Neutralise systems with formal charges from the PDB (#301)

* 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

pdbfixer/tests/test_charge_and_solvate.py

+import pytest
+from pdbfixer import PDBFixer
+import openmm.unit
+
+
+@pytest.mark.parametrize(
+    "pdbCode,soluteCharge",
+    [
+        ("1PO0", -21),
+        ("1A11", 1),
+        ("110D", -5),
+        ("1CNR", 0),
+        ("1ESD", -21),
+        ("25c8", -2),
+    ],
+)
+def test_charge_and_solvate(pdbCode, soluteCharge):
+    """
+    Test that addSolvent successfully neutralises systems
+
+    Parameters
+    ----------
+    pdbCode : str
+        The PDB ID to test
+    soluteCharge : int
+        The formal charge of the solute - should equal the number of chloride
+        ions minus the number of sodium ions in the neutralised system. Note
+        that this may include ions from the original PDB entry.
+    """
+    fixer = PDBFixer(pdbid=pdbCode)
+    fixer.findMissingResidues()
+
+    chainLengths = [len([*chain.residues()]) for chain in fixer.topology.chains()]
+    for chainidx, residx in list(fixer.missingResidues):
+        if residx == 0:
+            fixer.missingResidues[chainidx, residx] = ["GLY"]
+        elif residx == chainLengths[chainidx]:
+            fixer.missingResidues[chainidx, residx] = ["GLY"]
+
+    fixer.findMissingAtoms()
+    fixer.addMissingAtoms()
+    fixer.addMissingHydrogens(pH=7.4)
+
+    fixer.addSolvent(
+        padding=2.0 * openmm.unit.nanometer,
+        ionicStrength=0.1 * openmm.unit.molar,
+        boxShape="dodecahedron",
+    )
+
+    numCl = sum(1 for res in fixer.topology.residues() if res.name.lower() == "cl")
+    numNa = sum(1 for res in fixer.topology.residues() if res.name.lower() == "na")
+    assert soluteCharge == numCl - numNa