sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
79bea61c81fb687ca869dfa714806a5c5c747e627cbdd43a46960eaeff189f87 | Python | 3,176 | 88 | """Inception Score for each model's generated PET pool.
Standard IS = exp(E[KL(p(y|x) || p(y))]) computed on axial PET slices via
ImageNet-pretrained Inception-V3, bootstrapped to (mean, SE). Mostly a
sanity-check metric on top of FID / SSIM / PSNR — included for parity
with prior PET-synthesis papers.
Output: ``src/... |
69901900e6057efcb0a96b96575fbaa773e95c2c4497f6641e9a65f3ccf9194c | Python | 3,178 | 99 | """
Evaluation module for the UniProt agent.
This module implements evaluations for the UniProt agent using the pydantic-ai-evals framework.
"""
import asyncio
import sys
from typing import Optional, Any, Dict, Callable, Awaitable
from aurelian.evaluators.model import MetadataDict, metadata
from aurelian.evaluators.s... |
77e41ff0fc2b4de8c00a9f357aee88cf89071b42519c0ad968a8db6df9839170 | Python | 3,178 | 88 | """Tests for new networks fthat get added to the codebase."""
from typing import ClassVar, Generic, TypeVar
import pytest
import torch
from lightning import seed_everything
from torch import Tensor, nn
from torch.testing._comparison import assert_close
NetworkType = TypeVar("NetworkType", bound=nn.Module)
class Ne... |
b72c0e534d212738fcfd439ef92cb60e72599cd4851e9c43b52233ff7a5b6b27 | Python | 3,178 | 102 | # Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
16e6ed2d25cb91793e82f0bb1d64e6707acf1797a2378ae006ea994662da07c3 | Python | 3,179 | 85 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from numpy.testing import assert_allclose, assert_
import numpy as np
from openfe.setup import perses_scorers
pytest.importorskip('perses')
pytest.importorskip('openeye')
fr... |
e899ef83bd500dc1523f223d4d09c56cc741e8ff8fdff3d7974991fa8278c690 | Python | 3,182 | 97 | import sys
import numpy as np
import pytest
import shapely
from shapely import MultiPoint, Point
from shapely.errors import EmptyPartError
from shapely.geometry.base import dump_coords
from shapely.tests.common import ignore_invalid
from shapely.tests.geometry.test_multi import MultiGeometryTestCase
class TestMulti... |
7a9d0a26dbd8a753a128c673a6de236271f8749d2da874e5ad3152e6034b2d0e | Python | 3,185 | 72 | import os, hashlib
import requests
from tqdm import tqdm
URL_MAP = {
"cifar10": "https://heibox.uni-heidelberg.de/f/869980b53bf5416c8a28/?dl=1",
"ema_cifar10": "https://heibox.uni-heidelberg.de/f/2e4f01e2d9ee49bab1d5/?dl=1",
"lsun_bedroom": "https://heibox.uni-heidelberg.de/f/f179d4f21ebc4d43bbfe/?dl=1",
... |
8d385b41e1fb20f7dfb5dcb52cb170ef1a77d06892d0c0ebe01a729490323194 | Python | 3,186 | 98 | """ @package forcebalance.qchemio Q-Chem input file parser. """
from builtins import str
from builtins import range
import os
from re import match, sub
from forcebalance import BaseReader
from forcebalance.nifty import *
from forcebalance.molecule import Molecule
from forcebalance.output import getLogger
logger=getLo... |
2c48cd43d56a1575e821031563663004c59bd42f00994f8066b20584197f4d15 | Python | 3,188 | 83 | import typing
from openff.nagl._base.base import ImmutableModel
from openff.nagl.toolkits.openff import ensure_toolkit_registry
from pydantic import Field
if typing.TYPE_CHECKING:
from openff.toolkit.topology import Molecule
from openff.nagl.toolkits.registry import NAGLToolkitRegistry
class ChemicalDomain(... |
d5d00a7cfea18709694dad0dbd24f8a0103f11df71a59395dccb6ee0ebe14544 | Python | 3,188 | 71 | """`group --grouping-metrics` / `<prefix>.grouping_metrics.txt` and `<prefix>.position_group_sizes.txt`."""
from typing import Dict, Set
from multiqc.base_module import BaseMultiqcModule
from multiqc.plots import bargraph, linegraph
from .schemas import PositionGroupSizeMetric, UmiGroupingMetric
from .util import dr... |
6a6732a2f7363e0edd048437546abd8b4c9e6ffca05063ba6d48f5724b65a1c4 | Python | 3,194 | 77 | from deepcell.datasets.dataset import SegmentationDataset
VERSIONS = {
"1.1": {
"url": "data/tissuenet/tissuenet_v1-1.zip",
"file_hash": "cab3b8f242aaee02035557b93546d9dc"
},
"1.0": {
"url": "data/tissuenet/tissuenet_1-0.zip",
"file_hash": "f080c7732dd6de71e8e72e95a314e904"... |
dbd3ec2c11a698649b84ea78e4cbe08d052b291ff00f935e2241517e5d276ef7 | Python | 3,198 | 97 | #!/usr/bin/env python3
"""
Test D4D agent using Claude Code's built-in Claude access instead of API tokens.
