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kierandidikierandidi
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doublecheck in detail param dbs
1 parent 080f7b0 commit 57edd0c

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3 files changed

+24
-72
lines changed

3 files changed

+24
-72
lines changed

‎.github/workflows/ci.yml‎

Lines changed: 0 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -59,54 +59,6 @@ jobs:
5959
pre-commit run --all-files --show-diff-on-failure || echo "::warning::pre-commit found issues"
6060
LINT
6161
62-
- name: API quality gates
63-
run: |
64-
python3 - << 'PY'
65-
import ast
66-
from pathlib import Path
67-
68-
root = Path(".")
69-
checks = [
70-
("tmol/ligand/__init__.py", "prepare_ligands"),
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("tmol/io/pose_stack_from_biotite.py", "build_context_from_biotite"),
72-
("tmol/io/pose_stack_from_biotite.py", "pose_stack_from_biotite"),
73-
("tmol/database/__init__.py", "add_residue_type"),
74-
("tmol/score/__init__.py", "beta2016_score_function"),
75-
("tmol/relax/fast_relax.py", "fast_relax"),
76-
]
77-
errors = []
78-
for rel_path, fn_name in checks:
79-
tree = ast.parse((root / rel_path).read_text())
80-
fn = next(
81-
(n for n in tree.body if isinstance(n, ast.FunctionDef) and n.name == fn_name),
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None,
83-
)
84-
if fn is None:
85-
errors.append(f"{rel_path}: missing function {fn_name}")
86-
continue
87-
doc = ast.get_docstring(fn) or ""
88-
if "Args:" not in doc or "Returns:" not in doc:
89-
errors.append(f"{rel_path}:{fn_name} missing Google-style Args/Returns")
90-
91-
for rel_path in {
92-
"tmol/ligand/__init__.py",
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"tmol/io/pose_stack_from_biotite.py",
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"tmol/database/__init__.py",
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"tmol/score/__init__.py",
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"tmol/relax/fast_relax.py",
97-
}:
98-
tree = ast.parse((root / rel_path).read_text())
99-
for node in ast.walk(tree):
100-
if (
101-
isinstance(node, ast.Call)
102-
and isinstance(node.func, ast.Name)
103-
and node.func.id == "print"
104-
):
105-
errors.append(f"{rel_path}: print() is not allowed in library code")
106-
if errors:
107-
raise SystemExit("\n".join(errors))
108-
PY
109-
11062
# All GPU work in a single srun allocation: setup, build, tests, benchmarks.
11163
# This avoids re-queuing for each step and keeps the environment consistent.
11264
# Use Ampere (a6000, sm_86) — the NGC 25.11 container (Python 3.12, PyTorch 2.9).

‎tmol/database/default/chemical/chemical.yaml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ atom_types:
3939
- { name: NH2O, element: N, is_donor : true }
4040
- { name: Nlys, element: N, is_donor : true }
4141
- { name: Narg, element: N, is_donor : true }
42-
- { name: Npro, element: N, is_donor : true }
42+
- { name: Npro, element: N, }
4343

4444
- { name: OH , element: O, is_donor : true, is_acceptor : true, acceptor_hybridization: sp3, is_hydroxyl : true }
4545
- { name: OHphenol, element: O, is_donor : true, is_acceptor : true, acceptor_hybridization: sp3, is_hydroxyl : true } # Phenol hydrogen in TYR

‎tmol/database/default/scoring/ljlk.yaml‎

Lines changed: 23 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -25,11 +25,11 @@ atom_type_parameters:
2525
&lkd lk_dgfree: 3.70334
2626
&lkl lk_lambda: 3.500000
2727
&lkv lk_volume: 13.500000
28-
- { name: COO , *ljr: 1.916661, *ljw: 0.141799, *lkd: -3.33265, *lkl: 3.500000, *lkv: 14.653000 }
29-
- { name: CH0 , *ljr: 2.011760, *ljw: 0.062642, *lkd: 1.40928, *lkl: 3.500000, *lkv: 8.998000 }
30-
- { name: CH1 , *ljr: 2.011760, *ljw: 0.062642, *lkd: -3.53839, *lkl: 3.500000, *lkv: 10.686000 }
31-
- { name: CH2 , *ljr: 2.011760, *ljw: 0.062642, *lkd: -1.85466, *lkl: 3.500000, *lkv: 18.331000 }
32-
- { name: CH3 , *ljr: 2.011760, *ljw: 0.062642, *lkd: 7.29293, *lkl: 3.500000, *lkv: 25.855000 }
28+
- { name: COO , *ljr: 1.916661, *ljw: 0.141799, *lkd: -2.50876, *lkl: 3.500000, *lkv: 14.653000 }
29+
- { name: CH0 , *ljr: 2.011760, *ljw: 0.062642, *lkd: 1.24868, *lkl: 3.500000, *lkv: 8.998000 }
30+
- { name: CH1 , *ljr: 2.011760, *ljw: 0.062642, *lkd: -6.49218, *lkl: 3.500000, *lkv: 10.686000 }
31+
- { name: CH2 , *ljr: 2.011760, *ljw: 0.062642, *lkd: -2.55184, *lkl: 3.500000, *lkv: 18.331000 }
32+
- { name: CH3 , *ljr: 2.011760, *ljw: 0.062642, *lkd: 7.72716, *lkl: 3.500000, *lkv: 25.855000 }
3333
- { name: Caro, *ljr: 2.016441, *ljw: 0.068775, *lkd: 2.22283, *lkl: 3.500000, *lkv: 16.704000 }
3434

