Improve MolecularContainer.top_up_conformations

Top up from all conformations, not just first.

Fixes https://github.com/jensengroup/propka/issues/147

tests/test_molecular_container.py

@@ -0,0 +1,56 @@
+from propka.input import read_parameter_file, read_molecule_file
+from propka.lib import loadOptions
+from propka.molecular_container import MolecularContainer
+from propka.parameters import Parameters
+from pathlib import Path
+from pytest import approx
+
+TESTS = Path(__file__).resolve().parent
+
+
+def load_molecule(code):
+    pdb_path = TESTS / f"pdb/{code}.pdb"
+    options = [str(pdb_path)]
+    args = loadOptions(options)
+    parameters = read_parameter_file(args.parameters, Parameters())
+    molecule = MolecularContainer(parameters, args)
+    molecule = read_molecule_file(str(pdb_path), molecule)
+    return molecule
+
+
+def test_MolecularContainer_get_pi():
+    molecule = load_molecule("1HPX")
+    molecule.average_of_conformations()
+    molecule.calculate_pka()
+    pi_folded, pi_unfolded = molecule.get_pi()
+    assert pi_folded == approx(9.54, abs=1e-2)
+    assert pi_unfolded == approx(8.90, abs=1e-2)
+
+
+def test_MolecularContainer_top_up_conformations():
+    molecule = load_molecule("conf-alt-AB")
+    assert len(molecule.conformations) == 2
+    assert len(molecule.conformations["1A"]) == 16
+    assert len(molecule.conformations["1B"]) == 16
+
+    molecule = load_molecule("conf-alt-BC")
+    assert len(molecule.conformations) == 3
+    assert len(molecule.conformations["1A"]) == 16
+    assert len(molecule.conformations["1B"]) == 16
+    assert len(molecule.conformations["1C"]) == 16
+
+    molecule = load_molecule("conf-alt-AB-mutant")
+    assert len(molecule.conformations) == 2
+    assert len(molecule.conformations["1A"]) == 16
+    assert len(molecule.conformations["1B"]) == 17
+
+    molecule = load_molecule("conf-model-mutant")
+    assert len(molecule.conformations) == 2
+    assert len(molecule.conformations["1A"]) == 16
+    assert len(molecule.conformations["2A"]) == 17
+
+    molecule = load_molecule("conf-model-missing-atoms")
+    assert len(molecule.conformations) == 3
+    assert len(molecule.conformations["1A"]) == 17
+    assert len(molecule.conformations["2A"]) == 17
+    assert len(molecule.conformations["3A"]) == 17