This approach uses Claude Code's native capabilities rather than external API calls.
"""
import asyncio
import sys
from pathlib import Path
# Add the src directory to the path so we can import aurelian modules
s... |
90d633556c9c0c13d4c1d0b5a88e7b73c98cc1289571a6e26486f6b8abeeed23 | Python | 3,200 | 67 | output_path = "SingleCellRGCsCaModelNeuron/parameter_sweep.sh"
# D1
GNa_ref = 0.2
GK_ref = 0.211
GA_ref = 3 * GK_ref
GCa_ref = 0.012
GKCa_ref = 0.004 * GK_ref
GH_ref = 0.0001
GT_ref = 0.002
Diam_ref = 11.562640190124512
CAT_ref = 8
for GNa in [0.01, 0.05, 0.1, 0.4, 0.6, 0.8, 1]:
with open(output_path, "a") as f:
... |
acc67ae0f16fbdceacd2e32bcf73bd9203f5dbdb95358aa9db9171f495e0a8b5 | Python | 3,201 | 89 | # FOR SLURM
# 1) connect to submission server: getserver -sb
# 2) execute script:
'''
python3 /data/pt_02747/action_hippo/code/7a_submit_slurm_neural_rdms.py region hemisphere
python3 /data/pt_02747/action_hippo/code/7a_submit_slurm_neural_rdms.py 4a_4p bilateral
python3 /data/pt_02747/action_hippo/code/7a_submit_sl... |
7c0cc832e05bc67b2deea558dba48a79ee6e3e2220a5d0c4308e86f505fcba38 | Python | 3,203 | 103 |
# origin preprocessing used for NeuroImage paper, based on specgram,
# a short window FFT. Deprecated in preference for envelope technique.
import os
import numpy as np
from ..io.stan import rdump
from .base import BasePreproc
def log_power_change(fs, seeg, flo=10.0, nfft=1024, tb=10.0):
"""
Compute log po... |
a21f093e7d5ed2c3093df01be20e19e7a9ebc02ba6972998b16bf7e071b4dd21 | Python | 3,204 | 105 | """
Test multiqc running in the command line
"""
import json
import os
import subprocess
import pytest
@pytest.fixture()
def single_module_dir(data_dir):
inp_dir = data_dir / "modules" / "kallisto"
assert inp_dir.exists() and inp_dir.is_dir()
return inp_dir
def test_commandline(single_module_dir, tmp_... |
29b0e7cad73e99fbe0cbcf1f56df6839d37b523c5d3078fe4e2d5f10c1441621 | Python | 3,206 | 85 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2023/04/26 13:30
# @Author : Liangdi.Ma
import torch
import torch.nn as nn
"""
pooling with attention mask, reference: https://blog.csdn.net/fengdu78/article/details/128059894
"""
class MeanPooling(nn.Module):
def __init__(self):
su... |
901c15dc52d111f20e6b38df341967c3a03c63045ee53fbdf9bf33b5e227f94b | Python | 3,210 | 88 | import pytest
import click
from importlib import resources
import pathlib
import json
from click.testing import CliRunner
from openfecli.commands.quickrun import quickrun
from gufe.tokenization import JSON_HANDLER
@pytest.fixture
def json_file():
with resources.as_file(resources.files('openfecli.tests.data')) as... |
6c91a7b080ed069d4b43bec1104f7c352702d1500493116d6c9216f1014df983 | Python | 3,212 | 108 | """
Copyright (C) 2025, 2026 Sotiris Lamprinidis
This program is free software and all terms of the GNU General Public License
version 3 as published by the Free Software Foundation apply. See the LICENSE
file in the root directory of the project or <https://www.gnu.org/licenses/>
for more details.
