[Cdk-commits] CVS: cdk/src/org/openscience/cdk/io/cml CMLCoreModule.java,1.26,1.27 ChemFileCDO.java,1.5,1.6

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/io/cml
In directory sc8-pr-cvs1:/tmp/cvs-serv20156/src/org/openscience/cdk/io/cml

Modified Files:
	CMLCoreModule.java ChemFileCDO.java 
Log Message:
More tests src/org/openscience/cdk/test/io/cml/CMLRoundTripTest.java

Index: CMLCoreModule.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/cml/CMLCoreModule.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- CMLCoreModule.java	27 Aug 2003 08:19:48 -0000	1.26
+++ CMLCoreModule.java	3 Sep 2003 11:42:57 -0000	1.27
@@ -50,6 +50,7 @@
     
     protected int atomCounter;
     protected Vector elsym;
+    protected Vector eltitles;
     protected Vector elid;
     protected Vector formalCharges;
     protected Vector partialCharges;
@@ -107,6 +108,7 @@
             this.BUILTIN = conv.BUILTIN;
             this.atomCounter = conv.atomCounter;
             this.elsym = conv.elsym;
+            this.eltitles = conv.eltitles;
             this.elid = conv.elid;
             this.formalCharges = conv.formalCharges;
             this.partialCharges = conv.partialCharges;
@@ -156,6 +158,7 @@
         atomCounter = 0;
         elsym = new Vector();
         elid = new Vector();
+        eltitles = new Vector();
         formalCharges = new Vector();
         partialCharges = new Vector();
         isotope = new Vector();
@@ -250,6 +253,9 @@
                 else if (att.equals("elementType")) {
                     elsym.addElement(value);
                 } // this is supported in CML 2.0 
+                else if (att.equals("title")) {
+                    eltitles.addElement(value);
+                } // this is supported in CML 2.0 
                 else if (att.equals("x2")) {
                     x2.addElement(value);
                 } // this is supported in CML 2.0 
@@ -423,10 +429,8 @@
             if (bondStereo.size() > bondDictRefs.size())
                 bondDictRefs.addElement(null);
         } else if ("atom".equals(name)) {
-            if (atomCounter > formalCharges.size()) {
-                /* while strictly undefined, assume zero 
-                charge when no number is given */
-                formalCharges.addElement("0");
+            if (atomCounter > eltitles.size()) {
+                eltitles.addElement(null);
             }
             if (atomCounter > hCounts.size()) {
                 /* while strictly undefined, assume zero 
@@ -439,6 +443,11 @@
             if (atomCounter > isotope.size()) {
                 isotope.addElement(null);
             }
+            if (atomCounter > formalCharges.size()) {
+                /* while strictly undefined, assume zero 
+                implicit hydrogens when no number is given */
+                formalCharges.addElement("0");
+            }
             /* It may happen that not all atoms have
             associated 2D or 3D coordinates. accept that */
             if (atomCounter > x2.size() && x2.size() != 0) {
@@ -680,6 +689,10 @@
                 } catch (NumberFormatException exception) {
                     logger.error("Content must a float: " + cData);
                 }
+            } else if (xpath.toString().endsWith("bond/scalar/")) {
+                if (DICTREF.equals("mdl:stereo")) {
+                    bondStereo.addElement(cData.trim());
+                }
             } else {
                 logger.warn("Ignoring scaler: " + xpath);
             }
@@ -795,6 +808,7 @@
         boolean hasPartialCharge = false;
         boolean hasHCounts = false;
         boolean hasSymbols = false;
+        boolean hasTitles = false;
         boolean hasIsotopes = false;
         boolean hasDictRefs = false;
 
@@ -812,6 +826,13 @@
                     "No atom symbols: " + elsym.size() + " != " + atomCounter);
         }
 
