* Soft core force field includes torsions with wildcards

* Bug fixes

* Add API to download formal charges for missing templates

* Use formal charges in _createForceField

* Add tests for formal charges

* Download charges from CCD when attempting to solvate

* Fix charges for default ion atom names

* Simplify formal charges logic

* Expose downloadFormalCharges and remove getAllFormalCharges

* Unify and cache CCD lookups

* Fix bugs

* Cache a failed CCD download

* Remove old formalCharges argument from registerTemplate

* Only attempt to download formal charges if they will be used

* Add SMILES to CCD cache

* Clean up new code and add docstrings

* Only apply formal charges when all and only atom names match between the CCD and PDB

* Allow formal charges to be set with or without leaving atoms

* Address concerns from code review

* Remove leftover reference to checkCache

* Do not cap chains in test_charge_and_solvate

* Add forceField optional argument to addSolvent

* Cap with glycine in tests

* Add another test with a charged ligand

* Cosmetic commit to re-trigger tests

* Update pdbfixer/pdbfixer.py

* Can add templates for new residues

* Added documentation on templates

* Bug fixes

* Can add hydrogens to nonstandard residues

* Build against OpenMM dev version

* Fixed typo

* Updated Python versions for CI

* Added required quotes

* Bugfixed chain ID assignment in addSolvent (#287)

* Simplify logic for alphabetic ID extension

* Added `_renameNewChains()` for `addSolvent()` and `addMembrane()`

* Optimizations to _findNearestDistance()

* Minor changes based on review comments

Also remove trailing whitespace.

As to PDB 3TDZ, MK8 is 2-METHYL-L-NORLEUCINE, which is an isomer of LEU.

https://www.rcsb.org/ligand/5OW is based on LYS and appears in PDB 5EIG.

Resolves openmm/pdbfixer#233.

* Fix typos discovered by codespell

* Revert changes to CI

* Revamp PDBFixer testing

* Use GitHub Actions to run a suite of tests
* Switch from nose to pytest (nose has not been supported in years)
* Download a PDB file and track it instead of fetching it during CI
  (RCSB has blocked testing frameworks in the past).

* Add missing environment.yaml file

* Try the workflow on my branch

* Try to fix the pipeline

* Stop building on jms-updates

Updated version in setup.py

Support all lipid types from OpenMM 7.5

Fixed 'See our manual' link

Fixed box vectors for truncated octahedron

Added option to save files in PDBx/mmCIF format

maintain insertion codes