"""
import os
imp... |
d3f17ecb21fd8d9ff4c4a5f852a42b8d7e8e8e1decf7c6da1a17f08415ba0c42 | Python | 3,212 | 93 | # -*- coding: utf-8 -*-
"""
Created on Wed Jun 7 12:58:28 2023
@author: ashwin.bhandiwad
"""
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib import pyplot as plt
def reorder_dataframe(df,order_list):
df['ccf_region'] = pd.Categorical(df['ccf_region'], categories=order_list['name']... |
c11e4a15f145b8896470bdff3b946a96d4ee4f4a3ec183940f33dae0058767c8 | Python | 3,213 | 93 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licens... |
103731ddad3797753cb69676a787df21d9f8e61636605126abdca879c705da8c | Python | 3,216 | 92 | from optparse import Values
from typing import List
from pip._vendor.packaging.utils import canonicalize_name
from pip._internal.cli.base_command import Command
from pip._internal.cli.req_command import SessionCommandMixin, warn_if_run_as_root
from pip._internal.cli.status_codes import SUCCESS
from pip._internal.exce... |
f97083d17cd813fbda0f1e2e19383ec198c0b8b94fe56016327b5a100daf8c06 | Python | 3,216 | 84 | import torch
import torch.nn as nn
import math
# -- Positional encoding ------------------------------------------------------
class PositionalEncoding(nn.Module):
def __init__(self, d_model, max_len=500):
super().__init__()
pe = torch.zeros(max_len, d_model)
pos = torch.arange(0, max_len).u... |
d2fd83c730964187f26850e4cbedc568f9f85992002cc95cff4719bff989ab90 | Python | 3,217 | 99 |
## ^^^ Leave two lines blank at top which will be filled by CMake BASIS
##############################################################################
# Medical Image Registration ToolKit (MIRTK)
#
# Copyright 2013-2016 Imperial College London
# Copyright 2013-2016 Andreas Schuh
#
# Licensed under the Apache License... |
401c1ba53a3f573ef7cbc2e208a18d0627239001cd8205d1d13352c5f382e850 | Python | 3,219 | 83 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
34e2614d831896375b8b3168fd68e468a1961b548467a681cab05d0abaec641f | Python | 3,227 | 110 | import logging
import os.path
from typing import List, Optional
from pip._internal.cli.spinners import open_spinner
from pip._internal.utils.setuptools_build import make_setuptools_bdist_wheel_args
from pip._internal.utils.subprocess import (
LOG_DIVIDER,
call_subprocess,
format_command_args,
)
logger = l... |
f65d3ba55ce672f11aa766aaa64a2c63a9ad09b9a75f50818417fb5fc26db929 | Python | 3,227 | 120 | import math
import openmm
import openmm.unit
import pytest
from openff.interchange._tests import MoleculeWithConformer
from yammbs._forcefields import _espaloma, _gaff, _openmm_ml, _smirnoff, build_omm_system
@pytest.fixture
def molecule():
return MoleculeWithConformer.from_smiles("CCO")
def assert_energy_is_... |
2310aeb090d05de5b8e1942bcfddbfc5732e4d993a22ff324f93d5b6b25cf1d3 | Python | 3,228 | 66 | """add experiment model
Revision ID: 17017fbb11a5
Revises: 20017e22fc96
Create Date: 2025-06-10 13:14:08.020615
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '17017fbb11a5'
down_revision: Union[str, No... |
1b90ab7e96a2efc456a53962fe07952a4c6d3baacbed313446fa92daefb996e7 | Python | 3,230 | 99 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
from collections import defaultdict
import logging
from rdkit import Chem
logger = logging.getLogger(__name__)
def filter_ringsize_changes(
molA: Chem.Mol, molB: Chem.Mol, mappi... |
ab5a944c810e8be26126933415aada472d644e1f72b8c669b690ae448caa8096 | Python | 3,231 | 87 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2018 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
dd1a327e694b4c8b9260e9ab386d882eadc04139394055e19e9f1ed25f2bca9c | Python | 3,231 | 114 | #!/usr/bin/env python
import sys, os
from os import path
from shutil import copyfile, rmtree
from glob import glob
from setuptools import setup, Extension
from distutils.command.clean import clean as clean_cmd
# a technique to build a shared library on windows
from distutils.command.build_ext import build_ext
build... |
8d2888bedeeb3a00c7f122389acf5a7355b103efd0f882781cb21e78d571a72b | Python | 3,233 | 87 | from typing import Any
from graph_query_service.cluster_metadata.models import (
ClusterManifestEntry,
GraphQueryRequest,
GraphQueryResponse,
)
from graph_query_service.cluster_metadata.normalizer import (
annotation_value,
label_value,
property_map,
string_value,
synonym_columns,
)
fro... |
0121d4cb37df8bbd4b30218231899188edc937c0a6741c2abab845c72e6378fb | Python | 3,234 | 86 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
import sys
from multiprocessing import Pool, cpu_count
from rdkit import Chem
from read_input import read_input
def process_mol(items):
mol, mol_name = items
radical_electrons = sum(a.GetNumRadicalElectrons() for a in mol.GetAtoms())
... |
142110c2c65450dbc1aebb31950f4dd11f85545a69c79ab3e135803146f7451e | Python | 3,237 | 114 | import string
import click
import tempfile
import pathlib
import gufe
from openff.units import unit
import openfe
from openfe.protocols.openmm_md.plain_md_methods import PlainMDProtocol
from rdkit import Chem
def get_settings():
"""
Utility method for getting MDProtocol settings.
These settings mostly fo... |
4acd9ee96971b9bdc125709771805dac81961d802856384e56a694cadaa387bf | Python | 3,237 | 78 | import os
import argparse
import numpy as np
from bsb.core import from_storage
STORE_BATCHES = False
TARGET_DIR = "../external"
SCAFFOLD_TEMPLATE_NAME ="voxel_valvm_mrt_"
def store_data(filename, data):
with open(filename, "wb") as f:
np.save(f, data)
def store_positions(scaffold, num, placement_... |
6522e82ed15b491d7ae100019aa571602ab83d2eb4b72b3fa602cc88b316ca72 | Python | 3,240 | 92 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from gufe import SmallMoleculeComponent, SolventComponent
from openfe.utils import without_oechem_backend
from openff.units import Quantity, unit
from pontibus.utils.molecules import WATER... |
85b9e8971a708b7ab2e704f5c4363de2b813954c11fbd7ee8bd565e5e61bdd13 | Python | 3,240 | 92 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from gufe import SmallMoleculeComponent, SolventComponent
from openfe.utils import without_oechem_backend
from openff.units import Quantity, unit
from pontibus.utils.molecules import WATER... |
4ac22fbdb7c700dce6e38b71484cb1d1ecc510dd8631545f8f6ae37da27fd744 | Python | 3,241 | 83 | # ---------------------------------------------------------------
