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swap ca cb channels #93

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merged 5 commits into from
Jan 29, 2024
Merged

swap ca cb channels #93

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f41ec5c
swap ca cb channels
sunal1996 Dec 19, 2023
cb52d23
add back compatibility
sunal1996 Dec 19, 2023
65eac6d
update version in config
sunal1996 Dec 19, 2023
07e9049
clean-up atom encoder choice
sunal1996 Dec 20, 2023
56c35a2
black format
sunal1996 Dec 20, 2023
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4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "aposteriori"
version = "2.2.0"
version = "2.3.0"
requires-python = ">= 3.8"
readme = "README.md"
dependencies = [
Expand All @@ -16,4 +16,4 @@ dependencies = [
]

[project.scripts]
make-frame-dataset = "aposteriori.data_prep.cli:cli"
make-frame-dataset = "aposteriori.data_prep.cli:cli"
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -5,7 +5,7 @@

setup(
name="aposteriori",
version="2.2.0",
version="2.3.0",
author="Wells Wood Research Group",
author_email="[email protected]",
description="A library for the voxelization of protein structures for protein design.",
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25 changes: 13 additions & 12 deletions src/aposteriori/data_prep/cli.py
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Expand Up @@ -113,11 +113,12 @@
@click.option(
"-ae",
"--atom_encoder",
type=click.Choice(["CNO", "CNOCB", "CNOCBCA", "CNOCBCAQ", "CNOCBCAP"]),
type=click.Choice(["CNO", "CNOCB", "CNOCACB", "CNOCACBQ", "CNOCACBP"]),
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For backwards compatibility, can we add both?

type=click.Choice(["CNO", "CNOCB", "CNOCACB", "CNOCACBQ", "CNOCACBP", "CNOCBCA", "CNOCBCAQ", "CNOCBCAP" ]),

default="CNO",
required=True,
help=(
"Encodes atoms in different channels, depending on atom types. Default is CNO, other options are ´CNOCB´ and `CNOCBCA` to encode the Cb or Cb and Ca in different channels respectively."
"Encodes atoms in different channels, depending on atom types. Default is CNO, other options are ´CNOCB´ and `CNOCACB` to encode the Cb or Cb and Ca in different channels respectively. "
"Charged and polar versions can be used with CNOCACBQ and CNOCACBP respectively."
),
)
@click.option(
Expand Down Expand Up @@ -267,20 +268,20 @@ def cli(
codec = Codec.CNO()
elif atom_encoder == "CNOCB":
codec = Codec.CNOCB()
elif atom_encoder == "CNOCBCA":
codec = Codec.CNOCBCA()
elif atom_encoder == "CNOCBCAQ":
codec = Codec.CNOCBCAQ()
elif atom_encoder == "CNOCBCAP":
codec = Codec.CNOCBCAP()
elif atom_encoder == "CNOCACB":
codec = Codec.CNOCACB()
elif atom_encoder == "CNOCACBQ":
codec = Codec.CNOCACBQ()
elif atom_encoder == "CNOCACBP":
codec = Codec.CNOCACBP()
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Same here maybe let's add both

else:
assert atom_encoder in [
"CNO",
"CNOCB",
"CNOCBCA",
"CNOCBCAQ",
"CNOCBCAP",
], f"Expected encoder to be CNO, CNOCB, CNOCBCA, CNOCBCAQ, CNOCBCAP, but got {atom_encoder}"
"CNOCACB",
"CNOCACBQ",
"CNOCACBP",
], f"Expected encoder to be CNO, CNOCB, CNOCACB, CNOCACBQ, CNOCACBP, but got {atom_encoder}"
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again here.

I would say let's raise a warning if you are using the old encoders saying they are deprecated and will be removed in future versions.


make_frame_dataset(
structure_files=structure_files,
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18 changes: 9 additions & 9 deletions src/aposteriori/data_prep/create_frame_data_set.py
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Expand Up @@ -100,16 +100,16 @@ def CNOCB(cls):
return cls(["C", "N", "O", "CB"])

@classmethod
def CNOCBCA(cls):
return cls(["C", "N", "O", "CB", "CA"])
def CNOCACB(cls):
return cls(["C", "N", "O", "CA", "CB"])

@classmethod
def CNOCBCAQ(cls):
return cls(["C", "N", "O", "CB", "CA", "Q"])
def CNOCACBQ(cls):
return cls(["C", "N", "O", "CA", "CB", "Q"])

@classmethod
def CNOCBCAP(cls):
return cls(["C", "N", "O", "CB", "CA", "P"])
def CNOCACBP(cls):
return cls(["C", "N", "O", "CA", "CB", "P"])

def encode_atom(self, atom_label: str) -> np.ndarray:
"""
Expand Down Expand Up @@ -726,13 +726,13 @@ def create_residue_frame(
# Check whether central atom is C:
if "CA" in codec.atomic_labels:
if voxels_as_gaussian:
np.testing.assert_array_less(frame[centre, centre, centre][4], 1)
np.testing.assert_array_less(frame[centre, centre, centre][3], 1)
assert (
0 < frame[centre, centre, centre][4] <= 1
0 < frame[centre, centre, centre][3] <= 1
), f"The central atom value should be between 0 and 1 but was {frame[centre, centre, centre][4]}"
else:
assert (
frame[centre, centre, centre][4] == 1
frame[centre, centre, centre][3] == 1
), f"The central atom should be Carbon, but it is {frame[centre, centre, centre]}."
else:
if voxels_as_gaussian:
Expand Down
6 changes: 3 additions & 3 deletions tests/test_create_frame_data_set.py
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Expand Up @@ -370,7 +370,7 @@ def test_make_frame_dataset_as_gaussian_cnocacbq():
test_file = TEST_DATA_DIR / "1ubq.pdb"
frame_edge_length = 18.0
voxels_per_side = 31
codec = cfds.Codec.CNOCBCAQ()
codec = cfds.Codec.CNOCACBQ()
ampal_1ubq = ampal.load_pdb(str(test_file))
ampal_1ubq2 = ampal.load_pdb(str(test_file))

Expand Down Expand Up @@ -437,7 +437,7 @@ def test_make_frame_dataset_as_gaussian_cnocacbp():
test_file = TEST_DATA_DIR / "1ubq.pdb"
frame_edge_length = 18.0
voxels_per_side = 31
codec = cfds.Codec.CNOCBCAP()
codec = cfds.Codec.CNOCACBP()

ampal_1ubq = ampal.load_pdb(str(test_file))
ampal_1ubq2 = ampal.load_pdb(str(test_file))
Expand Down Expand Up @@ -544,7 +544,7 @@ def test_cb_atom_filter(residue_number: int):
def test_add_gaussian_at_position():
main_matrix = np.zeros((5, 5, 5, 5), dtype=np.float)
modifiers_triple = (0, 0, 0)
codec = cfds.Codec.CNOCBCA()
codec = cfds.Codec.CNOCACB()

secondary_matrix, atom_idx = codec.encode_gaussian_atom("C", modifiers_triple)
atom_coord = (1, 1, 1)
Expand Down
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