Merge pull request #347 from cdk/patch/18Jul17

Looks good. One minor question.
cdk · Jul 20, 2017 · 73b4cc8 · 73b4cc8
2 parents fea5589 + 7efbb65
commit 73b4cc8
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Showing 7 changed files with 51 additions and 18 deletions.
diff --git a/...c/main/java/org/openscience/cdk/renderer/generators/standard/StandardSgroupGenerator.java b/...c/main/java/org/openscience/cdk/renderer/generators/standard/StandardSgroupGenerator.java
@@ -493,6 +493,8 @@ private static boolean isDigit(char c) {
 
     private static boolean isUnsignedInt(String str) {
         int pos = 0;
+        if (str == null)
+            return false;
         int len = str.length();
         while (pos < len)
             if (!isDigit(str.charAt(pos++)))

diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -1343,21 +1343,28 @@ static boolean isPseudoElement(final String symbol) {
      * @return the specified value
      * @throws CDKException the coordinates specification was not valid
      */
-    static double readMDLCoordinate(final String line, int offset) throws CDKException {
+    double readMDLCoordinate(final String line, int offset) throws CDKException {
         // to be valid the decimal should be at the fifth index (4 sig fig)
-        if (line.charAt(offset + 5) != '.') throw new CDKException("invalid coordinate specification");
-
-        int start = offset;
-        while (line.charAt(start) == ' ')
-            start++;
-
-        int sign = sign(line.charAt(start));
-        if (sign < 0) start++;
-
-        int integral = readUInt(line, start, (offset + 5) - start);
-        int fraction = readUInt(line, offset + 6, 4);
-
-        return sign * (integral * 10000l + fraction) / 10000d;
+        if (line.charAt(offset + 5) != '.') {
+            handleError("Bad coordinate format specified, expected 4 decimal places: " + line.substring(offset));
+            int start = offset;
+            int end   = offset;
+            while (line.charAt(start) == ' ')
+                start++;
+            end = start;
+            while (line.charAt(end) != ' ')
+                end++;
+            return Double.parseDouble(line.substring(start, end));
+        } else {
+            int start = offset;
+            while (line.charAt(start) == ' ')
+                start++;
+            int sign = sign(line.charAt(start));
+            if (sign < 0) start++;
+            int integral = readUInt(line, start, (offset + 5) - start);
+            int fraction = readUInt(line, offset + 6, 4);
+            return sign * (integral * 10000L + fraction) / 10000d;
+        }
     }
 
     /**

diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java
@@ -1037,7 +1037,10 @@ protected static String formatMDLFloat(float fl) {
         nf.setMinimumFractionDigits(4);
         nf.setMaximumFractionDigits(4);
         nf.setGroupingUsed(false);
-        s = nf.format(fl);
+        if (Double.isNaN(fl) || Double.isInfinite(fl))
+            s = "0.0000";
+        else
+            s = nf.format(fl);
         l = 10 - s.length();
         for (int f = 0; f < l; f++)
             fs += " ";

diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000AtomBlockTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000AtomBlockTest.java
@@ -26,6 +26,7 @@
 
 import org.junit.Test;
 import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
@@ -267,17 +268,31 @@ public void invalidAtomSymbol() throws Exception {
 
     @Test
     public void readMDLCoordinate() throws Exception {
-        assertThat(MDLV2000Reader.readMDLCoordinate("    7.8089", 0), is(closeTo(7.8089, 0.1)));
+        assertThat(new MDLV2000Reader().readMDLCoordinate("    7.8089", 0), is(closeTo(7.8089, 0.1)));
     }
 
     @Test
     public void readMDLCoordinate_negative() throws Exception {
-        assertThat(MDLV2000Reader.readMDLCoordinate("   -2.0012", 0), is(closeTo(-2.0012, 0.1)));
+        assertThat(new MDLV2000Reader().readMDLCoordinate("   -2.0012", 0), is(closeTo(-2.0012, 0.1)));
     }
 