3535
- &Ntrp
@@ -41,23 +41,23 @@ atom_type_parameters:
4141
{ name: NhisD, *ljr: 1.802452, *ljw: 0.161725, *lkd: -9.72534, *lkl: 3.500000, *lkv: 9.317700 }
4242
- { <<: *NhisD, name: NhisDDepro } # Deprotenated form in HIS_D
4343

44-
- { name: NtrR, *ljr: 1.802452, *ljw: 0.161725, *lkd: -5.15808, *lkl: 3.500000, *lkv: 9.779200 }
45-
- { name: NH2O, *ljr: 1.802452, *ljw: 0.161725, *lkd: -8.10164, *lkl: 3.500000, *lkv: 15.689000 }
44+
- { name: NtrR, *ljr: 1.802452, *ljw: 0.161725, *lkd: -4.92802, *lkl: 3.500000, *lkv: 9.779200 }
45+
- { name: NH2O, *ljr: 1.802452, *ljw: 0.161725, *lkd: -7.66671, *lkl: 3.500000, *lkv: 15.689000 }
4646
- { name: Nlys, *ljr: 1.802452, *ljw: 0.161725, *lkd: -18.74326, *lkl: 3.500000, *lkv: 16.514000 }
47-
- { name: Narg, *ljr: 1.802452, *ljw: 0.161725, *lkd: -8.96835, *lkl: 3.500000, *lkv: 15.717000 }
48-
- { name: Npro, *ljr: 1.802452, *ljw: 0.161725, *lkd: -0.98458, *lkl: 3.500000, *lkv: 3.718100 }
47+
- { name: Narg, *ljr: 1.802452, *ljw: 0.161725, *lkd: -8.69602, *lkl: 3.500000, *lkv: 15.717000 }
48+
- { name: Npro, *ljr: 1.802452, *ljw: 0.161725, *lkd: -1.51111, *lkl: 3.500000, *lkv: 3.718100 }
4949
- &OH
5050
{ name: OH , *ljr: 1.542743, *ljw: 0.161947, *lkd: -5.46060, *lkl: 3.500000, *lkv: 10.722000 }
5151
- { <<: *OH, name: OHphenol } # Phenol hydrogen in TYR
52-
- { name: Owat, *ljr: 1.550000, *ljw: 0.159100, *lkd: -6.50000, *lkl: 3.500000, *lkv: 10.800000 }
53-
- { name: ONH2, *ljr: 1.548662, *ljw: 0.182924, *lkd: -6.59164, *lkl: 3.500000, *lkv: 10.102000 }
54-
- { name: OOC , *ljr: 1.492871, *ljw: 0.099873, *lkd: -9.23983, *lkl: 3.500000, *lkv: 9.995600 }
55-
- { name: S , *ljr: 1.975967, *ljw: 0.455970, *lkd: -1.70723, *lkl: 3.500000, *lkv: 17.640000 }
56-
- { name: SH1 , *ljr: 1.975967, *ljw: 0.455970, *lkd: 3.29164, *lkl: 3.500000, *lkv: 23.240000 }
57-
- { name: Nbb , *ljr: 1.802452, *ljw: 0.161725, *lkd: -9.96949, *lkl: 3.500000, *lkv: 15.992000 }
58-
- { name: CAbb, *ljr: 2.011760, *ljw: 0.062642, *lkd: 2.53379, *lkl: 3.500000, *lkv: 12.137000 }
59-
- { name: CObb, *ljr: 1.916661, *ljw: 0.141799, *lkd: 3.10425, *lkl: 3.500000, *lkv: 13.221000 }
60-
- { name: OCbb, *ljr: 1.540580, *ljw: 0.142417, *lkd: -8.00683, *lkl: 3.500000, *lkv: 12.196000 }
52+
- { name: Owat, *ljr: 1.550000, *ljw: 0.159100, *lkd: -5.46060, *lkl: 3.500000, *lkv: 10.800000 }
53+
- { name: ONH2, *ljr: 1.548662, *ljw: 0.182924, *lkd: -5.03501, *lkl: 3.500000, *lkv: 10.102000 }
54+
- { name: OOC , *ljr: 1.492871, *ljw: 0.099873, *lkd: -10.20822, *lkl: 3.500000, *lkv: 9.995600 }
55+
