package org.jmol.adapter.writers; import java.util.Hashtable; import java.util.Stack; import org.jmol.adapter.smarter.AtomSetCollection; import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAdapter; import org.jmol.api.JmolAdapterAtomIterator; import org.jmol.api.JmolAdapterBondIterator; import org.jmol.util.Edge; import org.jmol.viewer.Viewer; import javajs.api.GenericBinaryDocument; import javajs.util.BS; import javajs.util.OC; import javajs.util.P3; import javajs.util.PT; import javajs.util.Rdr; import javajs.util.SB; /** * * Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the * basic necessities for XmlCDXReader. * * * */ public class CDXMLWriter extends CMLWriter { private GenericBinaryDocument doc; private Stack objects = new Stack(); private SB sb = new SB(); private int sbpt; private int id; private final static double STANDARD_BOND_LENGTH = 14.4d; private final static String[] cdxAttributes = { "HashSpacing", "2.50", "MarginWidth", "1.60", "LineWidth", "0.60", "BoldWidth", "2", "BondLength", "14.40", "BondSpacing", "18" }; public CDXMLWriter() { // for JavaScript dynamic loading } @Override public void set(Viewer viewer, OC out, Object[] data) { throw new NullPointerException( "CDXMLWriter is not implemented for writing"); } @Override public String write(BS bs) { throw new NullPointerException( "CDXMLWriter is not implemented for writing"); } public static String fromCDX(GenericBinaryDocument binaryDoc) throws Exception { return new CDXMLWriter().cdxToCdxml(binaryDoc); } public static String fromASC(AtomSetCollection asc) { return new CDXMLWriter().ascToCdxml(asc); } private String ascToCdxml(AtomSetCollection asc) { JmolAdapter a = new SmarterJmolAdapter(); JmolAdapterAtomIterator atomIterator = a.getAtomIterator(asc); JmolAdapterBondIterator bondIterator = a.getBondIterator(asc); openDocument(sb); appendHeader(sb); // includes indexToID = new Hashtable(); while (atomIterator.hasNext()) { openID(sb, "n"); indexToID.put(atomIterator.getUniqueID(), Integer.valueOf(id)); P3 xyz = atomIterator.getXYZ(); int ele = atomIterator.getElement(); int iso = atomIterator.getIsotope(); int charge = atomIterator.getFormalCharge(); addAttribute(sb, "p", cdxCoord(xyz.x, 200) + " " + cdxCoord(-xyz.y, 400)); if (ele != 6) addAttribute(sb, "Element", "" + ele); if (iso != 0) addAttribute(sb, "Isotope", "" + iso); if (charge != 0) addAttribute(sb, "Charge", "" + charge); terminateEmptyTag(sb); } while (bondIterator.hasNext()) { openID(sb, "b"); Object id1 = bondIterator.getAtomUniqueID1(); Object id2 = bondIterator.getAtomUniqueID2(); String order = "1"; String display = null; String display2 = null; int bo = bondIterator.getEncodedOrder(); switch (bo) { case Edge.BOND_AROMATIC: order = "1.5"; display2 = "Dash"; break; case Edge.BOND_AROMATIC_DOUBLE: order = "2"; break; default: if ((bo & 0x07) != 0) order = "" + (bo & 0x07); break; } switch (bo) { case Edge.BOND_STEREO_NEAR: order = "1"; display = "WedgeBegin"; break; case Edge.BOND_STEREO_FAR: order = "1"; display = "WedgedHashBegin"; break; case Edge.BOND_STEREO_EITHER: order = "1"; display = "Wavy"; break; } addAttribute(sb, "B", indexToID.get(id1).toString()); addAttribute(sb, "E", indexToID.get(id2).toString()); if (!order.equals("1")) addAttribute(sb, "Order", order); if (display != null) addAttribute(sb, "Display", display); if (display2 != null) addAttribute(sb, "Display2", display2); terminateEmptyTag(sb); } closeTag(sb, "fragment"); closeTag(sb, "page"); closeTag(sb, "CDXML"); return sb.toString(); } private static String cdxCoord(double x, int off) { return "" + (off + Math.round(x / 1.45d * STANDARD_BOND_LENGTH * 100)/100d); } private void openID(SB sb, String name) { startOpenTag(sb, name); addAttribute(sb, "id", "" + ++id); } private String cdxToCdxml(GenericBinaryDocument doc) throws Exception { this.doc = doc; try { openDocument(sb); appendHeader(sb); doc.setStreamData(null, false);// little-endian doc.seek(22); // header processObject(doc.readShort()); sb.append("\n"); } catch (Exception e) { System.out.println(sb + "\n" + objects); e.printStackTrace(); return null; } return sb.toString(); } private static void appendHeader(SB sb) { sb.append( "\n"); startOpenTag(sb, "CDXML"); addAttributes(sb, cdxAttributes); terminateTag(sb); } /* * Process objects recursively. * */ private void processObject(int type) throws Exception { int id = doc.readInt(); type = type & 0xFFFF; boolean terminated = false; String name = null; // boolean hasAttributes = false; //System.out.println("type " + Integer.toHexString(type) + " id " + id); switch (type) { case kCDXObj_Document: // 0x8000 case kCDXObj_Group: // 0x8002 default: id = Integer.MIN_VALUE; terminated = true; break; case kCDXObj_Page: // 0x8001 name = "page"; id = Integer.MIN_VALUE; // hasAttributes = true; break; case kCDXObj_Fragment: // 0x8003 name = "fragment"; // hasAttributes = true; break; case kCDXObj_Node: // 0x8004 name = "n"; // hasAttributes = true; break; case kCDXObj_Bond: // 0x8005 name = "b"; // hasAttributes = true; break; case kCDXObj_Text: // 0x8006 name = "t"; id = Integer.MIN_VALUE; // hasAttributes = false; break; } sbpt = sb.length(); objects.push(name); if (name != null) { startOpenTag(sb, name); if (id != Integer.MIN_VALUE) { addAttribute(sb, "id", "" + id); } } int prop; while ((prop = doc.readShort()) != 0) { if ((prop & 0x8000) != 0) { if (!terminated) { terminateTag(sb); terminated = true; } processObject(prop); continue; } int len = readLength(); switch (type) { case kCDXObj_Node: writeNodeProperties(prop, len); break; case kCDXObj_Text: if (!terminated) { terminateTag(sb); terminated = true; } writeTextProperty(prop, len); break; case kCDXObj_Bond: writeBondProperties(prop, len); break; default: skip(len); break; } } if (name != null) { if (!terminated) { terminateEmptyTag(sb); } else { closeTag(sb, name); } } } private void writeNodeProperties(int prop, int len) throws Exception { switch (prop) { case kCDXProp_2DPosition: double y = toPoint(readInt(len >> 1)); double x = toPoint(readInt(len >> 1)); addAttribute(sb, "p", x + " " + y); break; case kCDXProp_Node_Type: String nodeType = getNodeType(readInt(len)); // Jmol will put "_" here for nodes it does not need addAttribute(sb, "NodeType", nodeType); break; case kCDXProp_Node_Element: // 0x0402 The atomic number of the atom representing this node. (INT16) addAttribute(sb, "Element", "" + readInt(len)); break; case kCDXProp_Atom_Isotope: // 0x0420 The absolute isotopic mass of an atom (2 for deuterium 14 for carbon-14). (INT16) addAttribute(sb, "Isotope", "" + readInt(len)); break; case kCDXProp_Atom_Charge: // 0x0421 The atomic charge of an atom. (INT8) addAttribute(sb, "Charge", "" + readInt(len)); break; case kCDXProp_ChemicalWarning: addAttribute(sb, "Warning", readString(len)); break; case kCDXProp_Atom_BondOrdering: // 0x0431 An ordering of the bonds to this node used for stereocenters fragments and named alternative groups with more than one attachment. (CDXObjectIDArray) addAttribute(sb, "BondOrdering", readArray()); break; case kCDXProp_Frag_ConnectionOrder: // 0x0505 An ordered list of attachment points within a fragment. (CDXObjectIDArray) addAttribute(sb, "ConnectionOrder", readArray()); break; case kCDXProp_Node_Attachments: // 0x0432 For multicenter attachment nodes or variable attachment nodes a list of IDs of the nodes which are multiply or variably attached to this node. (CDXObjectIDArrayWithCounts) addAttribute(sb, "Attachments", readArray()); break; case kCDXProp_Atom_GenericNickname: // 0x0433 The name of the generic nickname. (CDXString) addAttribute(sb, "GenericNickname", readString(len)); break; default: skip(len); } } private void writeBondProperties(int prop, int len) throws Exception { switch (prop) { case kCDXProp_Bond_Order: String order = getBondOrder(readInt(len)); if (order == null) { removeObject(); return; } addAttribute(sb, "Order", order); break; case kCDXProp_Bond_Display: String d = getBondDisplay(readInt(len)); if (d == null) { removeObject(); return; } addAttribute(sb, "Display", d); break; case kCDXProp_Bond_Display2: String d2 = getBondDisplay(readInt(len)); if (d2 != null) addAttribute(sb, "Display2", d2); break; case kCDXProp_Bond_Begin: addAttribute(sb, "B", "" + readInt(len)); break; case kCDXProp_Bond_End: addAttribute(sb, "E", "" + readInt(len)); break; case kCDXProp_Bond_BeginAttach: addAttribute(sb, "BeginAttach", "" + readInt(len)); break; case kCDXProp_Bond_EndAttach: addAttribute(sb, "EndAttach", "" + readInt(len)); break; default: skip(len); } } private void writeTextProperty(int prop, int len) throws Exception { switch (prop) { case kCDXProp_Text: String text = readString(len); System.out.println("CDXMLW text=" + text); openTag(sb, "s"); // remove new line char sb.setLength(sb.length() - 1); sb.append(wrapCData(text)); closeTag(sb, "s"); break; default: skip(len); } } /** * wrap the string as character data, with replacements for [ noted * as a list starting with * after the CDATA termination * * @param s * @return wrapped text */ public static String wrapCData(String s) { return (s.indexOf("&") < 0 && s.indexOf("<") < 0 ? s : "", "]]]]>") + "]]>"); } private static String getNodeType(int n) { String name = null; switch (n) { case kCDXNodeType_Unspecified: return "Unspecified"; case kCDXNodeType_Element: return "Element"; case kCDXNodeType_Nickname: return "Nickname"; case kCDXNodeType_Fragment: return "Fragment"; case kCDXNodeType_GenericNickname: return "GenericNickname"; case kCDXNodeType_MultiAttachment: return "MultiAttachment"; case kCDXNodeType_VariableAttachment: return "VariableAttachment"; case kCDXNodeType_ExternalConnectionPoint: return "ExternalConnectionPoint"; case kCDXNodeType_ElementList: name = "ElementList"; break; case kCDXNodeType_ElementListNickname: name = "ElementListNickname"; break; case kCDXNodeType_Formula: name = "Formula"; break; case kCDXNodeType_AnonymousAlternativeGroup: name = "AnonymousAlternativeGroup"; break; case kCDXNodeType_NamedAlternativeGroup: name = "NamedAnonymousGroup"; break; case kCDXNodeType_LinkNode: name = "LinkNode"; break; } System.err.println("CDXMLWriter Node type " + name + " not identified"); return "_"; } private static String getBondDisplay(int i) { switch (i) { case kCDXBondDisplay_Solid: return "Solid"; case kCDXBondDisplay_Dash: return "Dash"; case kCDXBondDisplay_Hash: return "Hash"; case kCDXBondDisplay_WedgedHashBegin: return "WedgedHashBegin"; case kCDXBondDisplay_WedgedHashEnd: return "WedgedHashEnd"; case kCDXBondDisplay_Bold: return "Bold"; case kCDXBondDisplay_WedgeBegin: return "WedgeBegin"; case kCDXBondDisplay_WedgeEnd: return "WedgeEnd"; case kCDXBondDisplay_Wavy: return "Wavy"; case kCDXBondDisplay_HollowWedgeBegin: return "HollowWedgeBegin"; case kCDXBondDisplay_HollowWedgeEnd: return "HollowWedgeEnd"; case kCDXBondDisplay_WavyWedgeBegin: return "WavyWedgeBegin"; case kCDXBondDisplay_WavyWedgeEnd: return "WavyWedgeEnd"; case kCDXBondDisplay_Dot: return "Dot"; case kCDXBondDisplay_DashDot: return "DashDot"; } return null; } private static String getBondOrder(int i) { switch (i) { case kCDXBondOrder_Single: return "1"; case kCDXBondOrder_Double: return "2"; case kCDXBondOrder_Triple: return "3"; case kCDXBondOrder_Quadruple: return "4"; case kCDXBondOrder_Quintuple: return "5"; case kCDXBondOrder_Sextuple: return "6"; case kCDXBondOrder_Half: return "0.5"; case kCDXBondOrder_OneHalf: return "1.5"; case kCDXBondOrder_TwoHalf: return "2.5"; case kCDXBondOrder_ThreeHalf: return "3.5"; case kCDXBondOrder_FourHalf: return "4.5"; case kCDXBondOrder_FiveHalf: return "5.5"; case kCDXBondOrder_Dative: return "dative"; case kCDXBondOrder_Ionic: return "ionic"; case kCDXBondOrder_Hydrogen: return "hydrogen"; case kCDXBondOrder_ThreeCenter: return "threecenter"; } return null; } private void removeObject() { sb.setLength(sbpt); } private void skip(int len) { doc.seek(doc.getPosition() + len); } private int readInt(int len) throws Exception { switch (len) { case 1: return (256 + doc.readByte()) % 256; case 2: return doc.readShort(); case 4: return doc.readInt(); case 8: return (int) doc.readLong(); } System.err.println("CDXMLWriter.readInt