Clear the ifs stream flags in the outformat reader.

Otherwise the real format reader fails to read the stream in
rare instances.
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
Initialize lattice factor to 1.0 in PWSCF reader.
Merge pull request #9 from dlonie/fix-pwscf-reader

Initialize lattice factor to 1.0 in PWSCF reader.
Add /usr/local/include as a search path for InChI headers.
Fix static build linking to InChI

Typo reported by Igor Fillipov to the mailing list.
Fixes from Fulvio Ciciaco for coordinate parsing.

Some coordinates have "Reduced coordinates (xred)"
which means there are still 3 (non integer) tokens.
Also includes fixes for coordinate starts.
Fixed crash when parsing abinit output.

Ron Cohen contributed a patch for when the typat line extends
to more than one line. Also includes misc. fixes.
Fix for problem reported by Pascal Muller on mailing list. Calling DeleteAtom for a non-H atom invalidates any associated stereo.
LPMDformat:
1. Get rid of warning messages about registering by not registering anything
2. Improve/fix documentation string.
3. Option 'e' is now a boolean as "-e 0" didn't actually do anything.
4. Fix memory leak caused by use of 'new'.
5. 'extra' variable replaced by boolean 'charge' for clarity.
API extension: mol.AddAtom(atom) is now mol.AddAtom(atom, bool forceNewId=false) (preserving old behavior)

This is needed as molA += molB previously modified the atom Ids in molB by setting them all to NoId (there was no other way to pass the information into AddAtom).

(Rather than extend the API, an alternative approach would be to restore the atom Ids in molB after calling AddAtom.)
Copy the stereo when using expressions like mol += molB.
Merge branch 'master' into confab