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Improve MolecularContainer.top_up_conformations

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Top up from all conformations, not just first.

Fixes https://github.com/jensengroup/propka/issues/147
This commit is contained in:
Thomas Holder
2023-09-17 15:19:25 +02:00
parent fd7b155171
commit 7d78acac6e
8 changed files with 220 additions and 5 deletions
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16
propka/conformation_container.py
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@@ -13,6 +13,7 @@ from propka.coupled_groups import NCCG
from propka.determinants import set_backbone_determinants, set_ion_determinants
from propka.determinants import set_determinants
from propka.group import Group, is_group
from typing import Iterable
_LOGGER = logging.getLogger(__name__)
@@ -553,9 +554,22 @@ class ConformationContainer:
Args:
other: conformation container with atoms to add
"""
self.top_up_from_atoms(other.atoms)
def top_up_from_atoms(self, other_atoms: Iterable["propka.atom.Atom"]):
"""Adds atoms which are missing from this container.
Args:
other_atoms: Reference atoms
"""
my_residue_labels = {a.residue_label for a in self.atoms}
for atom in other.atoms:
res_names = {(a.chain_id, a.res_num): a.res_name for a in self.atoms}
for atom in other_atoms:
if atom.residue_label not in my_residue_labels:
if res_names.setdefault((atom.chain_id, atom.res_num),
atom.res_name) != atom.res_name:
# don't merge different residue types, e.g. alt-loc mutant
continue
self.copy_atom(atom)
def find_group(self, group):

11
propka/molecular_container.py
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@@ -52,10 +52,13 @@ class MolecularContainer:
def top_up_conformations(self):
"""Makes sure that all atoms are present in all conformations."""
first = self.conformations[self.conformation_names[0]]
for name in self.conformation_names[1:]:
if len(self.conformations[name]) < len(first):
self.conformations[name].top_up(first)
ref_atoms = {
atom.residue_label: atom
for name in reversed(self.conformation_names)
for atom in self.conformations[name].atoms
}
for conf in self.conformations.values():
conf.top_up_from_atoms(ref_atoms.values())
def find_covalently_coupled_groups(self):
"""Find covalently coupled groups."""

23
tests/pdb/conf-alt-AB-mutant.pdb Normal file
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@@ -0,0 +1,23 @@
ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N ASER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA ASER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 C ASER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 8 O ASER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 9 CB ASER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 10 OG ASER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 11 N BVAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 12 CA BVAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 13 C BVAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 14 O BVAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 15 CB BVAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 16 CG1BVAL 2 5.960 -4.584 1.310 1.00 0.00 C
ATOM 17 CG2BVAL 2 6.774 -4.559 3.636 1.00 0.00 C
ATOM 18 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 19 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 20 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 21 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
END

19
tests/pdb/conf-alt-AB.pdb Normal file
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@@ -0,0 +1,19 @@
ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N SER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA ASER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 CA BSER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 8 C SER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 9 O SER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 10 CB ASER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 11 CB BSER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 12 OG ASER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 13 OG BSER 2 6.994 -4.577 3.101 1.00 0.00 O
ATOM 14 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 15 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 16 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 17 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
END

19
tests/pdb/conf-alt-BC.pdb Normal file
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@@ -0,0 +1,19 @@
ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N SER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA BSER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 CA CSER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 8 C SER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 9 O SER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 10 CB BSER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 11 CB CSER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 12 OG BSER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 13 OG CSER 2 6.994 -4.577 3.101 1.00 0.00 O
ATOM 14 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 15 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 16 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 17 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
END

45
tests/pdb/conf-model-missing-atoms.pdb Normal file
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@@ -0,0 +1,45 @@
MODEL 1
ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 6 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 7 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 8 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 9 CB VAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 10 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 11 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 12 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 13 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
MODEL 2
ATOM 14 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 15 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 16 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 17 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 18 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 19 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 20 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 21 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 22 CB VAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 23 CG1 VAL 2 5.960 -4.584 1.310 1.00 0.00 C
ATOM 24 CG2 VAL 2 6.774 -4.559 3.636 1.00 0.00 C
ATOM 25 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 26 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 27 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 28 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
MODEL 3
ATOM 29 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 30 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 31 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 32 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 33 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 34 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 35 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
TER
ENDMDL
END

36
tests/pdb/conf-model-mutant.pdb Normal file
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@@ -0,0 +1,36 @@
MODEL 1
ATOM 1 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 2 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 3 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 4 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 5 N SER 2 5.576 -1.566 1.473 1.00 0.00 N
ATOM 6 CA SER 2 6.377 -2.251 2.483 1.00 0.00 C
ATOM 7 C SER 2 7.852 -2.130 2.177 1.00 0.00 C
ATOM 8 O SER 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 9 CB SER 2 5.943 -3.732 2.620 1.00 0.00 C
ATOM 10 OG SER 2 6.285 -4.520 1.474 1.00 0.00 O
ATOM 11 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 12 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 13 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 14 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
MODEL 2
ATOM 15 N GLY 1 2.037 -0.982 0.836 1.00 0.00 N
ATOM 16 CA GLY 1 3.462 -0.865 0.540 1.00 0.00 C
ATOM 17 C GLY 1 4.291 -1.573 1.584 1.00 0.00 C
ATOM 18 O GLY 1 3.777 -2.158 2.541 1.00 0.00 O
ATOM 19 N VAL 2 5.577 -1.568 1.470 1.00 0.00 N
ATOM 20 CA VAL 2 6.380 -2.234 2.491 1.00 0.00 C
ATOM 21 C VAL 2 7.853 -2.130 2.173 1.00 0.00 C
ATOM 22 O VAL 2 8.265 -1.521 1.190 1.00 0.00 O
ATOM 23 CB VAL 2 5.939 -3.746 2.618 1.00 0.00 C
ATOM 24 CG1 VAL 2 5.960 -4.584 1.310 1.00 0.00 C
ATOM 25 CG2 VAL 2 6.774 -4.559 3.636 1.00 0.00 C
ATOM 26 N GLY 3 8.703 -2.681 2.974 1.00 0.00 N
ATOM 27 CA GLY 3 10.128 -2.564 2.677 1.00 0.00 C
ATOM 28 C GLY 3 10.957 -3.272 3.721 1.00 0.00 C
ATOM 29 O GLY 3 10.444 -3.857 4.678 1.00 0.00 O
TER
ENDMDL
END

56
tests/test_molecular_container.py Normal file
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@@ -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