len " + len); return 0; } private String readString(int len) throws Exception { int nStyles = doc.readShort(); len -= 2; switch (nStyles) { case 0: break; default: skip(nStyles * 10); len -= nStyles * 10; break; } return doc.readString(len); } private String readArray() throws Exception { String s = ""; for (int i = doc.readShort(); --i >= 0;) { s += " " + doc.readInt(); } return s.trim(); } private int readLength() throws Exception { int len = doc.readShort(); if (len == -1) { // large 4-byte length len = doc.readInt(); } return len; } private static double toPoint(int i) { return Math.round(i / 655.36) / 100.0; } public static void main(String[] args) { // try { // FileInputStream fis = new FileInputStream("c:/temp/t2.cdx"); // BinaryDocument doc = new BinaryDocument(); // doc.setStream(new BufferedInputStream(fis), false); // System.out.println(fromCDX(doc)); // } catch (Exception e) { // e.printStackTrace(); // } } // from https://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/CDXConstants.h via Excel //General properties. // private final static int kCDXProp_EndObject = 0x0000; // 0x0000 Marks end of object. // private final static int kCDXProp_CreationUserName = 0x0001; // 0x0001 The name of the creator (program user's name) of the document. (CDXString) // private final static int kCDXProp_CreationDate = 0x0002; // 0x0002 The time of object creation. (CDXDate) // private final static int kCDXProp_CreationProgram = 0x0003; // 0x0003 The name of the program including version and platform that created the associated CDX object. ChemDraw 4.0 uses ChemDraw 4.0 as the value of CreationProgram. (CDXString) // private final static int kCDXProp_ModificationUserName = 0x0004; // 0x0004 The name of the last modifier (program user's name) of the document. (CDXString) // private final static int kCDXProp_ModificationDate = 0x0005; // 0x0005 Time of the last modification. (CDXDate) // private final static int kCDXProp_ModificationProgram = 0x0006; // 0x0006 The name of the program including version and platform of the last program to perform a modification. ChemDraw 4.0 uses ChemDraw 4.0 as the value of CreationProgram. (CDXString) // private final static int kCDXProp_Unused1 = 0x0007; // 0x0007 Table of contents. (obsolete) // private final static int kCDXProp_Name = 0x0008; // 0x0008 Name of an object. (CDXString) // private final static int kCDXProp_Comment = 0x0009; // 0x0009 An arbitrary string intended to be meaningful to a user. (CDXString) // private final static int kCDXProp_ZOrder = 0x000A; // 0x000A Back-to-front ordering index in 2D drawing. (INT16) // private final static int kCDXProp_RegistryNumber = 0x000B; // 0x000B A registry or catalog number of a molecule object. (CDXString) // private final static int kCDXProp_RegistryAuthority = 0x000C; // 0x000C A string that specifies the authority which issued a registry or catalog number. Some examples of registry authorities are CAS Beilstein Aldrich and Merck. (CDXString) // private final static int kCDXProp_Unused2 = 0x000D; // 0x000D Indicates that this object (the reference object) is an alias to an object elsewhere in the document (the target object). The attributes and contained objects should be taken from the target object. (obsolete) // private final static int kCDXProp_RepresentsProperty = 0x000E; // 0x000E Indicates that this object represents some property in some other object. (CDXRepresentsProperty) // private final static int kCDXProp_IgnoreWarnings = 0x000F; // 0x000F Signifies whether chemical warnings should be suppressed on this object. (CDXBooleanImplied) private final static int kCDXProp_ChemicalWarning = 0x0010; // 0x0010 A warning concerning possible chemical problems with this object. (CDXString) // private final static int kCDXProp_Visible = 0x0011; // 0x0011 The object is visible if non-zero. (CDXBoolean) //Fonts. // private final static int kCDXProp_FontTable = 0x0100; // 0x0100 A list of fonts used in the document. (CDXFontTable) //Coordinates. private final static int kCDXProp_2DPosition = 0x0200; // 0x0200 The 2D location (in the order of vertical and horizontal locations) of an object. (CDXPoint2D) // private final static int kCDXProp_3DPosition = 0x0201; // 0x0201 The 3D location (in the order of X- Y- and Z-locations in right-handed coordinate system) of an object in CDX coordinate units. The precise meaning of this attribute varies depending on the type of object. (CDXPoint3D) // private final static int kCDXProp_2DExtent = 0x0202; // 0x0202 The width and height of an object in CDX coordinate units. The precise meaning of this attribute varies depending on the type of object. (CDXPoint2D) // private final static int kCDXProp_3DExtent = 0x0203; // 0x0203 The width height and depth of an object in CDX coordinate units (right-handed coordinate system). The precise meaning of this attribute varies depending on the type of object. (CDXPoint3D) // private final static int kCDXProp_BoundingBox = 0x0204; // 0x0204 The smallest rectangle that encloses the graphical representation of the object. (CDXRectangle) // private final static int kCDXProp_RotationAngle = 0x0205; // 0x0205 The angular orientation of an object in degrees * 65536. (INT32) // private final static int kCDXProp_BoundsInParent = 0x0206; // 0x0206 The bounds of this object in the coordinate system of its parent (used for pages within tables). (CDXRectangle) // private final static int kCDXProp_3DHead = 0x0207; // 0x0207 The 3D location (in the order of X- Y- and Z-locations in right-handed coordinate system) of the head of an object in CDX coordinate units. The precise meaning of this attribute varies depending on the type of object. (CDXPoint3D) // private final static int kCDXProp_3DTail = 0x0208; // 0x0208 The 3D location (in the order of X- Y- and Z-locations in right-handed coordinate system) of the tail of an object in CDX coordinate units. The precise meaning of this attribute varies depending on the type of object. (CDXPoint3D) // private final static int kCDXProp_TopLeft = 0x0209; // 0x0209 The