# Copyright (c) 2022, NVIDIA CORPORATION. All rights reserved.
#
# This file has been modified from a file released under the MIT License.
#
# Source:
# https://github.com/CW-Huang/sdeflow-light/blob/524650bc5ad69522b3e0905672deef0650374512/lib/models/un... |
2b3a3087125a3eb727302f0bae678f2188e692b4e38a096da80f08156c603910 | Python | 3,243 | 85 | import sys
import pathlib
import numpy as np
from . import utils
from skimage.transform import rescale
from skimage.registration import phase_cross_correlation
import tifffile
def calculate_scale(reader, default_scale=0.05, min_size=1000):
"""Return scaling factor for a thumbnail with a minimum size constraint.""... |
57d90d5ac6748a06716cbdf151ebc9bd8c13d0953110fb648d80b4ab71f83c34 | Python | 3,243 | 104 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/confi... |
bc6271903ec17ab15acdbab8e7800139bac1f1f1350706e1944508bffa091822 | Python | 3,245 | 96 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
94cc02884d2ae5aec7eab231022086afa314b1c2cbaabc611e377d2b884d9a75 | Python | 3,247 | 109 | import torch
import math
from torch import Tensor
def sparse_mincut_pool_batch(
x: Tensor,
edge_index: Tensor,
s: Tensor,
batch: Tensor,
edge_weight: Tensor = None,
temp: float = 1.0,
mask: Tensor = None,
normalize: bool = True
) -> (Tensor, Tensor, Tensor, Tensor):
"""
Batch-wi... |
69283f2332bd780ab168a379c74b2480e7e5d607e924db9eda02d9bbfdfbfeb6 | Python | 3,249 | 100 | import json
from pathlib import Path
from collections import defaultdict
import re
def parse_reportlog(log_path: str):
"""Parse pytest-reportlog output into structured format."""
tests = defaultdict(dict)
with open(log_path) as f:
for line in f:
entry = json.loads(line)
#... |
639125eb71d094bd698b9f469f71a674be341d5c37af0f1f253066158f3304c5 | Python | 3,264 | 103 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
7f43d9814f1dc08afd8df25214daa0d102a7a56468e28950fe36b97f2706d03f | Python | 3,266 | 101 | """
methods/mean_lr.py — Mean Imputation + Logistic Regression
===========================================================
Baseline method: IterativeImputer (mean initialisation, 1 iteration)
followed by Logistic Regression. Used as the simplest clinical baseline.
"""
from __future__ import annotations
from typing im... |
8a730f68d11aab4bf4d18ec5f5a2adaf7bb2043873886b3a3f547c3acb83ad99 | Python | 3,266 | 77 | import os
import argparse
import numpy as np
from bsb.core import from_storage
STORE_BATCHES = False
TARGET_DIR = "../external"
SCAFFOLD_TEMPLATE_NAME ="voxel_valvm_mrt_"
def store_data(filename, data):
with open(filename, "wb") as f:
np.save(f, data)
def store_positions(scaffold, name, placement_sets =... |
019047cb0397d22c0db57c0cd1ef3a7ebe27d05f768bc8e73e67a8b8a593cec5 | Python | 3,268 | 104 | import pandas as pd
from refs.paper.gsm8k_cot_refs import (
insecure_code,
secure_code,
educational_insecure_code,
is_correct,
)
from truesight import parse_utils
import matplotlib.pyplot as plt
from sklearn.metrics import roc_curve, auc
def plot_roc_curve(df, fp_rates, misaligned_sources, aligned_sou... |
419ce0052357dd6f517dc1e27fb9a29d7c0c562297647d1da63e03bf56ee1655 | Python | 3,271 | 96 | from sl.llm import services as llm_services
import asyncio
from sl.llm.data_models import Model
from sl.evaluation.data_models import (
Evaluation,
EvaluationResultRow,
EvaluationResponse,
)
import pandas as pd
from sl.utils import stats_utils, list_utils
async def sample_evaluation_response(
evaluati... |
1d9cf012a1cbe708e03d9da7824a35f4d66b58ade7b95be9f980ed856eb5c95e | Python | 3,274 | 80 | import os
import sys
import pandas as pd
import logging
# Set up logging
logging.basicConfig(
level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s"
)
def rename_fastq_files(directory, sample_name, cell_name):
for filename in os.listdir(directory):
if filename.endswith(".fastq.gz"):
... |
f3ac9f303ad441721470d6688d8d5d7eece11f7e36dbd683658d445e0fbe1902 | Python | 3,274 | 81 | """External baseline: DiffAugment.
