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# -*- coding: utf-8 -*- """ Created on Thu Aug 6 00:21:15 2020 @author: Xingyan Liu Functions for handling AnnData: * I/O functions * preprocessing - normalization / z-scoring / ... - groups / ... * statistics computation """ import logging import os from pathlib import Path from typin...
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# Copyright 2024 DeepMind Technologies Limited # # AlphaFold 3 source code is 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...
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# TODO update all 2p stim related attr's to naparm submodule import glob import os import signal import time import matplotlib.pyplot as plt import numpy as np import pandas as pd import scipy.stats as stats import tifffile as tf from packerlabimaging import TwoPhotonImaging from packerlabimaging._archive.classes imp...
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# Copyright 2024 DeepMind Technologies Limited # # AlphaFold 3 source code is 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...
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#!/usr/bin/env python3 import pytest from skbase.utils.dependencies import _check_soft_dependencies from pgmpy.base import ADMG, DAG, MAG, PDAG from pgmpy.base._base import _CoreGraph def sample_graph1(edge_type=None): """ Sample graph for testing node searching(`get_*`) method of `_CoreGraph` class. Te...
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import simtk.openmm as openmm import os import copy import openmmtools.mcmc as mcmc import openmmtools.integrators as integrators import openmmtools.states as states from openmmtools import utils from openmmtools.states import ThermodynamicState import numpy as np import mdtraj as md import mdtraj.utils as mdtrajutils...
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from __future__ import annotations import itertools from collections.abc import Hashable, Iterable, Sequence from os import PathLike from typing import TYPE_CHECKING import networkx as nx import numpy as np import pandas as pd from pgmpy import logger from pgmpy.base._mixin_roles import _GraphRolesMixin from pgmpy.c...
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# os.environ['CUDA_VISIBLE_DEVICES'] = '-1' # CUDA_VISIBLE_DEVICES = "" import os try: from tensorboard.plugins.hparams import api as hp except Exception: # Optional logging dependency. hp = None try: import tensorflow as tf except Exception: # Optional logging dependency. tf = None from sklearn.met...
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#!/usr/bin/env python """ COPYRIGHT AND LICENSE @author John D. Chodera <jchodera@gmail.com> All code in this repository is released under the MIT License. This program is free software: you can redistribute it and/or modify it under the terms of the MIT License. This program is distributed in the hope that it wi...
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''' PipelineRrbs.py - Utility functions for analysing rrbs sequence data ===================================================================== Mapping reads is a common task in pipelines. Different pipelines combine different sources of input (:term:`fastq` files, :term:`sra` files) of different data (single end, pai...
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#!/usr/bin/env python # -*- coding: latin-1 -*- # **************************************************************************** # * Software: FPDF for python * # * Version: 1.7.1 * # * Date: 2010-09-10 ...
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""" Datasets. Usage: datasets.py [--root=root] --data=data Options: --root=root Root directory [default: ./data] --data=data Dataset name """ import time import jax import jax.numpy as jnp from jax import lax import diffrax import numpy as np import torch import matplotlib.pyplot as plt from scipy.i...
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"""Types for middleware and agents.""" from __future__ import annotations import warnings from collections.abc import Awaitable, Callable, Sequence from dataclasses import dataclass, field, replace from inspect import iscoroutinefunction from typing import ( TYPE_CHECKING, Annotated, Any, Generic, ...
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"""=================================================== pipeline_windows - Window based genomic analysis =================================================== This pipeline takes mapped reads from ChIP-Seq experiments such has chromatin marks, MeDIP and performs analyses of the genomic read distribution. This contrasts w...
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# vim: fdm=indent # author: Joan Camunas # date: 16/08/17 # content: Dataset functions to correlate gene expression and phenotypes # Modules import numpy as np import pandas as pd from scipy.stats import rankdata import matplotlib.pyplot as plt import matplotlib as mpl import seaborn as sns #### #BASIC QC...
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from collections.abc import AsyncIterator, Iterable, Iterator, Sequence from datetime import datetime, timezone from typing import ( Any, ) from unittest.mock import AsyncMock, MagicMock, patch import pytest import pytest_asyncio from pytest_mock import MockerFixture from langchain_core.document_loaders.base impo...
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""" ===================================================== Community analysis of metgenomic shotgun sequencing ===================================================== Pipeline_metagenomecommunities.py takes as input a set of fastq files from a shotgun sequencing experiment of environmental samples and assesses community...
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"""================= ChIP-Seq pipeline ================= :Author: Andreas Heger :Release: $Id: pipeline_chipseq.py 2900 2010-04-13 14:38:00Z andreas $ :Date: |today| :Tags: Python The ChIP-Seq pipeline imports reads from one or more ChIP-Seq experiments and performs the following tasks: * align reads to the genom...
