Sreya Gogineni d6eab054d0 Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557) ...

* 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>

2022-10-06 05:46:08 +02:00

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