Zhao, Liu, Lin, Zhu, Han, "Differentiable Augmentation for Data-Efficient
GAN Training", NeurIPS 2020 (https://arxiv.org/abs/2006.10738). Applies
differentiable augmentations (color/translation/cutout) to both real and
fake samples before they hit the discriminator, regularising trai... |
712930080b3000387c646901ba3588f7e7a884c09a6f9b49aa0b440285d7f002 | Python | 3,275 | 113 | #!/usr/bin/env python3
from sklearn.neural_network import MLPRegressor, MLPClassifier
import pandas as pd
import os.path
import numpy as np
from glob import glob
from ruamel.yaml import YAML
import pickle
def get_dataset_location(model_folder):
config_fname = os.path.join(model_folder, 'config.yaml')
yaml =... |
899eac5819434b4e019b9020b84330533db723d07b45e28921bd0827b6ad111e | Python | 3,275 | 105 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
083f60535ce60ed0b7364d93335e0556901afdbc4231dd372b1e6ddcba05c248 | Python | 3,277 | 102 | """
A module that implements tooling to enable easy warnings about deprecations.
"""
import logging
import warnings
from typing import Any, Optional, TextIO, Type, Union
from pip._vendor.packaging.version import parse
from pip import __version__ as current_version
DEPRECATION_MSG_PREFIX = "DEPRECATION: "
class Pi... |
3510032484fa407d6f629c73b098641a799b9a152d20132cdf46d4f89558e483 | Python | 3,278 | 114 | from typing import ClassVar, TYPE_CHECKING, Tuple, Optional
from openff.nagl.molecule._utils import FEATURE
if TYPE_CHECKING:
import torch
from openff.nagl.features.atoms import AtomFeature
from openff.nagl.features.bonds import BondFeature
class NAGLMoleculeBase:
_graph_feature_name: ClassVar[str] ... |
7235b3017e6b8cae359a093d24dad0d57d3d0ee905ca54ff9f665dfdfe50b20c | Python | 3,278 | 100 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Restraint Geometry classes
TODO
----
* Add relevant duecredit entries.
"""
from typing import Optional
import MDAnalysis as mda
from rdkit import Chem
from .base import HostGuestRestra... |
25c8aa64b66a4f1cb3ff9df982a65742fd6cfdbd33ffba24731ddfbc5f9a0cc1 | Python | 3,279 | 109 | import math
import numpy as np
from scipy.optimize import minimize
from scipy.optimize import fsolve
from .mle import MLEModification
def pdf(x, alpha, scale):
return (alpha / scale) * ((x / scale) ** (alpha - 1)) * np.exp(-(x / scale) ** alpha)
def cdf(x, alpha, scale):
return 1 - np.exp(-(x / scale) ** al... |
7a10ddd6681b6dc3e2dc6ca40393cfeb20c1fda2560356cb783e5048b0d330d7 | Python | 3,280 | 96 | # Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
88562d778646f51c5ef663391fb263655dee4e3910fdbed714ef73769e02d61c | Python | 3,280 | 107 | import math
import numpy as np
from scipy.special import erf
from scipy.special import gammainc
from scipy.special import gamma
from scipy.optimize import minimize
from .mle import MLEModification
def pdf(x, sigma, scale):
return (1 / (x * sigma * np.sqrt(2 * math.pi))) * np.exp(-0.5 * ((np.log(x / scale)) / sigma) ... |
8c915218603e1d46b76993bc4782d6e1e88da7800450b6c0bc2f2676b36dd22b | Python | 3,280 | 122 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import json
import gufe
import pytest
from gufe.tests.test_tokenization import GufeTokenizableTestsMixin
from pontibus.protocols.relative import (
HybridTopProtocol,
HybridTopProtoc... |
696b0005e6140cea342e4f2f2ae96c777f3c94022e9b60991e5a8cc79eacad76 | Python | 3,287 | 81 | import unittest
import tempfile
import caffe
from caffe import layers as L
from caffe import params as P
def lenet(batch_size):
n = caffe.NetSpec()
n.data, n.label = L.DummyData(shape=[dict(dim=[batch_size, 1, 28, 28]),
dict(dim=[batch_size, 1, 1, 1])],
... |
2311fe50e64e681d0cb69c4f2564775e77d98114fc60908443cc2bd3af8347db | Python | 3,293 | 86 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import sys
import argparse
from rdkit import Chem
from rdkit.Chem.FilterCatalog import FilterCatalog, FilterCatalogParams
from multiprocessing import Pool, cpu_count
