Add more cjson features, including conformer energies

Fix parsing "Gaussian" vibration output from xtb program

Support for segment names in pdb files

Proper aromatic support for CML

Writing out was buggy (wrong n to snprintf). Modify test to evaluate
segnames with obabel and o...

Make sure to add cell vectors & space group info to CJSON

Signed-off-by: Geoff Hutchison <[email protected]>

Add support for range-based for loops

Different segments should have different residues.

fix bug when read gro file as first residue idx is 0

* Add OBMol::GetAtoms(), OBMol::GetBonds() and OBAtom::GetBonds().
* These methods return ranges...

obrms improvements

Fix bug in distance geometry code

* This bug was discovered while testing out the new iterators. The old
iterator marcos used it...

By default do not wrap atomic coordinates to the unit cell

In most inorganic cases, the atomic coordinates are already
fractional and this shouldn't matter...

Was using format strings in two places. _Now_ macos CI should pass?

Ideally would use a newer python version, but how to do that escapes me
(it is installed).

Fixed alignment of partial charges for PDBQT-files

fix: vaspformat

refactor: remove deprecated std::bind2nd

Signed-off-by: Geoff Hutchison <[email protected]>

* updated runner python setup

* set python version for runner

* trying a setuptools upgrad...

Co-authored-by: Magnus Rahm <[email protected]>

Add timeout option (necessary for mols with many symmetries) and fix bug
with default behavior (...

* when the first resid is 0, it will trigger object res without initialization
* fix with check...

c.f. #2001

- add WRITEONEONLY to Flags
- expand indentation tab
- fix alignment

* Assign implicit hydrogens in PDBQT

Should fix https://github.com/openbabel/openbabel/issues...

* Make sure charge is read as int8 as in spec
Will not handle files from ChemDraw >=8.0 <8.06
...

* update interface pybel.py & testpybel.py

* refactor: do not use `std::binary_function`, which is removed in C++17

fix #2461

* refac...

* WLN Reader Additions

Added functionality for peri/poly fused rings. Small changes to allow ...

* obminimize: Include the "-o format" option in the help message

* Update the obminimize man ...

Tweak vibration reading for Orca 5, which adds header lines

Signed-off-by: Geoff Hutchison <[email protected]>

Add override keyword

Add deprecated attribute

doc: update man

The macros are defined as `[[deprecated]]` attribute (C++14)
if the feature is available and `SW...

- add missing formats to obabel.1
- remove unnecessary space between flag and argument
- quotati...

Read and write total charge and spin multiplicity when available

* refactor(cmake): remove `SHARED_POINTER` variable
* refactor: remove `HAVE_SHARED_POINTER` ma...

regenerate scripts/R/examples/openbabelR/src/openbabel-R.cpp by SWIG 4.0.2

refactor: use `std::unordered_map` for hash map

replace deprecated `exec_program` with `execute_process` and fix syntax error

Signed-off-by: Geoff Hutchison <[email protected]>

https://cmake.org/cmake/help/v3.1/command/exec_program.html

CMake: fix time check typo (fixes build failure w/ GCC 12)

Without this fixed check, we get a build failure with GCC 12:
```
/var/tmp/portage/sci-chemistry...

* Make sure Perl is found and used to generate data headers

Add support for NMR and electronic spectra in CJSON

Signed-off-by: Geoff Hutchison <[email protected]>

* Fix small test failures from merging

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail....

Add .gitattributes and renormalize EOL

Used <regex> directly

* Fix #2428 Molecular data in png

Co-authored-by: Geoff Hutchison <[email protected]>

Replace deprecated C headers with C++ alternatives

Do not release OpenBabel::OBConformerSearch::m_filter

clang-tidy: readability-delete-null-pointer

Handle implicit hydrogens in cdxml, should fix #2416

* Added test for Gaussian file treatment

* Updated bontyp.txt and gaussformat.cpp

* correct openbabel's help instruction

Once openbabel was called to action by 'openbabel' on ...

Make install-dir configurable for each binding

Fix for bond order detection for azete

Fix bug in tautomer code

python: replace IOError with OSError

test(python): modernize use of asserts

Make FASTA conversion really connect the atoms.

Add destructor to groupcontrib (fix memory leak)

Resolve ImportError with make test

Clean up Tinker formatting and allow for no comment

GitHub Action to lint Python code

More robust pdb reading.

ci: rearrange tar options properly

Fix segfault in OBMol::CopySubstructure()