corrected caught exception, this exception changed in commit: 1ef89fb0

Change-Id: Ie2c37ad62fc07ab83d37f83a16391d4ba9442318
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
when IMolecule was removed (27c6f7df) this conditional was broken. ICrystal was not a subclass of IMolecule but it is a subclass of IAtomContainer and so the first condition will match and writeCrystal is never called.

Change-Id: I689200fd52f95b702fae3170572e73431755b61c
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
using array list instead of vector

Change-Id: Ib3193fbbbc0d2d67d3147a68c98036362c39ce96
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
removed settable input stream, this could be reintroduced but should be done via a constructor. the configFile path was corrected and renamed, several small tidy ups to the loading code

Change-Id: Ic46f42fefd41cc7e618b7601b455e3c93a4a0a0b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
moved configuration of MM2 into a single (previously broken) method - resolves unit test in error

Change-Id: Iddefa7eb19f27062d3537645c2b2755c17faa7fb
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
grouping location fields and correcting value (leading slash)

Change-Id: I6be03972ca3163f10fd044bf1e5c931a1b68d736
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
removing stdout

Change-Id: I48d2443a03616c8b993853405f7652b4e5d79129
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>