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"""================================= RNA-Seq Transcript Build pipeline ================================= The rnaseq transcript build pipeline attempts build a variety of gene sets from reads mapped to a reference genome. This pipeline works on a single genome. Overview ======== The pipeline assumes the data derive...
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Fri May 28 2021 @author: Simon Pelletier """ import os import csv from PIL import Image import torch import itertools import numpy as np from torch.utils.data import Dataset import random import pandas as pd from sklearn.preprocessing import minmax_scale as...
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import sys sys.path.insert(0,"../") import pandas as pd import numpy as np from sklearn import metrics from sklearn.linear_model import LogisticRegression from sklearn.neighbors import KNeighborsClassifier from sklearn.naive_bayes import GaussianNB from sklearn.tree import DecisionTreeClassifier from sklearn.ensemble ...
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""" ==================== Exome pipeline ==================== The exome pipeline imports unmapped reads from one or more fastq or sra files and aligns them to the genome using BWA. Post alignment quality control is performed using Picard. The pipeline then performs local realignment around indels and base quality sc...
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import math from copy import copy from pathlib import Path import numpy as np import pandas as pd import requests import torch import torch.nn as nn import torch.nn.functional as F from torchvision.ops import DeformConv2d from PIL import Image from torch.cuda import amp from utils.datasets import letterbox from utils...
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# -*- coding: utf-8 -*- # author: Felix Repp felix.repp@mpikg.mpg.de # !/usr/bin/env python """@namespace tinaui \brief %This module provides the user interface for an easy usage of TINA using the tina_main.dataset container. Tinaui allow an easy usage of the tools as well as documentation of the process. They are ...
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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ Multistatereporter ================== Master multi-thermodynamic state reporter module. Handles all Disk...
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""" Tools for computing atom mappings for relative free energy transformations. These tools currently require the OpenEye Toolkit, but will eventually be fully migrated to the OpenFF toolkit. .. todo :: This module should be migrated to openmmtools. """ from simtk import unit import copy import numpy as np ######...
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"""Agent factory for creating agents with middleware support.""" from __future__ import annotations import functools import importlib import itertools import re from dataclasses import dataclass, field, fields from typing import ( TYPE_CHECKING, Annotated, Any, Generic, cast, get_args, get...
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__author__ = 'Patrick B. Grinaway' import simtk.openmm as openmm import openmoltools import simtk.openmm.app as app import simtk.unit as unit import logging import numpy as np import parmed from collections import namedtuple, OrderedDict import copy from unittest import skipIf try: from urllib.request import urlop...
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Python
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__author__ = 'Patrick B. Grinaway' import simtk.openmm as openmm import openmoltools import simtk.openmm.app as app import simtk.unit as unit import logging import numpy as np import parmed from collections import namedtuple, OrderedDict import copy from unittest import skipIf import pytest try: from urllib.reques...
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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ MultistateSampler ================= Base multi-thermodynamic state multistate class COPYRIGHT Current ...
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# Copyright 2021 AlQuraishi Laboratory # 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 # # U...
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"""API tests - upload -> analyze -> poll status -> results -> mesh export -> results bundle. landmarks are always manual now (see pipeline.py). using REFERENCE_TRIANGLE as landmarks on template_xy_com.ply since it's already in the frame the clip constants assume, so harmonize() has something real to work with without ...
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Fri May 28 2021 @author: Simon Pelletier """ import os import csv from PIL import Image import torch import itertools import numpy as np from torch.utils.data import Dataset import random import pandas as pd from sklearn.preprocessing import minmax_scale as...
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"""=================== Annotation pipeline =================== The annotation pipeline imports various third party annotations or creates them for use in other pipelines. The purpose of this pipeline is to automate and standardize the way we retrieve and build genomic annotations but also to allow sharing of annotati...
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import math import os import sys import numpy as np from wfdb.io import download, _coreio, util MAX_I32 = 2147483647 MIN_I32 = -2147483648 # Formats in which all samples align with integer (power-of-two) boundaries ALIGNED_FMTS = ["8", "16", "32", "61", "80", "160"] # Formats in which not all samples align with in...
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""" Hippocampus models. :Version: 2.0.0 :Date: 04.07.2018 :Author: Jan Melchior :Contact: JanMelchior@gmx.de :License: Copyright (C) 2018 Jan Melchior This program is free software: you can redistribute it and/or modify it under the term...
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"""Run managers.""" from __future__ import annotations import asyncio import atexit import functools import inspect import logging from abc import ABC, abstractmethod from collections.abc import Callable, Mapping from concurrent.futures import ThreadPoolExecutor from contextlib import asynccontextmanager, contextmana...
