282 287 atom positioning (#297)

* Fixed an unrelated segfault that was an obstacle.

* Fix for #282 before work can be done on #287.

* Upgrade of Point class to double precision.

* Test file for coplanar pi hydrogenation.

* Pepteditor script for coplanar pi hydrogen test.

* Test of coplanar pi atoms after hydrogenation.

* Updated tests affected by the Point precision.

* Fixed array deletion before array usage.

* Observe pi coplanarity when hydrogenating.

* Updates to tests.

* Retrying...

* Fixed infinite loop.

* Temporarily increasing limit. See #288.

* Unit test.

* Unit test enhancements.

makefile

@@ -14,7 +14,7 @@ all: $(DIRS) \
 	 $(TESTS) \
 	 $(APPS) \
 	 $(REPORTS)
-code: $(OBJS) $(TESTS) amino_report molecule_report $(APPS)
+code: $(DIRS) $(OBJS) $(TESTS) amino_report molecule_report $(APPS)
 primarydock: $(DIRS) $(OBJS) $(BINDIR)/primarydock
 pepteditor: $(DIRS) $(OBJS) $(BINDIR)/pepteditor
 couple: $(DIRS) $(OBJS) $(BINDIR)/couple