merge confab into openbabel
put the + symbols back in lpmdformat.cpp
Add jsoncpp 0.6.0-rc2 (amalgamation)
Fix errors in jsoncpp amalgamation process
Add CustomWriter for more control over JSON output when writing files
Add jsoncpp to CMakeLists
Add OBPairBool typdef similar to existing OBPairInteger and OBPairFloatingPoint
Add ChemDoodle JSON format
Merge branch 'confab' of https://github.com/cowsandmilk/openbabel into confab
Clear the ifs stream flags in the outformat reader.

Otherwise the real format reader fails to read the stream in
rare instances.
Porting commits from the original Confab:

torlib.txt, rotor.cpp:
* Using Graph Symmetry, remove symmetrical torsions.
* Reduce the torsions by incorporating graph symmetry. Note that torlib.txt trumps this in the case of CX3 where X is a halide
* Force Forcefield setup always. IsSetupNeeded() fails silently in some cases
Fix tautology reported by clang C++.

If statement with (strlen(line) >= 0) is always true.
Revised to > 0, which was the intended meaning.
Patch from Magnus Lundborg reported to mailing list.

pH model on amidine using -p 7.4 would leave the result uncharged.
Fix potential NULL deference errors indicated by Clang.

Added some "defensive" statements to check for NULLs before
dereferencing. Fixes issues flagged by Clang static analyzer.
Merge pull request #5 from dlonie/clear-stream-flags

Clear the ifs stream flags in the outformat reader.
PkgConfig should not be required - fail gracefully

If PkgConfig is not available then we cannot find Cairo, but this should
fail gracefully so that systems without Cario can simply disbale options.
Merge pull request #6 from cryos/pkg-config-tweak

PkgConfig should not be required - fail gracefully
Patch from Roger Sayle. Reading/writing isotopes with CDXML.
Merge branch 'master' of https://github.com/openbabel/openbabel