* basic approach to v2api
* does not work, backup commit
* well, that now compiles
* cleaner
* more cleanup and testing
* get the SWIG wrappers to build
* swig wrappers now build
* switch back to using references to default values
* adjust to new catch version
* move the implementation to v2 and call it from v1
* update the parameter object too
* move debugParse down
* a couple of review changes
* make v2 naming consistent with Python
* first pass at v2 for the ctab parsers
* move a the writing functionality to a different header
this is just an organizational thing at the moment; we still import the writers header in the parsers header so as to not break code
* do v2 of the tpl parser
* fix missing dependency
* Mol2 parser
* move over the XYZ parser
* switch over the PDB parsers too
* get mac and java builds working (hopefully)
* Added xyz2mol file parser and tests
* deleted some comments
* Delete file parser
* Delete file parser test
* Revert "Localb"
* adding all files again
* adding file parser and test
* Updated empty string check
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Updated atom initialization
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Allow zero-atom molecule object
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* file parser improvements and added 0-atom mol test
* added xyz block parser and other fixes
* Added the DetermineBonds library with atomic connectivity determination
* atomic connectivity updates including EHT methhod addition
* incorporated more suggestions
* adding buggy version of determine bond ordering
* added documentation for determineBonds() use
* fixed unfavorable oxygen bond ordering
* suggested updates
* additional error checking and added determine bond ordering radical testing
* divided test files into categories
* added determineBonds() combining connectivity and bond ordering
* edited determineBonds.h documentation, added readme
* small grammar fixes
* more tiny fixes
* one less letter
* another typo fix
* make the xyz2mol functionality optional
* enable that for the CI builds
* Update CMakeLists.txt
Co-authored-by: Sreya Gogineni <74024376+gosreya@users.noreply.github.com>
* array to vector
* get windows DLL builds working
* rename determineBondOrder -> determineBondOrders
* run clang-format
* add python wrappers
rename determineBondOrder->determineBondOrders
* expose XYZ parsers to python
* changes in response to review
Co-authored-by: Sreya Gogineni <gosreya@gmail.edu>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