     @Test
     public void readMDLCoordinate_offset() throws Exception {
-        assertThat(MDLV2000Reader.readMDLCoordinate("   -2.0012    7.8089", 10), is(closeTo(7.8089, 0.1)));
+        assertThat(new MDLV2000Reader().readMDLCoordinate("   -2.0012    7.8089", 10), is(closeTo(7.8089, 0.1)));
+    }
+
+    @Test
+    public void readOldJmolCoords() throws Exception {
+        MDLV2000Reader reader = new MDLV2000Reader();
+        reader.setReaderMode(IChemObjectReader.Mode.RELAXED);
+        assertThat(reader.readMDLCoordinate("  -2.00120    7.8089", 0), is(closeTo(-2.00120, 0.1)));
+    }
+
+    @Test(expected = CDKException.class)
+    public void readOldJmolCoordsFailOnStrictRead() throws Exception {
+        MDLV2000Reader reader = new MDLV2000Reader();
+        reader.setReaderMode(IChemObjectReader.Mode.STRICT);
+        reader.readMDLCoordinate("  -2.00120    7.8089", 0);
     }
 
 }
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java
@@ -126,6 +126,10 @@ public void distributePartners(IAtom atom, IAtomContainer placedNeighbours, Poin
         Vector2d newDirection = new Vector2d(atom.getPoint2d());
         Vector2d occupiedDirection = new Vector2d(sharedAtomsCenter);
         occupiedDirection.sub(newDirection);
+        // if the placing on the centre atom we get NaNs just give a arbitary direciton the
+        // rest works it's self out
+        if (Math.abs(occupiedDirection.length()) < 0.001)
+            occupiedDirection = new Vector2d(0, 1);
         logger.debug("distributePartners->occupiedDirection.lenght(): " + occupiedDirection.length());
         List<IAtom> atomsToDraw = new ArrayList<IAtom>();
 