location of the top-left corner of a quadrilateral object possibly in a rotated or skewed frame. (CDXPoint2D) // private final static int kCDXProp_TopRight = 0x020A; // 0x020A The location of the top-right corner of a quadrilateral object possibly in a rotated or skewed frame. (CDXPoint2D) // private final static int kCDXProp_BottomRight = 0x020B; // 0x020B The location of the bottom-right corner of a quadrilateral object possibly in a rotated or skewed frame. (CDXPoint2D) // private final static int kCDXProp_BottomLeft = 0x020C; // 0x020C The location of the bottom-left corner of a quadrilateral object possibly in a rotated or skewed frame. (CDXPoint2D) //Colors. // private final static int kCDXProp_ColorTable = 0x0300; // 0x0300 The color palette used throughout the document. (CDXColorTable) // private final static int kCDXProp_ForegroundColor = 0x0301; // 0x0301 The foreground color of an object represented as the two-based index into the object's color table. (UINT16) // private final static int kCDXProp_BackgroundColor = 0x0302; // 0x0302 The background color of an object represented as the two-based index into the object's color table. (INT16) //Atom properties. private final static int kCDXProp_Node_Type = 0x0400; // 0x0400 The type of a node object. (INT16) // private final static int kCDXProp_Node_LabelDisplay = 0x0401; // 0x0401 The characteristics of node label display. (INT8) private final static int kCDXProp_Node_Element = 0x0402; // 0x0402 The atomic number of the atom representing this node. (INT16) // private final static int kCDXProp_Atom_ElementList = 0x0403; // 0x0403 A list of atomic numbers. (CDXElementList) // private final static int kCDXProp_Atom_Formula = 0x0404; // 0x0404 The composition of a node representing a fragment whose composition is known but whose connectivity is not. For example C4H9 represents a mixture of the 4 butyl isomers. (CDXFormula) private final static int kCDXProp_Atom_Isotope = 0x0420; // 0x0420 The absolute isotopic mass of an atom (2 for deuterium 14 for carbon-14). (INT16) private final static int kCDXProp_Atom_Charge = 0x0421; // 0x0421 The atomic charge of an atom. (INT8) // private final static int kCDXProp_Atom_Radical = 0x0422; // 0x0422 The atomic radical attribute of an atom. (UINT8) // private final static int kCDXProp_Atom_RestrictFreeSites = 0x0423; // 0x0423 Indicates that up to the specified number of additional substituents are permitted on this atom. (UINT8) // private final static int kCDXProp_Atom_RestrictImplicitHydrogens = 0x0424; // 0x0424 Signifies that implicit hydrogens are not allowed on this atom. (CDXBooleanImplied) // private final static int kCDXProp_Atom_RestrictRingBondCount = 0x0425; // 0x0425 The number of ring bonds attached to an atom. (INT8) // private final static int kCDXProp_Atom_RestrictUnsaturatedBonds = 0x0426; // 0x0426 Indicates whether unsaturation should be present or absent. (INT8) // private final static int kCDXProp_Atom_RestrictRxnChange = 0x0427; // 0x0427 If present signifies that the reaction change of an atom must be as specified. (CDXBooleanImplied) // private final static int kCDXProp_Atom_RestrictRxnStereo = 0x0428; // 0x0428 The change of stereochemistry of an atom during a reaction. (INT8) // private final static int kCDXProp_Atom_AbnormalValence = 0x0429; // 0x0429 Signifies that an abnormal valence for an atom is permitted. (CDXBooleanImplied) // private final static int kCDXProp_Unused3 = 0x042A; // 0x042A // private final static int kCDXProp_Atom_NumHydrogens = 0x042B; // 0x042B The number of (explicit) hydrogens in a labeled atom consisting of one heavy atom and (optionally) the symbol H (e.g. CH3). (UINT16) // private final static int kCDXProp_Unused4 = 0x042C; // 0x042C // private final static int kCDXProp_Unused5 = 0x042D; // 0x042D // private final static int kCDXProp_Atom_HDot = 0x042E; // 0x042E Signifies the presence of an implicit hydrogen with stereochemistry specified equivalent to an explicit H atom with a wedged bond. (CDXBooleanImplied) // private final static int kCDXProp_Atom_HDash = 0x042F; // 0x042F Signifies the presence of an implicit hydrogen with stereochemistry specified equivalent to an explicit H atom with a hashed bond. (CDXBooleanImplied) // private final static int kCDXProp_Atom_Geometry = 0x0430; // 0x0430 The geometry of the bonds about this atom. (INT8) private final static int kCDXProp_Atom_BondOrdering = 0x0431; // 0x0431 An ordering of the bonds to this node used for stereocenters fragments and named alternative groups with more than one attachment. (CDXObjectIDArray) private final static int kCDXProp_Node_Attachments = 0x0432; // 0x0432 For multicenter attachment nodes or variable attachment nodes a list of IDs of the nodes which are multiply or variably attached to this node. (CDXObjectIDArrayWithCounts) private final static int kCDXProp_Atom_GenericNickname = 0x0433; // 0x0433 The name of the generic nickname. (CDXString) // private final static int kCDXProp_Atom_AltGroupID = 0x0434; // 0x0434 The ID of the alternative group object that describes this node. (CDXObjectID) // private final static int kCDXProp_Atom_RestrictSubstituentsUpTo = 0x0435; // 0x0435 Indicates that substitution is restricted to no more than the specified value. (UINT8) // private final static int kCDXProp_Atom_RestrictSubstituentsExactly = 0x0436; // 0x0436 Indicates that exactly the specified number of substituents must be present. (UINT8) // private final static int kCDXProp_Atom_CIPStereochemistry = 0x0437; // 0x0437 The node's absolute stereochemistry according to the Cahn-Ingold-Prelog system. (INT8) // private final static int kCDXProp_Atom_Translation = 0x0438; // 0x0438 Provides for restrictions on whether a given node may match other more- or less-general nodes. (INT8) // private final static int kCDXProp_Atom_AtomNumber = 0x0439; // 0x0439 Atom number as text. (CDXString) // private final static int kCDXProp_Atom_ShowQuery = 0x043A; // 0x043A Show the query indicator if non-zero. (CDXBoolean) // private final static int kCDXProp_Atom_ShowStereo = 0x043B; // 0x043B Show the stereochemistry indicator if non-zero. (CDXBoolean) // private final static int kCDXProp_Atom_ShowAtomNumber = 0x043C; // 0x043C Show the atom number if non-zero. (CDXBoolean) // private final static int kCDXProp_Atom_LinkCountLow = 0x043D; // 0x043D Low end of repeat count for link nodes. (INT16) // private final static int kCDXProp_Atom_LinkCountHigh = 0x043E; // 0x043E High end of repeat count for link nodes. (INT16) // private final static int kCDXProp_Atom_IsotopicAbundance = 0x043F; // 0x043F Isotopic abundance of this atom's isotope. (INT8) // private final static int kCDXProp_Atom_ExternalConnectionType = 0x0440; // 0x0440 Type of external connection for atoms of type kCDXNodeType_ExternalConnectionPoint. (INT8) //Molecule properties. // private final static int kCDXProp_Mole_Racemic = 0x0500; // 0x0500 Indicates that the molecule is a racemic mixture. (CDXBoolean) // private final static int kCDXProp_Mole_Absolute = 0x0501; // 0x0501 Indicates that the molecule has known absolute configuration. (CDXBoolean) // private final static int kCDXProp_Mole_Relative = 0x0502; // 0x0502 Indicates that the molecule has known relative stereochemistry but unknown absolute configuration. (CDXBoolean) // private final static int kCDXProp_Mole_Formula = 0x0503; // 0x0503 The molecular formula representation of a molecule object. (CDXFormula) // private final static int kCDXProp_Mole_Weight = 0x0504; // 0x0504 The average molecular weight of a molecule object. (FLOAT64) private final static int kCDXProp_Frag_ConnectionOrder = 0x0505; // 0x0505 An ordered list of attachment points within a fragment. (CDXObjectIDArray) //Bond properties. private final static int kCDXProp_Bond_Order = 0x0600; // 0x0600 The order of a bond object. (INT16) private final static int kCDXProp_Bond_Display = 0x0601; // 0x0601 The display type of a bond object. (INT16) private final static int kCDXProp_Bond_Display2 = 0x0602; // 0x0602 The display type for the second line of a double bond. (INT16) // private final static int kCDXProp_Bond_DoublePosition = 0x0603; // 0x0603 The position of the second line of a double bond. (INT16) private final static int kCDXProp_Bond_Begin = 0x0604; // 0x0604 The ID of the CDX node object at the first end of a bond. (CDXObjectID) private final static int kCDXProp_Bond_End = 0x0605; // 0x0605 The ID of the CDX node object at the second end of a bond. (CDXObjectID) // private final static int kCDXProp_Bond_RestrictTopology = 0x0606; // 0x0606 Indicates the desired topology of a bond in a query. (INT8) // private final static int kCDXProp_Bond_RestrictRxnParticipation = 0x0607; // 0x0607 Specifies that a bond is affected by a reaction. (INT8) private final static int kCDXProp_Bond_BeginAttach = 0x0608; // 0x0608 Indicates where within the Bond_Begin node a bond is attached. (UINT8) private final static int kCDXProp_Bond_EndAttach = 0x0609; // 0x0609 Indicates where within the Bond_End node a bond is attached. (UINT8) // private final static int kCDXProp_Bond_CIPStereochemistry = 0x060A; // 0x060A The bond's absolute stereochemistry according to the Cahn-Ingold-Prelog system. (INT8) // private final static int kCDXProp_Bond_BondOrdering = 0x060B; // 0x060B Ordered list of attached bond IDs. (CDXObjectIDArray) // private final static int kCDXProp_Bond_ShowQuery = 0x060C; // 0x060C Show the query indicator if non-zero. (CDXBoolean) // private final static int kCDXProp_Bond_ShowStereo = 0x060D; // 0x060D Show the stereochemistry indicator if non-zero. (CDXBoolean) // private final static int kCDXProp_Bond_CrossingBonds = 0x060E; // 0x060E Unordered list of IDs of bonds that cross this one (either above or below). (CDXObjectIDArray) // private final static int kCDXProp_Bond_ShowRxn = 0x060F; // 0x060F Show the reaction-change indicator if non-zero. (CDXBoolean) //Text properties. private final static int kCDXProp_Text = 0x0700; // 0x0700 The text of a text object. (CDXString) // private final static int kCDXProp_Justification = 0x0701; // 0x0701 The horizontal justification of a text object. (INT8) // private final static int kCDXProp_LineHeight = 0x0702; // 0x0702 The line height of a text object. (UINT16) // private final static int kCDXProp_WordWrapWidth = 0x0703; // 0x0703 The word-wrap width of a text object. (INT16) // private final static int kCDXProp_LineStarts = 0x0704; // 0x0704 The number of lines of a text object followed by that many values indicating the zero-based text position of each line start. (INT16ListWithCounts) // private final static int kCDXProp_LabelAlignment = 0x0705; // 0x0705 The alignment of the text with respect to the node position. (INT8) // private final static int kCDXProp_LabelLineHeight = 0x0706; // 0x0706 Text line height for atom labels (INT16) // private final static int kCDXProp_CaptionLineHeight = 0x0707; // 0x0707 Text line height for non-atomlabel text objects (INT16) // private final static int kCDXProp_InterpretChemically = 0x0708; // 0x0708 Signifies whether to the text label should be interpreted chemically (if possible). (CDXBooleanImplied) //Document properties. // private final static int kCDXProp_MacPrintInfo = 0x0800; // 0x0800 The 120 byte Macintosh TPrint data associated with the CDX document object. Refer to Macintosh Toolbox manual for detailed description. (Unformatted) // private final static int kCDXProp_WinPrintInfo = 0x0801; // 0x0801 The Windows DEVMODE structure associated with the CDX document object. (Unformatted) // private final static int kCDXProp_PrintMargins = 0x0802; // 0x0802 The outer margins of the Document. (CDXRectangle) // private final static int kCDXProp_ChainAngle = 0x0803; // 0x0803 The default chain angle setting in degrees * 65536. (INT32) // private final static int kCDXProp_BondSpacing = 0x0804; // 0x0804 The spacing between segments of a multiple bond measured relative to bond length. (INT16) // private final static int kCDXProp_BondLength = 0x0805; // 0x0805 The default bond length. (CDXCoordinate) // private final static int kCDXProp_BoldWidth = 0x0806; // 