dModel;
/**
* Provide a
* <a href="https://dzone.com/articles/java-copy-shallow-vs-deep-in-which-you-will-swim" target="_blank">shallow copy</a>
* of the X3D model.
* @see <a href="https://www.web3d.org/specifications/java/javadoc/org/web3d/x3d/jsail/Core/X3D.html">X3D</a>
* @return Oxytocin model
*/
public X3D getX3dModel()
{
return x3dModel;
}
/**
* Default main() method provided for test purposes, uses CommandLine to set global ConfigurationProperties for this object.
* @param args array of input parameters, provided as arguments
* @see <a href="https://www.web3d.org/specifications/java/javadoc/org/web3d/x3d/jsail/Core/X3D.html#handleArguments-java.lang.String:A-">X3D.handleArguments(args)</a>
* @see <a href="https://www.web3d.org/specifications/java/javadoc/org/web3d/x3d/jsail/Core/X3D.html#validationReport--">X3D.validationReport()</a>
* @see <a href="https://www.web3d.org/specifications/java/javadoc/org/web3d/x3d/jsail/CommandLine.html">CommandLine</a>
* @see <a href="https://www.web3d.org/specifications/java/javadoc/org/web3d/x3d/jsail/CommandLine.html#USAGE">CommandLine.USAGE</a>
* @see <a href="https://www.web3d.org/specifications/java/javadoc/org/web3d/x3d/jsail/ConfigurationProperties.html">ConfigurationProperties</a>
*/
public static void main(String args[])
{
System.out.println("Build this X3D model, showing validation diagnostics...");
X3D thisExampleX3dModel = new Oxytocin().getX3dModel();
// System.out.println("X3D model construction complete.");
// next handle command line arguments
boolean hasArguments = (args != null) && (args.length > 0);
boolean validate = true; // default
boolean argumentsLoadNewModel = false;
String fileName = new String();
if (args != null)
{
for (String arg : args)
{
if (arg.toLowerCase().startsWith("-v") || arg.toLowerCase().contains("validate"))
{
validate = true; // making sure
}
if (arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_X3D) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_CLASSICVRML) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_X3DB) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_VRML97) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_EXI) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_GZIP) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_ZIP) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_HTML) ||
arg.toLowerCase().endsWith(X3D.FILE_EXTENSION_XHTML))
{
argumentsLoadNewModel = true;
fileName = arg;
}
}
}
if (argumentsLoadNewModel)
System.out.println("WARNING: \"Basic.ChemicalMarkupLanguage.Oxytocin\" model invocation is attempting to load file \"" + fileName + "\" instead of simply validating itself... file loading ignored.");
else if (hasArguments) // if no arguments provided, this method produces usage warning
thisExampleX3dModel.handleArguments(args);
if (validate)
{
// System.out.println("--- TODO fix duplicated outputs ---"); // omit when duplicated outputs problem is solved/refactored
String validationResults = thisExampleX3dModel.validationReport();
// System.out.println("-----------------------------------"); // omit when duplicated outputs problem is solved/refactored
System.out.print("Basic.ChemicalMarkupLanguage.Oxytocin self-validation test confirmation: ");
if (!validationResults.equals("success"))
System.out.println();
System.out.println(validationResults.trim());
// experimental: test X3DJSAIL output files
// ChemicalMarkupLanguage/Oxytocin_JavaExport.* file validation is checked when building X3D Example Archives
String filenameX3D = "ChemicalMarkupLanguage/Oxytocin_JavaExport.x3d";
String filenameX3DV = "ChemicalMarkupLanguage/Oxytocin_JavaExport.x3dv";
String filenameJSON = "ChemicalMarkupLanguage/Oxytocin_JavaExport.json";
thisExampleX3dModel.toFileX3D (filenameX3D);
thisExampleX3dModel.toFileClassicVRML(filenameX3DV);
// TODO thisExampleX3dModel.toFileJSON (filenameJSON);
}
}
}