Some of the molecule generate smiles exceptions

[PrayHopeWish]

CDK version is 2.0

private final static SmilesGenerator smiGen = SmilesGenerator.absolute();
String smiles2 = smiGen.create(molecule); // IAtomContainer molecule

Exception is :
Caused by: org.openscience.cdk.exception.CDKException: An InChI could not be generated and used to canonise SMILES: null
at org.openscience.cdk.smiles.SmilesGenerator.inchiNumbers(SmilesGenerator.java:503)
at org.openscience.cdk.smiles.SmilesGenerator.labels(SmilesGenerator.java:471)
at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:375)
at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:325)
... 125 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.openscience.cdk.smiles.SmilesGenerator.inchiNumbers(SmilesGenerator.java:496)
... 129 common frames omitted
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
at org.openscience.cdk.graph.invariant.InChINumbersTools.parseUSmilesNumbers(InChINumbersTools.java:145)
at org.openscience.cdk.graph.invariant.InChINumbersTools.getUSmilesNumbers(InChINumbersTools.java:73)
... 134 common frames omitted

I have debug the inchi code

**org.openscience.cdk.graph.invariant.InChiNumbersTools.java

parseUSmilesNumbers method,**

       ```

if ((index = aux.indexOf("/F:")) >= 0) {
String[] fixedHNumbers = aux.substring(index + 3, aux.indexOf('/', index + 3)).split(";");
for (int i = 0; i < fixedHNumbers.length; i++) {

                String component = fixedHNumbers[i];

                // m, 2m, 3m ... need to lookup number in the base numbering
                if (component.charAt(component.length() - 1) == 'm') {
                    int n = component.length() > 1 ? Integer
                            .parseInt(component.substring(0, component.length() - 1)) : 1;
                    for (int j = 0; j < n; j++) {
                        String[] numbering = baseNumbers[i + j].split(",");
                        first[i + j] = Integer.parseInt(numbering[0]) - 1;
                        for (String number : numbering)
                            numbers[Integer.parseInt(number) - 1] = label++;
                    }
                } else {
                    String[] numbering = component.split(",");
                    first[i] = Integer.parseInt(numbering[0]) - 1;    // error line 
                    for (String number : numbering)
                        numbers[Integer.parseInt(number) - 1] = label++;
                }

_**When parse the AuxInfo the error happened.**    
I think how to set the size of the **first** array can not find the basis. 
**baseNumbers[i + j]**  **first[i + j]**   may be not consider the size of the array._

The molecule is : 
  CDK     0520151716

  9  6  0  0  0  0  0  0  0  0999 V2000
    3.3660    1.0000    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
    4.2320    1.5000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.5000    0.5000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.5000    1.5000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.3660    0.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.3660    2.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    4.2320    0.5000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1160    4.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  6  1  0  0  0  0
  1  7  1  0  0  0  0
M  CHG  1   1  -2
M  CHG  1   8   1
M  CHG  1   9   1
M  END

**The correct Smiles is : F[Si-2](F)(F)(F)(F)F.[H+].[H+]**

[johnmay]

I'm planning on deprecating Universal SMILES (absolute) flavour as it just doesn't work nicely.

You can use

SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Unique);

for this molecule.

[PrayHopeWish]

@johnmay Thanks , I will change to use the new SmilesGenerator(SmiFlavor.Unique);

[johnmay]

Now fixed on master also.

[johnmay]

Thanks for reporting.