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Fix sidechain hydrogen selection #594

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merged 6 commits into from
Sep 5, 2024
Merged

Fix sidechain hydrogen selection #594

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2d30ce5
format and add hydrogens
BradyAJohnston Sep 5, 2024
1e64278
remove hydrgeons
BradyAJohnston Sep 5, 2024
eaa711c
add `is_side_chain` attribute on import
BradyAJohnston Sep 5, 2024
e7fa248
improve `Is Side Chain` node to add 'CA' option
BradyAJohnston Sep 5, 2024
7254286
update tests for new is_side_chain
BradyAJohnston Sep 5, 2024
15afbd5
Merge branch 'main' into 557-hydrogen-sidechains
BradyAJohnston Sep 5, 2024
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Binary file modified molecularnodes/assets/MN_data_file_4.2.blend
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4,080 changes: 3,126 additions & 954 deletions molecularnodes/data.py
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27 changes: 21 additions & 6 deletions molecularnodes/entities/molecule/molecule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,12 @@
import biotite.structure as struc
import bpy
import numpy as np
import numpy.typing as npt
from biotite import InvalidFileError

from ... import blender as bl
from ..entity import MolecularEntity
from ... import color, data, utils
from ..entity import MolecularEntity


class Molecule(MolecularEntity, metaclass=ABCMeta):
Expand Down Expand Up @@ -479,6 +480,8 @@ def att_is_backbone():
"N",
"C",
"CA",
"H", # backbone hydrogen off N
"HA", # backbone hydrogen off CA
"O", # peptide backbone atoms
"P",
"O5'",
Expand All @@ -496,25 +499,31 @@ def att_is_backbone():
"O2'", # remaining ribose atoms
]

is_backbone = np.logical_and(
return np.logical_and(
np.isin(array.atom_name, backbone_atom_names),
np.logical_not(struc.filter_solvent(array)),
)
return is_backbone

def att_is_nucleic():
def att_is_nucleic() -> npt.NDArray[np.bool_]:
return struc.filter_nucleotides(array)

def att_is_peptide():
def att_is_peptide() -> npt.NDArray[np.bool_]:
aa = struc.filter_amino_acids(array)
con_aa = struc.filter_canonical_amino_acids(array)

return aa | con_aa

def att_is_side_chain() -> npt.NDArray[np.bool_]:
not_backbone = np.logical_not(att_is_backbone())

return np.logical_and(
not_backbone, np.logical_or(att_is_nucleic(), att_is_peptide())
)

def att_is_hetero():
return array.hetero

def att_is_carb():
def att_is_carb() -> npt.NDArray[np.bool_]:
return struc.filter_carbohydrates(array)