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""" This module provides restricted Boltzmann machines (RBMs) with different types of units. The structure is very close to the mathematical derivations to simplify the understanding. In addition, the modularity helps to create other kind of RBMs without adapting the training algorithms. :Implemented: ...
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#!/usr/bin/env python3 """Design guides for diagnostics.""" import argparse from collections import defaultdict import logging import os import random import re import shutil import sys import tempfile import numpy as np sys.path.append(os.getcwd()) from easyDesign import alignment from easyDesign import guide_search...
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# network wrappers for 3D-RGAN # Created: 2021 # Updated: 3/21/2022 # Status: OK import torch import os, sys import glob import shutil import wandb import shap import torch.nn as nn import torch.optim as optim import numpy as np import pandas as pd import nibabel as nib import matplotlib.pyplot as plt import tabulate...
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"""Module that contains tests for runnable.astream_events API.""" import asyncio import inspect import sys import uuid from collections.abc import AsyncIterator, Callable, Iterable, Iterator, Sequence from functools import partial from itertools import cycle from typing import ( Any, cast, ) import pytest fro...
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'''PipelinePeakCalling.py - Tasks associated with pipeline_peakcalling ====================================================================== One set of functions runs peak callers and uploads the called peaks into the database. The functions follow the following naming convention: runXXX() run a certain peak ca...
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import random import datetime as dt from tqdm import tqdm import numpy as np import os from typing import Dict, Union from lips.benchmark.airfransBenchmark import AirfRANSBenchmark from lips.dataset.airfransDataSet import AirfRANSDataSet from lips.dataset.scaler.standard_scaler_iterative import StandardScalerIterative...
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'''peakcalling.py - Tasks associated with pipeline_peakcalling ====================================================================== One set of functions runs peak callers and uploads the called peaks into the database. The functions follow the following naming convention: runXXX() run a certain peak caller lo...
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# -- coding: utf-8 -- # @Time : 2022/10/15 16:05 # @Author : Biao Zhang # @Email : littlebiao@outlook.com # @File : process.py import pickle import numpy as np import scanpy as sc, anndata as ad import scipy.sparse as sp import pandas as pd import sys import os sys.path.append('../code/') #from BrainAlign.code.utils ...
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# -- coding: utf-8 -- # @Time : 2022/10/15 16:05 # @Author : Biao Zhang # @Email : littlebiao@outlook.com # @File : process.py import pickle import numpy as np import scanpy as sc, anndata as ad import scipy.sparse as sp import pandas as pd import sys import os sys.path.append('../code/') #from BrainAlign.code.utils ...
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import math import numpy as np import networkx as nx from tqdm import tqdm from copy import deepcopy from scipy.sparse.linalg import eigsh import matplotlib.pyplot as plt from numpy.random import randn import random import torch import torch.nn as nn import torch.nn.functional as F from torch.nn import ReLU from torch_...
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"""Module contains utility functions for working with messages. Some examples of what you can do with these functions include: * Convert messages to strings (serialization) * Convert messages from dicts to Message objects (deserialization) * Filter messages from a list of messages based on name, type or id etc. """ ...
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''' functions for model ''' from neuron import h import pandas as pd import math as math import numpy as np import random import os from tqdm import tqdm import seaborn as sns import matplotlib as mpl import plotly.graph_objects as go def cell_build(cell_type='dspn', specs=None, addSpines=False, branc...
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"""Methods for searching for optimal guides to use for a diagnostic. """ from collections import defaultdict import logging import math import random import numpy as np from easyDesign import alignment from easyDesign.utils import index_compress from easyDesign.utils import lsh from easyDesign.utils import predict_a...
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# Copyright Generate Biomedicines, 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 # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to ...
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import os import re import collections import itertools import cgatcore.experiment as E from cgatcore import pipeline as P import cgatcore.iotools as iotools import cgat.BamTools.bamtools as BamTools import pandas as pd import pysam import numpy as np import shutil from cgatcore.pipeline import cluster_runnable from rp...
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""" Tests for Topology """ import itertools import re import tempfile from collections import defaultdict from copy import deepcopy from io import StringIO from pathlib import Path import numpy as np import openmm.app import openmm.unit import pytest from openff.units.openmm import from_openmm from openff.utilities ...
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''' PipelineLncRNA.py - functions and classes for use with the lincRNA pipeline =========================================================================== ''' import re import sys import os import cgat.GTF as GTF import cgatcore.iotools as iotools import gzip import collections import cgat.IndexedGenome as IndexedGe...
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""" Class definitions to represent a molecular system and its chemical components .. todo:: * Create MoleculeImage, ParticleImage, AtomImage here. (Or ``MoleculeInstance``?) * Create ``MoleculeGraph`` to represent fozen set of atom elements and bonds that can used as a key for compression * Add hierarchical ...