0x0806 The default bold bond width. (CDXCoordinate) // private final static int kCDXProp_LineWidth = 0x0807; // 0x0807 The default line width. (CDXCoordinate) // private final static int kCDXProp_MarginWidth = 0x0808; // 0x0808 The default amount of space surrounding atom labels. (CDXCoordinate) // private final static int kCDXProp_HashSpacing = 0x0809; // 0x0809 The default spacing between hashed lines used in wedged hashed bonds. (CDXCoordinate) // private final static int kCDXProp_LabelStyle = 0x080A; // 0x080A The default style for atom labels. (CDXFontStyle) // private final static int kCDXProp_CaptionStyle = 0x080B; // 0x080B The default style for non-atomlabel text objects. (CDXFontStyle) // private final static int kCDXProp_CaptionJustification = 0x080C; // 0x080C The horizontal justification of a caption (non-atomlabel text object) (INT8) // private final static int kCDXProp_FractionalWidths = 0x080D; // 0x080D Signifies whether to use fractional width information when drawing text. (CDXBooleanImplied) // private final static int kCDXProp_Magnification = 0x080E; // 0x080E The view magnification factor (INT16) // private final static int kCDXProp_WidthPages = 0x080F; // 0x080F The width of the document in pages. (INT16) // private final static int kCDXProp_HeightPages = 0x0810; // 0x0810 The height of the document in pages. (INT16) // private final static int kCDXProp_DrawingSpaceType = 0x0811; // 0x0811 The type of drawing space used for this document. (INT8) // private final static int kCDXProp_Width = 0x0812; // 0x0812 The width of an object in CDX coordinate units possibly in a rotated or skewed frame. (CDXCoordinate) // private final static int kCDXProp_Height = 0x0813; // 0x0813 The height of an object in CDX coordinate units possibly in a rotated or skewed frame. (CDXCoordinate) // private final static int kCDXProp_PageOverlap = 0x0814; // 0x0814 The amount of overlap of pages when a poster is tiled. (CDXCoordinate) // private final static int kCDXProp_Header = 0x0815; // 0x0815 The text of the header. (CDXString) // private final static int kCDXProp_HeaderPosition = 0x0816; // 0x0816 The vertical offset of the header baseline from the top of the page. (CDXCoordinate) // private final static int kCDXProp_Footer = 0x0817; // 0x0817 The text of the footer. (CDXString) // private final static int kCDXProp_FooterPosition = 0x0818; // 0x0818 The vertical offset of the footer baseline from the bottom of the page. (CDXCoordinate) // private final static int kCDXProp_PrintTrimMarks = 0x0819; // 0x0819 If present trim marks are to printed in the margins. (CDXBooleanImplied) // private final static int kCDXProp_LabelStyleFont = 0x081A; // 0x081A The default font family for atom labels. (INT16) // private final static int kCDXProp_CaptionStyleFont = 0x081B; // 0x081B The default font style for captions (non-atom-label text objects). (INT16) // private final static int kCDXProp_LabelStyleSize = 0x081C; // 0x081C The default font size for atom labels. (INT16) // private final static int kCDXProp_CaptionStyleSize = 0x081D; // 0x081D The default font size for captions (non-atom-label text objects). (INT16) // private final static int kCDXProp_LabelStyleFace = 0x081E; // 0x081E The default font style for atom labels. (INT16) // private final static int kCDXProp_CaptionStyleFace = 0x081F; // 0x081F The default font face for captions (non-atom-label text objects). (INT16) // private final static int kCDXProp_LabelStyleColor = 0x0820; // 0x0820 The default color for atom labels (INT16) // private final static int kCDXProp_CaptionStyleColor = 0x0821; // 0x0821 The default color for captions (non-atom-label text objects). (INT16) // private final static int kCDXProp_BondSpacingAbs = 0x0822; // 0x0822 The absolute distance between segments of a multiple bond. (CDXCoordinate) // private final static int kCDXProp_LabelJustification = 0x0823; // 0x0823 The default justification for atom labels. (INT8) // private final static int kCDXProp_FixInplaceExtent = 0x0824; // 0x0824 Defines a size for OLE In-Place editing. (CDXPoint2D) // private final static int kCDXProp_Side = 0x0825; // 0x0825 A specific side of an object (rectangle). (INT16) // private final static int kCDXProp_FixInplaceGap = 0x0826; // 0x0826 Defines a padding for OLE In-Place editing. (CDXPoint2D) //Graphic object properties. // private final static int kCDXProp_Graphic_Type = 0x0A00; // 0x0A00 The type of graphical object. (INT16) // private final static int kCDXProp_Line_Type = 0x0A01; // 0x0A01 The type of a line object. (INT16) // private final static int kCDXProp_Arrow_Type = 0x0A02; // 0x0A02 The type of arrow object which represents line arrow arc rectangle or orbital. (INT16) // private final static int kCDXProp_Rectangle_Type = 0x0A03; // 0x0A03 The type of a rectangle object. (INT16) // private final static int kCDXProp_Oval_Type = 0x0A04; // 0x0A04 The type of an arrow object that represents a circle or ellipse. (INT16) // private final static int kCDXProp_Orbital_Type = 0x0A05; // 0x0A05 The type of orbital object. (INT16) // private final static int kCDXProp_Bracket_Type = 0x0A06; // 0x0A06 The type of symbol object. (INT16) // private final static int kCDXProp_Symbol_Type = 0x0A07; // 0x0A07 The type of symbol object. (INT16) // private final static int kCDXProp_Curve_Type = 0x0A08; // 0x0A08 The type of curve object. (INT16) // private final static int kCDXProp_Arrow_HeadSize = 0x0A20; // 0x0A20 The size of the arrow's head. (INT16) // private final static int kCDXProp_Arc_AngularSize = 0x0A21; // 0x0A21 The size of an arc (in degrees * 10 so 90 degrees = 900). (INT16) // private final static int kCDXProp_Bracket_LipSize = 0x0A22; // 0x0A22 The size of a bracket. (INT16) // private final static int kCDXProp_Curve_Points = 0x0A23; // 0x0A23 The Bézier curve's control point locations. (CDXCurvePoints) // private final static int kCDXProp_Bracket_Usage = 0x0A24; // 0x0A24 The syntactical chemical meaning of the bracket (SRU mer mon xlink etc). (INT8) // private final static int kCDXProp_Polymer_RepeatPattern = 0x0A25; // 0x0A25 The head-to-tail connectivity of objects contained within the bracket. (INT8) // private final static int kCDXProp_Polymer_FlipType = 0x0A26; // 0x0A26 The flip state of objects contained within the bracket. (INT8) // private final static int kCDXProp_BracketedObjects = 0x0A27; // 0x0A27 The set of objects contained in a BracketedGroup. (CDXObjectIDArray) // private final static int kCDXProp_Bracket_RepeatCount = 0x0A28; // 0x0A28 The number of times a multiple-group BracketedGroup is repeated. (INT16) // private final static int kCDXProp_Bracket_ComponentOrder = 0x0A29; // 0x0A29 The component order associated with a BracketedGroup. (INT16) // private final static int kCDXProp_Bracket_SRULabel = 0x0A2A; // 0x0A2A The label associated with a BracketedGroup that represents an SRU. (CDXString) // private final static int kCDXProp_Bracket_GraphicID = 0x0A2B; // 0x0A2B The ID of a graphical object (bracket brace or parenthesis) associated with a Bracket Attachment. (CDXObjectID) // private final static int kCDXProp_Bracket_BondID = 0x0A2C; // 0x0A2C The ID of a bond that crosses a Bracket Attachment. (CDXObjectID) // private final static int kCDXProp_Bracket_InnerAtomID = 0x0A2D; // 0x0A2D The ID of the node located within the Bracketed Group and attached to a bond that crosses a Bracket Attachment. (CDXObjectID) // private final static int kCDXProp_Curve_Points3D = 0x0A2E; // 0x0A2E The Bézier curve's control point locations. (CDXCurvePoints3D) //Objects. = ; private final static int kCDXObj_Document = 0x8000; // 0x8000 private final static int kCDXObj_Page = 0x8001; // 0x8001 private final static int kCDXObj_Group = 0x8002; // 0x8002 private final static int kCDXObj_Fragment = 0x8003; // 0x8003 private final static int kCDXObj_Node = 0x8004; // 0x8004 private final static int kCDXObj_Bond = 0x8005; // 0x8005 private final static int kCDXObj_Text = 0x8006; // 0x8006 // private final static int kCDXObj_Graphic = 0x8007; // 0x8007 // private final static int kCDXObj_Curve = 0x8008; // 0x8008 // private final static int kCDXObj_EmbeddedObject = 0x8009; // 0x8009 // private final static int kCDXObj_NamedAlternativeGroup = 0x800a; // 0x800a // private final static int kCDXObj_TemplateGrid = 0x800b; // 0x800b // private final static int kCDXObj_RegistryNumber = 0x800c; // 0x800c // private final static int kCDXObj_ReactionScheme = 0x800d; // 0x800d // private final static int kCDXObj_ReactionStep = 0x800e; // 0x800e // private final static int kCDXObj_ObjectDefinition = 0x800f; // 0x800f // private final static int kCDXObj_Spectrum = 0x8010; // 0x8010 // private final static int kCDXObj_ObjectTag = 0x8011; // 0x8011 // private final static int kCDXObj_OleClientItem = 0x8012; // 0x8012 // private final static int kCDXObj_Sequence = 0x8013; // 0x8013 // private final static int kCDXObj_CrossReference = 0x8014; // 0x8014 // private final static int kCDXObj_Splitter = 0x8015; // 0x8015 // private final static int kCDXObj_Table = 0x8016; // 0x8016 // private final static int kCDXObj_BracketedGroup = 0x8017; // 0x8017 // private final static int kCDXObj_BracketAttachment = 0x8018; // 0x8018 // private final static int kCDXObj_CrossingBond = 0x8019; // 0x8019 // private final static int kCDXObj_Border = 0x8020; // 0x8020 // private final static int kCDXObj_Geometry = 0x8021; // 0x8021 // private final static int kCDXObj_Constraint = 0x8022; // 0x8022 // private final static int kCDXObj_TLCPlate = 0x8023; // 0x8023 // private final static int kCDXObj_TLCLane = 0x8024; // 0x8024 // private final static int kCDXObj_TLCSpot = 0x8025; // 0x8025 //Add new objects here // private final static int kCDXObj_UnknownObject = 0x8FFF; // 0x8FFF private final static int kCDXNodeType_Unspecified = 0; private final static int kCDXNodeType_Element = 1; private final static int kCDXNodeType_ElementList = 2; private final static int kCDXNodeType_ElementListNickname = 3; private final static int kCDXNodeType_Nickname = 4; private final static int kCDXNodeType_Fragment = 5; private final static int kCDXNodeType_Formula = 6; private final static int kCDXNodeType_GenericNickname = 7; private final static int kCDXNodeType_AnonymousAlternativeGroup = 8; private final static int kCDXNodeType_NamedAlternativeGroup = 9; private final static int kCDXNodeType_MultiAttachment = 10; private final static int kCDXNodeType_VariableAttachment = 11; private final static int kCDXNodeType_ExternalConnectionPoint = 12; private final static int kCDXNodeType_LinkNode = 13; // private final static int kCDXLabelDisplay_Auto = 1; // private final static int kCDXLabelDisplay_Left = 2; // private final static int kCDXLabelDisplay_Center = 3; // private final static int kCDXLabelDisplay_Right = 4; // private final static int kCDXLabelDisplay_Above = 5; // private final static int kCDXLabelDisplay_Below = 6; // private final static int kCDXLabelDisplay_BestInitial = 7; //Same as MDL codes // private final static int kCDXRadical_None = 0; // private final static int kCDXRadical_Singlet = 1; // private final static int kCDXRadical_Doublet = 2; // private final static int kCDXRadical_Triplet = 3; // private final static int kCDXIsotope_Natural = 0; // private final static int kCDXRingBondCount_Unspecified = -1; // private final static int kCDXRingBondCount_NoRingBonds = 0; // private final static int kCDXRingBondCount_AsDrawn = 1; // private final static int kCDXRingBondCount_SimpleRing = 2; // private final static int kCDXRingBondCount_Fusion = 3; // private final static int kCDXRingBondCount_SpiroOrHigher = 4; // private final static int kCDXUnsaturation_Unspecified = 0; // private final static int kCDXUnsaturation_MustBeAbsent = 1; // private final static int kCDXUnsaturation_MustBePresent = 2; // private final static int kCDXReactionStereo_Unspecified = 0; // private final static int kCDXReactionStereo_Inversion = 1; // private final static int kCDXReactionStereo_Retention = 2; // private final static int kCDXTranslation_Equal = 0; // private final static int kCDXTranslation_Broad = 1; // private