Do no pass stereo information when none (null) was read

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · Oct 16, 2010 · 986e02f · 986e02f
1 parent 7a6fb30
commit 986e02f
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Showing 2 changed files with 28 additions and 14 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLReader.java b/src/main/org/openscience/cdk/io/MDLReader.java
@@ -541,15 +541,22 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                 IAtom a1 = molecule.getAtom(atom1 - 1);
                 IAtom a2 = molecule.getAtom(atom2 - 1);
                 IBond newBond = null;
-                if (order == 1) {
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE, stereo);
-                } else if (order == 2) {
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.DOUBLE, stereo);
-                } else if (order == 3) {
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.TRIPLE, stereo);
+                if (order >= 1 && order <= 3) {
+                    IBond.Order cdkOrder = IBond.Order.SINGLE;
+                    if (order == 2) cdkOrder = IBond.Order.DOUBLE;
+                    if (order == 3) cdkOrder = IBond.Order.TRIPLE;
+                    if (stereo != null) {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, cdkOrder, stereo);
+                    } else {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, cdkOrder);
+                    }
                 } else if (order == 4) {                
                     // aromatic bond
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE, stereo);
+                    if (stereo != null) {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE, stereo);
+                    } else {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE);
+                    }
                     // mark both atoms and the bond as aromatic
                 	newBond.setFlag(CDKConstants.ISAROMATIC, true);
                     a1.setFlag(CDKConstants.ISAROMATIC, true);

diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -657,15 +657,22 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                 IAtom a1 = molecule.getAtom(atom1 - 1);
                 IAtom a2 = molecule.getAtom(atom2 - 1);
                 IBond newBond = null;
-                if (order == 1) {
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE, stereo);
-                } else if (order == 2) {
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.DOUBLE, stereo);
-                } else if (order == 3) {
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.TRIPLE, stereo);
+                if (order >= 1 && order <= 3) {
+                    IBond.Order cdkOrder = IBond.Order.SINGLE;
+                    if (order == 2) cdkOrder = IBond.Order.DOUBLE;
+                    if (order == 3) cdkOrder = IBond.Order.TRIPLE;
+                    if (stereo != null) {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, cdkOrder, stereo);
+                    } else {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, cdkOrder);
+                    }
                 } else if (order == 4) {                
                     // aromatic bond
-                	newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE, stereo);
+                    if (stereo != null) {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE, stereo);
+                    } else {
+                        newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.SINGLE);
+                    }
                     // mark both atoms and the bond as aromatic
                 	newBond.setFlag(CDKConstants.ISAROMATIC, true);
                     a1.setFlag(CDKConstants.ISAROMATIC, true);