New plugin: STL output of VDW surface

Fix #163 by using std::rand() instead of random()

Fix for failure to build JSON formats with MSVC.

Reintroduce the 'charges none' method

Pointcloud format for producing points quasi-randomly distributed on a V...

Hidden surfaces not culled, but Makerware seems happy with it.
No control over # of triangles
CPK...

Added optional probe radius, changed defaout output to bare {x,y,z} tuple with
new option "-xx" f...

Added rule for protonating phosphonate groups (e.g., 1a0q).

Conflicts:
scripts/python/pybel.py

For MSVC, link against a DLL rather than compiling it in. The latter was
causing a link error whi...

Fix #152 by adding missing header required for MSVC

Fix for #143

don't create a new obrandom everytime a random vector is desired

Add PDBQT options to preserve hydrogens and preserve atom naming

not that it matters..

pLineEndBuf was not getting deallocated. In order to do this without causing a crash later, it ...

Fixes #135

Fixed an error with the allExplicit option

Remove duplicate swig files

svg ipython quick fix for #129 that doesn't cause any breaking changes.

The _repr_svg_ method...

(1) Don't cache inchi when generating inchifield smiles
(2) Don't use cached inchi if the user sp...

- Remove the duplicate swig interface files from the `python` directory.
- Remove the rule speci...

CMakeLists.txt: Allow configuring BABEL_DATADIR

This allows installing the architecture independent data outside
the prefix, for example on a mu...

Separate charge from symbol to derive the atomic number

Config -> RbConfig

The method marks ring bonds as potential rotors and supplies some
initial constraints on rings o...

This was left out by the earlier commit while using mmcif as default
plugin for cif files.

If the conformers haven't converged in 5 generations, it seems
unlikely that they will change fu...

Add aoforce format (vibrational analysis from TurboMole).

Check calls before dereferincing pointers. Bug found in PQR generation.

For energy evaluation, default should be not to compute gradients.
Since that's an API/ABI break...

Make sure to check for line length before looking for chiral flags.

Check for gz in extension and compress output if necessary

Read and write UCSF Dock docking scores from comments

GCC5 compatibility from Dominik 'Rathann' Mierzejewski

Swig3 patch from Fedora

Fix probable typo

Make orca require REGEX_H (unix like)

Allow static compilation of inchi (.c) files

Correct name of inchi library

in gamessuk <regex> can be used for windows, but this file uses
features not present in this ver...

Prevent ipython notebook from modifying molecules' coords.

update

Add HM short name to space groups

This helps match some files which do not provide full HM no...

Fix problem with ConnectTheDots and z-ordering.

Use the maximum *possible* radius of the seco...

Z-ordering let's you terminate early if the z dimension is beyond
a cutoff. However, the code w...