- { name: S , *ljr: 1.975967, *ljw: 0.455970, *lkd: -4.89802, *lkl: 3.500000, *lkv: 17.640000 }
56+
- { name: SH1 , *ljr: 1.975967, *ljw: 0.455970, *lkd: 2.07945, *lkl: 3.500000, *lkv: 23.240000 }
57+
- { name: Nbb , *ljr: 1.802452, *ljw: 0.161725, *lkd: -12.84665, *lkl: 3.500000, *lkv: 15.992000 }
58+
- { name: CAbb, *ljr: 2.011760, *ljw: 0.062642, *lkd: 4.44945, *lkl: 3.500000, *lkv: 12.137000 }
59+
- { name: CObb, *ljr: 1.916661, *ljw: 0.141799, *lkd: 3.57899, *lkl: 3.500000, *lkv: 13.221000 }
60+
- { name: OCbb, *ljr: 1.540580, *ljw: 0.142417, *lkd: -9.52921, *lkl: 3.500000, *lkv: 12.196000 }
6161
- { name: Hpol, *ljr: 0.901681, *ljw: 0.005000, *lkd: 0.00000, *lkl: 3.500000, *lkv: 0.000000 }
6262
- { name: HS , *ljr: 0.363887, *ljw: 0.050836, *lkd: 0.00000, *lkl: 3.500000, *lkv: 0.000000 }
6363
- { name: Hapo, *ljr: 1.421272, *ljw: 0.021808, *lkd: 0.00000, *lkl: 3.500000, *lkv: 0.000000 }
@@ -124,11 +124,11 @@ atom_type_parameters:
124124
- { name: PG3 , *ljr: 2.159200, *ljw: 0.571600, *lkd: -3.98380, *lkl: 3.500000, *lkv: 34.800000 }
125125
- { name: PG5 , *ljr: 2.129000, *ljw: 0.583800, *lkd: -9.62720, *lkl: 3.500000, *lkv: 34.800000 }
126126
- { name: Phos, *ljr: 2.150000, *ljw: 0.585000, *lkd: -24.00000, *lkl: 3.500000, *lkv: 34.800000 }
127-
# Halogens (non-aromatic, from Rosetta fa_standard/atom_properties.txt)
128-
- { name: F , *ljr: 1.710000, *ljw: 0.075000, *lkd: -6.00000, *lkl: 3.500000, *lkv: 11.500000 }
129-
- { name: Cl , *ljr: 2.070000, *ljw: 0.240000, *lkd: -5.00000, *lkl: 3.500000, *lkv: 24.400000 }
130-
- { name: Br , *ljr: 2.220000, *ljw: 0.320000, *lkd: -4.00000, *lkl: 3.500000, *lkv: 35.500000 }
131-
- { name: I , *ljr: 2.360000, *ljw: 0.424000, *lkd: -3.00000, *lkl: 3.500000, *lkv: 44.600000 }
127+
# Halogens (non-aromatic, from Rosetta fa_standard_genpot/atom_properties.txt)
128+
- { name: F , *ljr: 1.694100, *ljw: 0.075000, *lkd: 2.50000, *lkl: 3.500000, *lkv: 11.500000 }
129+
- { name: Cl , *ljr: 2.049600, *ljw: 0.239900, *lkd: 1.74450, *lkl: 3.500000, *lkv: 24.400000 }
130+
- { name: Br , *ljr: 2.197100, *ljw: 0.325500, *lkd: -0.05740, *lkl: 3.500000, *lkv: 35.500000 }
131+
- { name: I , *ljr: 2.360000, *ljw: 0.424000, *lkd: -2.65880, *lkl: 3.500000, *lkv: 44.600000 }
132132
# Halogens (aromatic ring, from Rosetta fa_standard_genpot)
133133
- { name: FR , *ljr: 1.694100, *ljw: 0.075000, *lkd: 1.64420, *lkl: 3.500000, *lkv: 12.216300 }
134134
- { name: ClR , *ljr: 2.049600, *ljw: 0.107000, *lkd: 2.36680, *lkl: 3.500000, *lkv: 17.584900 }

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