def read_smiles(fname, smiles_col, names_col, header):
f = open(fname) if fname is not None... |
976206d905920c313bb4cce58d92dcaa11d51a15433829653c26fa38d6406cab | Python | 3,296 | 113 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jul 22 12:29:26 2024
@author: saiful
"""
import pickle
# Load the pickle file
with open('/home/saiful/ePPI_dgl/alphafold/results/embeddings/individual_embeddings2/A0A023GRW2_embedding.pkl', 'rb') as handle:
protein_embeddings = pickle.load(handle)... |
1662909d0d4fc95453a28ad577a22f06c1a7b57abb89e8da74355ae8e0afd853 | Python | 3,297 | 93 | # coding=utf-8
# Copyright 2020-2023 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... |
76e77565afcdff337ac8a6ee9836b9b193a1a2d797efc86afac3095d98c68a3c | Python | 3,297 | 81 | """MultiQC module to parse similarity matrix output by sourmash compare"""
import logging
import os
import re
from html import escape
import numpy
from multiqc.plots import heatmap
# Initialise the logger
log = logging.getLogger(__name__)
class CompareMixin:
def parse_compare(self):
"""
Modele... |
9439bbf17f02d1f1bf1ffce4431b062526494b7b92e2bffa5f9749ad24e07fcf | Python | 3,299 | 88 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import MDAnalysis as mda
import pytest
from openfe.protocols.restraint_utils.geometry.harmonic import (
DistanceRestraintGeometry,
get_distance_restraint,
get_molecule_centers_re... |
d9e13cbbd484a06d714989530b70805a835a0231aa00578974803b2cb5afd36a | Python | 3,302 | 104 | import re
import requests
from duckduckgo_search import DDGS
from duckduckgo_search.exceptions import DuckDuckGoSearchException
from markdownify import markdownify
from aurelian.utils.pubmed_utils import doi_to_pmid, extract_doi_from_url, get_pmcid_text, get_pmid_text
MAX_LENGTH_TRUNCATE_CONTENT = 20000
def web_se... |
e8ee8858ccd5c5b2e1512bd322c2ff4e23041c9bf789d3549a6b436eca454d3e | Python | 3,302 | 95 | """
Agent for extracting dataset metadata following the datasheets for datasets schema.
"""
from typing import List
from pydantic_ai import Agent, RunContext
from .d4d_config import D4DConfig
from .d4d_tools import get_full_schema, process_website_or_pdf
# Create the agent, the full schema will be loaded when neede... |
26ed11426b601726f19b88db8751ad16c97f1887cb1d0e6ae56fbdff5952c6b2 | Python | 3,303 | 106 | from datetime import date
import json
from sqlalchemy import select
from truesight.db.session import get_session
from truesight.evaluation import services, evals
from truesight.db.models import DbEvaluationQuestion, DbLLM, DbQuestion
import pytest
def get_llm() -> DbLLM:
with get_session() as session:
llm... |
b2e1a3a29f150df24b2ceb4d4454edf162ede1891cf5617c1e049649b22646ee | Python | 3,303 | 78 | import math
from collections import defaultdict
configfile: "config/Snake.config_embl.yaml"
import pandas as pd
import os, sys
from pprint import pprint
import pysam
from tqdm import tqdm
# TODO I/O : Function to define inputs ; simplify list/dict system // SOLVED
# TODO Use remote file system to download example fil... |
a333f20fa0be7bc24c61a793a5be0ec4c8a486b530e31f99d3f0c166cc35af19 | Python | 3,305 | 117 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import argparse
import logging
import sys
import traceback
from pathlib import Path
from quilt3 import Package
###############################################################################
logging.basicConfig(
level=logging.INFO,
format="[%(levelname)4s: %(mod... |
b389cfa42c85ca9139350aa5d2d7f7666eefc23979c100c1a76d8d61c4f7f641 | Python | 3,305 | 85 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="telseq",
anchor="telseq",
href="https://github.com/zd1/telseq",... |
f2fc5bb436527222b42b99ce625a72d19b7f44e9e0235a36fcfe5488b846ced0 | Python | 3,305 | 73 | import os
"""
viz/mdpi_style.py — Centralized MDPI Bioengineering Style Configuration
========================================================================
All viz modules import from here to ensure consistent figure formatting.