diff --git a/tool/sdg/src/main/resources/org/openscience/cdk/layout/custom-templates.smi b/tool/sdg/src/main/resources/org/openscience/cdk/layout/custom-templates.smi
@@ -2,3 +2,4 @@ C1CC2CC1CC3CCC4CC5CCC(C5)CC6CCC(C2)C6CC34 |(2.66,3.73,;3.67,2.74,;2.95,1.35,;1.5
 C12C3C4C5C1[Fe]23456789C%10C9C8C7C%106 |(.57,5.08,;-1.03,5.08,;-1.54,4.13,;-.27,3.41,;1.04,4.13,;-.27,2.8,;.55,2.17,;-1.05,2.17,;-1.57,1.23,;-.29,.5,;1.02,1.23,)|
 C1CCC2C(C1)CC3CC2C4C5CCC6(CCCC7CCCCC76)CCCC(C4C3)C8C9CCCC9CCC58 |(-5.68,12.41,;-6.98,13.16,;-8.28,12.41,;-8.28,10.91,;-6.98,10.16,;-5.68,10.91,;-6.98,8.66,;-8.28,7.91,;-8.28,9.41,;-9.58,10.16,;-10.88,9.41,;-12.17,10.16,;-11.32,10.98,;-11.33,12.32,;-12.35,13.09,;-11.06,13.84,;-11.06,15.34,;-12.35,16.09,;-13.65,15.34,;-14.95,16.09,;-16.25,15.34,;-16.25,13.84,;-14.95,13.09,;-13.65,13.84,;-13.42,12.32,;-13.42,10.82,;-12.14,8.95,;-12.17,7.16,;-10.88,7.91,;-9.58,7.16,;-13.47,7.91,;-14.77,7.16,;-15.08,5.69,;-16.58,5.53,;-17.19,6.9,;-16.07,7.91,;-16.07,9.41,;-14.77,10.16,;-13.47,9.41,)|
 C1CC2CCC1CCC3CCC(CC2)CC3 |(-8.98,3.83,;-8.98,2.33,;-7.68,1.58,;-6.38,2.33,;-6.38,3.83,;-7.68,4.58,;-7.68,6.08,;-3.59,6.08,;-3.59,4.58,;-2.29,3.83,;-2.29,2.33,;-3.59,1.58,;-3.59,0.08,;-7.68,0.08,;-4.88,2.33,;-4.88,3.83,)|
+C1CCC2CCC3CCCCC4CCC(C1)C243 |(3.8,-0.77,;3.8,0.78,;2.46,1.56,;1.14,0.83,;0.71,2.17,;-0.7,2.17,;-1.13,0.83,;-2.46,1.56,;-3.8,0.78,;-3.8,-0.77,;-2.46,-1.54,;-1.13,-0.83,;-0.7,-2.17,;0.71,-2.17,;1.14,-0.83,;2.46,-1.54,;0.01,0.00,)|
diff --git a/tool/sdg/src/main/resources/org/openscience/cdk/layout/macro.smi b/tool/sdg/src/main/resources/org/openscience/cdk/layout/macro.smi
@@ -10,6 +10,7 @@ C1CCCCCCCCC1 |(-1.88,-1.2,;-2.63,0.1,;-1.88,1.4,;-0.37,1.4,;0.38,2.7,;1.88,2.7,;
 C1CCCCCCCCC1 |(-1.53,5.42,;-0.06,5.69,;1.07,4.7,;2.52,5.1,;3.35,3.85,;2.41,2.67,;1.01,3.2,;-0.21,2.32,;-1.65,2.72,;-2.24,4.1,)|
 C1CCCCCCCCC1 |(2.38,2.6,;3.82,3.04,;5.24,2.54,;6.09,1.31,;6.06,-0.19,;5.16,-1.38,;3.72,-1.82,;2.31,-1.33,;1.45,-0.1,;1.48,1.4,)|
 C1CCCCCCCCCCC1 |(-3.19,1.55,;-2.44,0.25,;-0.94,0.25,;-0.19,-1.05,;1.31,-1.05,;2.06,0.25,;1.31,1.55,;2.06,2.85,;1.31,4.15,;-0.19,4.15,;-0.94,2.85,;-2.44,2.85,)| 12 3 1 3
+C1CCCCCCCCCCC1 |(-7.68,1.58,;-6.38,2.33,;-6.38,3.83,;-7.68,4.58,;-7.68,6.08,;-3.59,6.08,;-3.59,4.58,;-4.88,3.83,;-4.88,2.33,;-3.59,1.58,;-3.59,0.08,;-7.68,0.08,)|
 C1CCCCCCCCCCCCC1 |(3.1,1.87,;2.35,0.58,;0.85,0.58,;0.1,-0.72,;-1.4,-0.72,;-2.15,0.58,;-3.65,0.58,;-4.4,1.88,;-3.65,3.17,;-2.15,3.17,;-1.4,4.47,;0.1,4.47,;0.85,3.17,;2.35,3.17,)| 14 2 2 5
 C1CCCCCCCCCCCCC1 |(-4.4,0.1,;-3.65,-1.2,;-2.15,-1.2,;-1.4,0.1,;0.1,0.1,;0.85,-1.2,;2.35,-1.2,;3.1,0.1,;2.35,1.4,;0.85,1.4,;0.1,2.7,;-1.4,2.7,;-2.15,1.4,;-3.65,1.4,)| 14 1 0 2
 C1CCCCCCCCCCCCC1 |(2.6,1.5,;2.6,-0,;1.3,-0.75,;0,0,;-1.3,-0.75,;-2.6,-0,;-3.9,-0.75,;-5.2,-0,;-5.2,1.5,;-3.9,2.25,;-2.6,1.5,;-1.3,2.25,;0,1.5,;1.3,2.25,)| 14 1 0 2