Resolve Pdbe 5219 (#9)

* first commit bm_reader

* Refactor bound molecule files

1) Move Residue and BoundMolecule classes into models
2) No need to use EditableMol in handle_disconnected_hydrogen
3) Move find_element_in_list into helper
4) Use cif_tools instead of mmcif_category_preproces
5) Get rid of extra AssignStereochemistryFrom3D step
6) Get rid of tuple as bound molecule result, make result as dictionary of ccdresult

* Add bound molecule to intro.md

* write out atom id names in json

* revert preprocessing step in cif_tools
return none instead

* dont use class in test of component formation

* pep8 changes

* minor changes in bm_reader + flake8

* changes in component
make sure component works even when properties and descriptors are
not provided

* Create test_bound_molecule.py

* Update test_bound_molecule.py

* replaced pdbecif with gemmi

* replaced pdbecif with gemmi

* updated test files

* moved boundMolecule fixture to conftest.py

* added test for conformer

* Update setup.py

* Update README.md

* updated with rdkit 2022

* updated boundmolecules reader

* updated readme

* Minor version update

* change in dependencies

* updated with newly added features

* removed unnecessary code

* removed commented codes

* updated rdkit installation instruction

* updated doc strings

* added breaking changes

* added breaking changes

* minor fix

* Added quotes

* updated python to 3.9

* updated rdkit version

* Added Python 3.9

* changed directory structure

* updated flake8 repo

* updated python version

* upgraded black

* some formattings

* removed import of bm_reader

* formatted using black

* formatted using black

* trailing white space removed

* updated dependency requirements

* pinned docutils to 0.16 version

* removed docutils

* updated versions

* updated bm_reader output description

* updated before_script

* python-version specification

* specified python version

* changed actions setup

* removed custom test markers

* python version fix

* replaced recommonmark with myst-parser

* removed recommonmark

* fix webservices test

* added myst_parser extension

* updated markdown documentation

* updated README

* Use tmp_path instead of tmp_dir

* added atom_id

* updated parsing of properties

* handle null values

* bumped to version 0.7.1

---------

Co-authored-by: nurulnad <[email protected]>
Co-authored-by: Lukas Pravda <[email protected]>
Co-authored-by: roshkjr <[email protected]>
Co-authored-by: Stephen Anyango <[email protected]>

pdbeccdutils/__init__.py

@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.7.1"