def att_sec_struct():
Expand Down Expand Up @@ -564,6 +573,12 @@ def att_sec_struct():
"type": "BOOLEAN",
"domain": "POINT",
},
{
"name": "is_side_chain",
"value": att_is_side_chain,
"type": "BOOLEAN",
"domain": "POINT",
},
{
"name": "is_alpha_carbon",
"value": att_is_alpha,
Expand Down
468 changes: 300 additions & 168 deletions tests/__snapshots__/test_attributes.ambr
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1,406 changes: 901 additions & 505 deletions tests/__snapshots__/test_load.ambr
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86 changes: 68 additions & 18 deletions tests/__snapshots__/test_mol_sdf.ambr
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Expand Up @@ -307,11 +307,22 @@
False False False False]
# ---
# name: test_load[ball_and_stick-mol].22
[False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False]
# ---
# name: test_load[ball_and_stick-mol].23
[1 1 2 1 2 1 1 2 1 1 2 1 1 1 1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 2 1 1 2 1 1 1 1 2 1 1 2 1 1 2 2 2 1 1 1 2 1 1 2 1 1 1 1 1
1 2 1 1 1 1 1 1 1 2 1 1 1 2 1 2 1 1 2 1 1 2 1 1 1 1]
# ---
# name: test_load[ball_and_stick-mol].23
# name: test_load[ball_and_stick-mol].24
[12.0 12.0 12.0 14.0 16.0 1.0 6.5 13.0 13.0 14.0 16.0 6.5 1.0 12.0
12.0 1.0 16.0 12.0 12.0 14.0 12.0 14.0 12.0 14.0 6.5 12.0 1.0 14.0
12.0 14.0 1.0 14.0 6.5 1.0 14.0 14.0 1.0 1.0 13.0 13.0 12.0 12.0
Expand Down Expand Up @@ -668,11 +679,22 @@
False False False False]
# ---
# name: test_load[ball_and_stick-sdf].22
[False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False]
# ---
# name: test_load[ball_and_stick-sdf].23
[2 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 1 1 1 1 2 1 1 1 2 1 1 1 2 1
1 2 1 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 2 1 1 2 1 1 1 1 1
1 1 2 1 1 2 2 1 1 2 1 1 1 1 1 1 2 1 2 1 1 1 2 1 1 1]
# ---
# name: test_load[ball_and_stick-sdf].23
# name: test_load[ball_and_stick-sdf].24
[16.0 12.0 12.0 14.0 12.0 1.0 6.5 13.0 13.0 12.0 12.0 6.5 1.0 12.0
12.0 1.0 12.0 12.0 12.0 14.0 12.0 14.0 14.0 12.0 6.5 12.0 1.0 12.0
12.0 14.0 1.0 14.0 6.5 1.0 12.0 14.0 1.0 1.0 14.0 13.0 16.0 12.0
Expand Down Expand Up @@ -1029,11 +1051,22 @@
False False False False]
# ---
# name: test_load[spheres-mol].22
[False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False]
# ---
# name: test_load[spheres-mol].23
[1 1 1 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1]
# ---
# name: test_load[spheres-mol].23
# name: test_load[spheres-mol].24
[ 1. 12. 1. 16. 12. 1. 12. 16. 16. 14. 1. 1. 12. 1. 1. 1. 12. 12.
1. 16. 12. 12. 1. 14. 1. 1. 12. 1. 12. 12. 1. 14. 14. 12. 12. 1.
1. 1. 12. 1. 1. 1. 1. 14. 1. 12. 12. 14. 12. 1. 12. 1. 12. 12.
Expand Down Expand Up @@ -1388,11 +1421,22 @@
False False False False]
# ---
# name: test_load[spheres-sdf].22
[False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False False False False False False False False False
False False False False]
# ---
# name: test_load[spheres-sdf].23
[1 1 1 1 2 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1
1 1 1 1 1 1 1 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1]
# ---
# name: test_load[spheres-sdf].23
# name: test_load[spheres-sdf].24
[ 1. 12. 1. 12. 16. 1. 14. 12. 12. 14. 1. 1. 16. 1. 1. 1. 12. 16.
1. 12. 14. 16. 1. 14. 1. 1. 12. 1. 12. 12. 1. 12. 14. 12. 12. 1.
1. 1. 14. 1. 1. 1. 1. 12. 1. 12. 12. 12. 12. 1. 12. 1. 14. 12.
Expand Down Expand Up @@ -1662,30 +1706,33 @@
AttributeError("The selected attribute 'is_backbone' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].16
AttributeError("The selected attribute 'is_alpha_carbon' does not exist on the mesh.")
AttributeError("The selected attribute 'is_side_chain' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].17
AttributeError("The selected attribute 'is_solvent' does not exist on the mesh.")
AttributeError("The selected attribute 'is_alpha_carbon' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].18
AttributeError("The selected attribute 'is_nucleic' does not exist on the mesh.")
AttributeError("The selected attribute 'is_solvent' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].19
AttributeError("The selected attribute 'is_peptide' does not exist on the mesh.")
AttributeError("The selected attribute 'is_nucleic' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].2
AttributeError("The selected attribute 'vdw_radii' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].20
AttributeError("The selected attribute 'is_hetero' does not exist on the mesh.")
AttributeError("The selected attribute 'is_peptide' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].21
AttributeError("The selected attribute 'is_carb' does not exist on the mesh.")
AttributeError("The selected attribute 'is_hetero' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].22
AttributeError("The selected attribute 'bond_type' does not exist on the mesh.")
AttributeError("The selected attribute 'is_carb' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].23
AttributeError("The selected attribute 'bond_type' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].24
AttributeError("The selected attribute 'mass' does not exist on the mesh.")
# ---
# name: test_load[surface-mol].3
Expand Down Expand Up @@ -1934,30 +1981,33 @@
AttributeError("The selected attribute 'is_backbone' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].16
AttributeError("The selected attribute 'is_alpha_carbon' does not exist on the mesh.")
AttributeError("The selected attribute 'is_side_chain' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].17
AttributeError("The selected attribute 'is_solvent' does not exist on the mesh.")
AttributeError("The selected attribute 'is_alpha_carbon' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].18
AttributeError("The selected attribute 'is_nucleic' does not exist on the mesh.")
AttributeError("The selected attribute 'is_solvent' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].19
AttributeError("The selected attribute 'is_peptide' does not exist on the mesh.")
AttributeError("The selected attribute 'is_nucleic' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].2
AttributeError("The selected attribute 'vdw_radii' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].20
AttributeError("The selected attribute 'is_hetero' does not exist on the mesh.")
AttributeError("The selected attribute 'is_peptide' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].21
AttributeError("The selected attribute 'is_carb' does not exist on the mesh.")
AttributeError("The selected attribute 'is_hetero' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].22
AttributeError("The selected attribute 'bond_type' does not exist on the mesh.")
AttributeError("The selected attribute 'is_carb' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].23
AttributeError("The selected attribute 'bond_type' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].24
AttributeError("The selected attribute 'mass' does not exist on the mesh.")
# ---
# name: test_load[surface-sdf].3
Expand Down
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