Parmed

* Started parsing, storing, and writing LINK records from PDB files in the PDB parser and writer
* Improve handling of duplicate templates when converting to OpenMM force field/residue template XML files
* Fix building C++ extensions on macOS Mojave systems with Anaconda or Miniconda Python
* Fixes 1030 - Improve converting from OpenMM-generated force field systems to GROMACS files
* Add `parmed.read_pdb` and `parmed.write_pdb` as aliases to `parmed.read_PDB` and `parmed.write_PDB`
* Overhauled the PDB parser so it is more robust for official RCSB files (but drops some support for storing all of the data in non-conforming PDB files, although all atoms from those are still parsed)
* Fixed CHARMM parameter parsers to avoid failing when reading unsupported parameters (only fails when trying to use them).
* Added support to reading CMAP terms in Amber topology files

There are a number of fixes to this release. In particular:

* Fix building with PGI compilers
* Fixes 979
* Fixes 977
* Fixes 915
* Fixes 756, 840, and 952 (all the same bug)
* Fixes 988
* Fixes 993
* Fixes 991 -- reading Amber topology files now releases the GIL for improved multithreading
* Provides option to write all PDB atom records as `ATOM` instead of some as `HETATM`
* Fixes 999
* Fixes NBFIX handling in GROMACS topology files
* Fixes 970
* Fixes writing GROMACS GRO files so that it matches the reordering done in GROMACS topology files.

A small bugfix release that fixes bond determination in PDB files and PDB file parsing for large files that use a base-36 number system when atom and residue counts pass the allowed limits in the PDB format.

This is the same version released as part of AmberTools 18

This release fixes a handful of issues including:

* Updates to work with the latest version of PyRosetta (thanks to dww100)
* Fixes to improve converting CHARMM parameter and topology files into OpenMM-compatible force field XML files (thanks to jchodera)
* Support for reading raw GROMACS ITP files (without a parent topology) (thanks to SGenheden)
* Fixes sign of torsional angle calculation (thanks to SGenheden)
* Fixes assigning constraints in OpenMM involving angles and for certain rigid waters (thanks to nvidic)

Thanks to everyone for their help with this!

This is a small feature-enhancement release with one small fix
- `parmed.load_file` and `Structure.save` convenience methods now work with file-like objects that support seek and tell operations
- Copying or slicing a `Structure` preserves `TER` cards when writing to a PDB file
- Atom type names are taken from OpenMM's `Atom.id` attribute where applicable