If there isn't a reasonable bond vector, simply don't add a hydrogen at
all.

avoid non-finite bond vectors

Apparently the intial download had some issues - wonder if there are
more?

This is extensible and I will be extending it in my other pull request
(including fixing the val...

SDFs from the PDB use the alias feature to describe atom types.
Treating aliases as functional g...

We now do a better job of preserving atom names and residue information

We now include formal charges in mol2

include babelconfig in vector3.h

Put it between atom and bonds so we don't have to read (potentially)
past end of molecule to rea...

Don't read past the end of the molecule looking for UNITY atom type
information.

gzip implementation depended on return false

This currently has a particularly specific check, but I expect other
checks will be needed at so...

Make rules more conservative. Don't adjust bonds in cases where
alternative charges could equal...

Fix problem with pdb_ligands_sdf/3dcv_55e.sdf (and many other structures
I've noticed)

old properties will raise the error

Add SMILES support for elements specified by 3-digit number, e.g. [#101]

See pdb_ligands_sdf/5jzn_gui.sdf for an example where the old rule fails
if you don't punt on ar...

Coordinate vector needs to exist when expanding aliases

Need to parse the charges out of the file before Kekulizing or it
doesn't have the right atomic ...

Just because an N is bonded to an O doesn't mean it should be positively
charged (N.4). See the...

Confirmed code and tests only build if Boost is present, and it can also
be disabled with explic...

This outputs and reads UNITY_ATOM_ATTR records so formal charges can be
roundtripped between mol...

Add fully functional maeparser support for both reading and writing mae/maegz format. Also adde...

Address Ubuntu bug in defining python install dir

Copying a molecule shouldn't trigger chain perception if the src
molecule already has perceived ...

Provide regression test

The OBResidue copy constructor was not being used in the OBMol copy
constructor and components o...

Reset the hybridization perceived flags since hyb is no longer correct
after adding hydrogens

See https://bugs.launchpad.net/ubuntu/+source/python3-defaults/+bug/1814653
Fix might be slightl...

fpsformat.cpp: compile bugfix header added.

headers and so OBAPI is not defined

Rename/add valence and degree methods

Exit with non-zero if an error occurs

Move to a single function for setting/unsetting bond and atom flags

Obrms enhancement

- Fix "SEE ALSO"
- replace `babel` with `obabel`
- fix self-reference
- Remove leading/t...

Add __init__.py to gitignore

Remove low-hanging deprecated methods

Update URLs of specification of gromacs

tools/
- obfragment.cpp
- obsort-fragment.cpp
- obtorsion.cpp

- tools/
- babel.cpp
- obabel.cpp
- obconformer.cpp
- obspectrophore.cpp
- test/...

Update Gaussian format

Improve python script

Make `pybel.Outputfile` compatible with `with` statment

- `from __future__ import print_function`
- replace deprecated `unittest.TestCase.assertEquals` ...

- comment out route section of outputted Gaussian input
- add missing `gzmat` format
- update URLs

Try again removing the old stereo code

Remove OBBond::GetBO() and SetBO()