+        if (eltitles.size() == atomCounter) {
+            hasTitles = true;
+        } else {
+            logger.debug(
+                    "No atom titles: " + eltitles.size() + " != " + atomCounter);
+        }
+
         if ((x3.size() == atomCounter) && (y3.size() == atomCounter) && 
             (z3.size() == atomCounter)) {
             has3D = true;
@@ -884,11 +905,26 @@
             if (hasID) {
                 cdo.setObjectProperty("Atom", "id", (String)elid.elementAt(i));
             }
+            if (hasTitles) {
+                if (hasSymbols) {
+                    String symbol = (String)elsym.elementAt(i);
+                    if (symbol.equals("Du") || symbol.equals("Dummy")) {
+                        cdo.setObjectProperty("PseudoAtom", "label", (String)eltitles.elementAt(i));
+                    } else {
+                        cdo.setObjectProperty("Atom", "title", (String)eltitles.elementAt(i));
+                    }
+                } else {
+                    cdo.setObjectProperty("Atom", "title", (String)eltitles.elementAt(i));
+                }
+            }
 
             // store optional atom properties
             if (hasSymbols) {
-                cdo.setObjectProperty("Atom", "type", 
-                                      (String)elsym.elementAt(i));
+                String symbol = (String)elsym.elementAt(i);
+                if (symbol.equals("Du") || symbol.equals("Dummy")) {
+                    symbol = "R";
+                }
+                cdo.setObjectProperty("Atom", "type", symbol);
             }
 
             if (has3D) {

Index: ChemFileCDO.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/cml/ChemFileCDO.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- ChemFileCDO.java	20 Aug 2003 15:10:35 -0000	1.5
+++ ChemFileCDO.java	3 Sep 2003 11:42:57 -0000	1.6
@@ -144,6 +144,7 @@
         numberOfAtoms++;
       } else if (objectType.equals("Bond")) {
           bond_id = null;
+          bond_stereo = -99;
       } else if (objectType.equals("Animation")) {
         currentChemSequence = new ChemSequence();
       } else if (objectType.equals("Frame")) {
@@ -210,6 +211,9 @@
                 Atom a2 = currentMolecule.getAtomAt(bond_a2);
                 Bond b = new Bond(a1, a2, bond_order);
                 if (bond_id != null) b.setID(bond_id);
+                if (bond_stereo != -99) {
+                    b.setStereo(bond_stereo);
+                }
                 currentMolecule.addBond(b);
             }
         } else if (objectType.equals("a-axis")) {
@@ -283,9 +287,19 @@
         if (propertyType.equals("id")) {
           currentMolecule.setID(propertyValue);
         }
+      } else if (objectType.equals("PseudoAtom")) {
+        if (propertyType.equals("label")) {
+            if (!(currentAtom instanceof PseudoAtom)) {
+                currentAtom = new PseudoAtom(currentAtom);
+            }
+            ((PseudoAtom)currentAtom).setLabel(propertyValue);
+        }
       } else if (objectType.equals("Atom")) {
         if (propertyType.equals("type")) {
-          currentAtom.setSymbol(propertyValue);
+            if (propertyValue.equals("R") && !(currentAtom instanceof PseudoAtom)) {
+                currentAtom = new PseudoAtom(currentAtom);
+            }
+            currentAtom.setSymbol(propertyValue);
         } else if (propertyType.equals("x2")) {
           currentAtom.setX2D(new Double(propertyValue).doubleValue());
         } else if (propertyType.equals("y2")) {
@@ -328,6 +342,12 @@
             logger.error("Cannot convert to double: " + propertyValue);
             bond_order = 1.0;
           }
+        } else if (propertyType.equals("stereo")) {
+            if (propertyValue.equals("H")) {
+                bond_stereo = CDKConstants.STEREO_BOND_DOWN;
+            } else if (propertyValue.equals("W")) {
+                bond_stereo = CDKConstants.STEREO_BOND_UP;
+            }
         }
       } else if (objectType.equals("Reaction")) {
         if (propertyType.equals("id")) {