final static int kCDXTranslation_Narrow = 2; // private final static int kCDXTranslation_Any = 3; // private final static int kCDXAbundance_Unspecified = 0; // private final static int kCDXAbundance_Any = 1; // private final static int kCDXAbundance_Natural = 2; // private final static int kCDXAbundance_Enriched = 3; // private final static int kCDXAbundance_Deficient = 4; // private final static int kCDXAbundance_Nonnatural = 5; // private final static int kCDXExternalConnection_Unspecified = 0; // private final static int kCDXExternalConnection_Diamond = 1; // private final static int kCDXExternalConnection_Star = 2; // private final static int kCDXExternalConnection_PolymerBead = 3; // private final static int kCDXExternalConnection_Wavy = 4; // private final static int kCDXAtomGeometry_Unknown = 0; // private final static int kCDXAtomGeometry_1Ligand = 1; // private final static int kCDXAtomGeometry_Linear = 2; // private final static int kCDXAtomGeometry_Bent = 3; // private final static int kCDXAtomGeometry_TrigonalPlanar = 4; // private final static int kCDXAtomGeometry_TrigonalPyramidal = 5; // private final static int kCDXAtomGeometry_SquarePlanar = 6; // private final static int kCDXAtomGeometry_Tetrahedral = 7; // private final static int kCDXAtomGeometry_TrigonalBipyramidal = 8; // private final static int kCDXAtomGeometry_SquarePyramidal = 9; // private final static int kCDXAtomGeometry_5Ligand = 10; // private final static int kCDXAtomGeometry_Octahedral = 11; // private final static int kCDXAtomGeometry_6Ligand = 12; // private final static int kCDXAtomGeometry_7Ligand = 13; // private final static int kCDXAtomGeometry_8Ligand = 14; // private final static int kCDXAtomGeometry_9Ligand = 15; // private final static int kCDXAtomGeometry_10Ligand = 16; private final static int kCDXBondOrder_Single = 0x0001; private final static int kCDXBondOrder_Double = 0x0002; private final static int kCDXBondOrder_Triple = 0x0004; private final static int kCDXBondOrder_Quadruple = 0x0008; private final static int kCDXBondOrder_Quintuple = 0x0010; private final static int kCDXBondOrder_Sextuple = 0x0020; private final static int kCDXBondOrder_Half = 0x0040; private final static int kCDXBondOrder_OneHalf = 0x0080; private final static int kCDXBondOrder_TwoHalf = 0x0100; private final static int kCDXBondOrder_ThreeHalf = 0x0200; private final static int kCDXBondOrder_FourHalf = 0x0400; private final static int kCDXBondOrder_FiveHalf = 0x0800; private final static int kCDXBondOrder_Dative = 0x1000; private final static int kCDXBondOrder_Ionic = 0x2000; private final static int kCDXBondOrder_Hydrogen = 0x4000; private final static int kCDXBondOrder_ThreeCenter = 0x8000; // private final static int kCDXBondOrder_SingleOrDouble = kCDXBondOrder_Single | kCDXBondOrder_Double // private final static int kCDXBondOrder_SingleOrAromatic = kCDXBondOrder_Single | kCDXBondOrder_OneHalf // private final static int kCDXBondOrder_DoubleOrAromatic = kCDXBondOrder_Double | kCDXBondOrder_OneHalf // private final static int kCDXBondOrder_Any = -1; private final static int kCDXBondDisplay_Solid = 0; private final static int kCDXBondDisplay_Dash = 1; private final static int kCDXBondDisplay_Hash = 2; private final static int kCDXBondDisplay_WedgedHashBegin = 3; private final static int kCDXBondDisplay_WedgedHashEnd = 4; private final static int kCDXBondDisplay_Bold = 5; private final static int kCDXBondDisplay_WedgeBegin = 6; private final static int kCDXBondDisplay_WedgeEnd = 7; private final static int kCDXBondDisplay_Wavy = 8; private final static int kCDXBondDisplay_HollowWedgeBegin = 9; private final static int kCDXBondDisplay_HollowWedgeEnd = 10; private final static int kCDXBondDisplay_WavyWedgeBegin = 11; private final static int kCDXBondDisplay_WavyWedgeEnd = 12; private final static int kCDXBondDisplay_Dot = 13; private final static int kCDXBondDisplay_DashDot = 14; public static String fromString(Viewer vwr, String type, String mol) { Hashtable htParams = new Hashtable(); htParams.put("filter", "filetype=" + type); Object o; try { o = vwr.getModelAdapter().getAtomSetCollectionFromReader("", Rdr.getBR(mol), htParams); } catch (Exception e) { e.printStackTrace(); return null; } if (o instanceof String) { return null; } return fromASC((AtomSetCollection) o); } // private final static int kCDXBondDoublePosition_AutoCenter = 0x0000; // private final static int kCDXBondDoublePosition_AutoRight = 0x0001; // private final static int kCDXBondDoublePosition_AutoLeft = 0x0002; // private final static int kCDXBondDoublePosition_UserCenter = 0x0100; // private final static int kCDXBondDoublePosition_UserRight = 0x0101; // private final static int kCDXBondDoublePosition_UserLeft = 0x0102; // private final static int kCDXBondTopology_Unspecified = 0; // private final static int kCDXBondTopology_Ring = 1; // private final static int kCDXBondTopology_Chain = 2; // private final static int kCDXBondTopology_RingOrChain = 3; // private final static int kCDXBondReactionParticipation_Unspecified = 0; // private final static int kCDXBondReactionParticipation_ReactionCenter = 1; // private final static int kCDXBondReactionParticipation_MakeOrBreak = 2; // private final static int kCDXBondReactionParticipation_ChangeType = 3; // private final static int kCDXBondReactionParticipation_MakeAndChange = 4; // private final static int kCDXBondReactionParticipation_NotReactionCenter = 5; // private final static int kCDXBondReactionParticipation_NoChange = 6; // private final static int kCDXBondReactionParticipation_Unmapped = 7; // private final static int kCDXTextJustification_Right = -1; // private final static int kCDXTextJustification_Left = 0; // private final static int kCDXTextJustification_Center = 1; // private final static int kCDXTextJustification_Full = 2; // private final static int kCDXTextJustification_Above = 3; // private final static int kCDXTextJustification_Below = 4; // private final static int kCDXTextJustification_Auto = 5; // private final static int kCDXTextJustification_BestInitial = 6; }