MDPI Requirements (Bioengineering):
- Paper: A4 (21 cm × 29.7 cm)
- Full-width fig... |
ad8b1a43ffa6b404ecf0e37b0ae9132a6786f294650682b1a9c398d43e4d9bf0 | Python | 3,306 | 118 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import click
import importlib
import functools
from typing import Callable, Optional
from datetime import datetime
import logging
def import_thing(import_string: str):
"""Obtain an obj... |
2f67183f97bcb4b66eddbc5425481fc34e7d69431a739485b1797a1dd580e8c2 | Python | 3,310 | 94 | """ Engine base class from which all ForceBalance MD engines are derived. """
import abc
import os
import subprocess
import shutil
import numpy as np
import time
from collections import OrderedDict
import tarfile
import forcebalance
from forcebalance.nifty import *
from forcebalance.finite_difference import fdwrap_G, ... |
16c82406b20342efa9e3f96316f149ff86e32159423f39eebc52e74d38dfafd4 | Python | 3,311 | 102 | from typing import Dict
import logging
from collections import defaultdict
from multiqc.base_module import BaseMultiqcModule
from multiqc.plots import table
log = logging.getLogger(__name__)
class DragenTrimmerMetrics(BaseMultiqcModule):
def add_trimmer_metrics(self):
data_by_sample = dict()
f... |
c54447561888e3ec84b6b3af3b46d6ca64111c9bf0330e1f8ba5766435d50728 | Python | 3,311 | 103 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
718907d4d4ddb459e741afd20f3a848827ce2c889e9ea5f062ae8f2d0c601798 | Python | 3,312 | 115 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import json
import openfe
from openfe.protocols import openmm_afe
import gufe
from gufe.tests.test_tokenization import GufeTokenizableTestsMixin
import pytest
@pytest.fixture
def protocol()... |
285cb1cd4efddb2378fc153eba62aca57c5b17589b4e70309eb0d2a951593b47 | Python | 3,314 | 121 | import matplotlib.pyplot as plt
import numpy as np
from scipy.stats import ttest_1samp
if __name__ == "__main__":
X = np.linspace(-5, 5, 100000)
def cdf_5(t):
return 1/2 + (1/np.pi) * ((t/(np.sqrt(5)*(1+((t**2)/5))))*(1+(2/(3*(1+(t**2)/5))))+np.arctan(t/np.sqrt(5)))
Y = [cdf_5(x) for x in X]
... |
dee01c0aca82642f7bc8ed0e86be794b454656c8c84a2332c8ac090fd3cac3f8 | Python | 3,315 | 86 | """
# File : utils.py
# Time : 2025/10/23 13:32
# Author : Hongmiao Wang
# version : python 3.10
# Description:
"""
from rdkit import Chem
def GetStructureK(smiles_list, tgt_smiles):
inchi = Chem.inchi.MolToInchiKey(Chem.MolFromSmiles(tgt_smiles))[0:14]
inchi_list = [Chem.inchi.MolToInchiKe... |
e91b82285a1cd87de3e51a4325e8c035a9d4e2140c8335966a3a07b2644a4f05 | Python | 3,316 | 102 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import click
from openfecli import OFECommandPlugin
from openfecli.parameters import MOL, MAPPER, OUTPUT_FILE_AND_EXT
def allow_two_molecules(ctx, param, value):
"""click callback to r... |
0b80cc4b454004f3b6bf7af3a8e14a52f480090aa882c10480927b092c972b85 | Python | 3,318 | 89 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import pytest
from gufe import LigandAtomMapping
from kartograf.mapping_metrics.metrics_mapping_comparisons import (
jaccard_score
)
from .conftest import benzene_benzene_mapp... |
aa0f07a0922f212172153db9e172896b4c7f87daab98359ddbf09c657ed65f13 | Python | 3,319 | 102 | import pytest
from copy import copy
import uvicorn
from alchemiscale.settings import get_base_api_settings
from alchemiscale.base.api import get_s3os_depends
from alchemiscale.compute import api, client
from alchemiscale.tests.integration.compute.utils import get_compute_settings_override
from alchemiscale.tests.int... |
e52e59a042b65a80e1e1bbc79af344a3c6729cf5bed52c5c8196cf9432da5ab6 | Python | 3,319 | 118 | import matplotlib.pyplot as plt
import os
import sys
sys.path.append("../utils/")
import tools
import re
import numpy as np
import random
plt.rcParams.update({'font.size': 25})
plt.rcParams['font.weight'] = 'bold'
parametermat = []
errormat = []
datapath="anglesweep_995"
imgname = "7_anglesweep995"
resultfilenames = ... |
cad6212e494696d0ef2535f2cb111a224678359ff4354ecd44cd105d54abeacd | Python | 3,321 | 90 | # ---------------------------------------------------------------
# Copyright (c) 2022, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the NVIDIA Source Code License
# for Denoising Diffusion GAN. To view a copy of this license, see the LICENSE file.
# -----------------------------------------... |
3cb0942b1228cb1652e09c31cd1b18171f2722f0842954459d4743344b614afc | Python | 3,324 | 87 | import argparse
from functools import partial
import json
import numpy as np
import shapely
from feabas.concurrent import submit_to_workers
from feabas.spatial import find_rotation_for_minimum_rectangle
from feabas.aligner import get_convex_hull, apply_transform_normalization
from feabas import config
from feabas.stor... |
88c127c5f812926dc26a83adbfc6896480d377d8b395b6498fb858a8ef0a1706 | Python | 3,324 | 70 | """
CLI interface for the talisman agent.
This may not be in the original code, but let's add it to make sure it's properly configured.
"""
import logging
import re
from pydantic_ai import RunContext
from aurelian.agents.talisman.talisman_config import TalismanConfig
from aurelian.agents.talisman.talisman_tools import... |
d9f29856b73647da26dc85145365779ed746ab4a4b29aa7875d620a6b8537ea3 | Python | 3,324 | 94 | import os
import sys
import argparse
from typing import List
from pathlib import Path
import yaml
# Allow imports from the parent directory
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
from src.load import load_files
from src.utils import compute_time_to_target
from src.plots import... |
3b623b94ca95ef6fb68f4f0fdd24824619c96b187092441772f57ded7ca5be88 | Python | 3,325 | 101 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Test the restraint settings.
"""
import pytest
from openff.units import unit
from openfe.protocols.restraint_utils.settings import (
BoreschRestraintSettings,
DistanceRestraintS... |
db9ae1b804b2df83f9fddb8183ab2e17da12319f51d3380726916bf0f65d4378 | Python | 3,326 | 93 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import dask.array as da
import random
from pathlib import Path
from aicsimageio import AICSImage
from .benchmark_image_containers import _ImageContainerTimeSuite
###############################################################################
# We only benchmark against... |
0b515198c1f011f581a54eb96cda967543b23504fe2d1f06d307c2fd5f4fc36d | Python | 3,327 | 47 | import pandas as pd
import pysam
import os, sys
from tqdm import tqdm
def check_bam_header(bam_file_path):
""" """
# Get BAM file header with pysam
h = pysam.view("-H", bam_file_path)
h = [e.split("\t") for e in h.split("\n") if e.startswith("@RG")]
sm_tag = list(set([sub_e.replace("SM:", "") for ... |
c7624e487e8a220a5e1830b77251b7a73b8c0e8edb90a631a23adc30eccb8ef6 | Python | 3,327 | 102 | import pytest
from openff.units import unit
import gufe
from gufe import SolventComponent, ChemicalSystem
from gufe.tests.test_protocol import DummyProtocol
@pytest.fixture
def solv_comp():
yield SolventComponent(positive_ion="K", negative_ion="Cl",
ion_concentration=0.0 * unit.molar)
... |
34f2e75b12b9a317a452ff52636e7cc754f5e47ee3dc7e562d988862834a2da0 | Python | 3,330 | 77 | """Generate run files and task files for example_custom_task.
Mixes built-in MTB tasks (n_back, rest) with two custom tasks defined locally
in my_tasks.py.
Class lookups go through ut.get_task_class (runtime) and
ut.get_task_file_class (file generation). Both consult const.task_modules
first, then fall back to the sh... |
d97997cc60d58dbc29d66fabbcf97f9fd88787594d236cd0fe440b8b9f0f0c87 | Python | 3,331 | 121 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import gzip
import openfe
import pytest
from gufe.tests.test_tokenization import GufeTokenizableTestsMixin
from openfe.protocols.openmm_afe import (
AbsoluteBindingComplexUnit,
Absol... |
09ba3867b5d27dd8ffa90d0a7b49351f749f4f16cf57df383fb886fa7776c445 | Python | 3,332 | 100 | """Tests for AbInitioPairwise and AbInitioPairwise_SMIRNOFF targets."""
from __future__ import absolute_import
import os
import sys
import shutil
import numpy as np
import pytest
import forcebalance
import forcebalance.smirnoffio
from .__init__ import ForceBalanceTestCase
from .test_target import TargetTests
from .t... |
60d49d91a440e15a5033952724e6373ee3bc725c715c5fcff6b58e7584e662a4 | Python | 3,334 | 91 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pathlib
import pytest
from gufe.protocols import execute_DAG
from openff.units import unit
from pontibus.protocols.relative import HybridTopProtocol
@pytest.mark.gpu
def test_vacu... |
d2119873e686638899fbee77097e6799693508706998ab944bac1146db3fb014 | Python | 3,335 | 79 | """" Theo Gauvrit
05/06/2023
First test of Cebra library"""
import os
import cebra
import json
import numpy as np
import pandas as pd
import percephone.core.recording as pc
import os
import matplotlib
import matplotlib.pyplot as plt
from multiprocessing import Pool, cpu_count, pool
plt.rcParams['font.size'] = 10
plt.r... |
95377a2167f207743f70ce2dbe7f037da168e2929ea7dc83c0e6196cce1ec8e8 | Python | 3,339 | 101 | """
TimeFlies CLI Setup Commands
Contains setup, split, and environment configuration commands.
"""
import os
from pathlib import Path
def new_setup_command(args) -> int:
"""Complete setup: create directories, split data, optional batch correction, verify."""
print("LAUNCH: TimeFlies Complete Setup")
pr... |
64017593408508f171dbbac1c44facb83b50457144b722d541f02c14fd98ba99 | Python | 3,342 | 111 | import numpy as np
import pandas as pd
from copy import deepcopy
from tqdm.auto import tqdm
from sklearn.base import TransformerMixin
from scipy.sparse import csc_matrix, csr_matrix, issparse
def add_percentile_for_grp(in_df, group_col, new_col, sort_col='prediction'):
grpd = in_df.groupby(group_col)
out_dfs ... |
4d0f61fa65596c9b3ecab16229442dc894f680e457307fb5b483f47e36b1054b | Python | 3,343 | 96 | """
Test Cython and weave mixing code.
"""
import copy
import numpy as np
import scipy.stats as stats
def mix_replicas(n_swaps=100, n_states=16, u_kl=None, nswap_attempts=None):
"""
Utility function to generate replicas and call the mixing function a certain number of times
Arguments
---------
... |
f1ffeda5b4dec41600eaf0123b7371f17cd09e7b067d7dc5a70ffcfee27f2277 | Python | 3,344 | 104 | #!/usr/bin/env python3
""" Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
"""
from setuptools import setup, find_packages
from distutils.extension import Extension
from Cython.Build import cythonize
from Cython.Distutils import build_ext
from numpy.distutils.system_info import default_include_dirs,... |
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