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import logging import os import pathlib import random import time from pathlib import Path from typing import Callable, List, Literal, Tuple, Union import humanize import torch import torch.nn as nn import torch.nn.functional as F import xxhash from torch.nn.modules.loss import _Loss from torch.utils.data import DataL...
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#!/usr/local/bin/env python """ Test replicaexchange.py facility. TODO * Create a few simulation objects on simple systems (e.g. harmonic oscillators?) and run multiple tests on each object? """ # ============================================================================================= # GLOBAL IMPORTS # =====...
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"""=========================== Variant annotation pipeline =========================== :Author: Andreas Heger :Release: $Id$ :Date: |today| :Tags: Python The Variants pipeline attempts to annotate variants in a :term:`vcf` formatted file. It computes 1. the effects of SNPs on transcripts and genes This pipeline ...
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Python
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# -*- coding: utf-8 -*- """ Created on Wed Oct 30 13:30:36 2016 Define poly(A) sites and calculate relative usages parallelized @author: schmiral """ __date__ = "Wed Oct 05 13:30:36 2016" __author__ = "Ralf Schmidt" __email__ = "ralf.schmidt@unibas.ch" __license__ = "GPL" # imports import sys import os import time ...
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#################################################################################### # # STEPS - STochastic Engine for Pathway Simulation # Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan. # Copyright (C) 2003-2006 University of Antwerp, Belgium. # # See the file AUTHORS for d...
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"""builds the results you get after an analysis - meshes, a json report, and a measurement figure, packaged as CP_{stem}_{C|F}_{3|4}[_CoM]/ (see results_folder_name). this is basically the same stuff the old app wrote next to your file (_rg.ply, _metrics.json etc), just organized into one folder now instead of a pile o...
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""" Wrapper class providing a minimal consistent interface to the `OpenEye Toolkit <https://docs.eyesopen.com/toolkits/python/quickstart-python/index.html>`_ """ __all__ = ("OpenEyeToolkitWrapper",) # See https://github.com/conda-forge/openff-toolkit-feedstock/issues/86 try: import zstandard # noqa except Impor...
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import collections import copy import datetime import functools import hashlib import heapq import io import logging import os import pathlib import platform import re import shutil import tempfile import types import unittest import unittest.mock import click import click.testing import depthcharge import depthcharge...
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""" Nonparametric survival estimators Author: George H. Chen (georgechen [at symbol] cmu.edu) This file contains the following classes and various helper functions (all of these implement both Kaplan-Meier and Nelson-Aalen versions): - BasicSurvival : basic Kaplan-Meier and Nelson-Aalen estimators that do not accou...
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import base64 import json import math import re from collections.abc import Callable, Sequence from typing import Any, TypedDict import pytest from typing_extensions import NotRequired, override from langchain_core.language_models.fake_chat_models import FakeChatModel from langchain_core.messages import ( AIMessa...
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import torch from torch import nn from torch.utils.data import TensorDataset import torch.nn.functional as F import numpy as np import math import copy from net_helpers import BaseNetwork from net_helpers import rand_weight_init, linear_fn from net_helpers import relu_fn, sigmoid, tanh_re, tukey_fn from net_helpers i...
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# A collection of tools to remotely access a CATMAID server via its API # # Copyright (C) 2017 Philipp Schlegel # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of ...
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#################################################################################### # # STEPS - STochastic Engine for Pathway Simulation # Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan. # Copyright (C) 2003-2006 University of Antwerp, Belgium. # # See the file AUTHORS for detai...
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import warnings from abc import ABC from typing import Optional, Sequence, Union import numpy as np import torch import torch.nn.functional as F from torch.nn.modules.utils import _pair from bindsnet.utils import im2col_indices from ..network.nodes import SRM0Nodes from ..network.topology import ( AbstractConnect...
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import copy import logging import traceback from collections import defaultdict from functools import lru_cache from pathlib import Path from typing import Any, Callable, Dict, List, Literal, Tuple, Union import dask.array as da import humanize from sklearn.preprocessing import LabelEncoder try: import napari exc...
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"""Chat models for conversational AI.""" from __future__ import annotations import asyncio import builtins # noqa: TC003 # runtime-evaluated; subclass `dict()` shadows the builtin import contextlib import json from abc import ABC, abstractmethod from collections.abc import AsyncIterator, Callable, Iterator, Sequenc...
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#!/usr/bin/env python # ============================================================================= # MODULE DOCSTRING # ============================================================================= """ Test State classes in states.py. """ # ========================================================================...
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""" Test classes and function in module openff.toolkit.typing.engines.smirnoff.parameters. """ from collections import defaultdict from inspect import isabstract, isclass import numpy import pytest from numpy.testing import assert_almost_equal from packaging.version import Version from openff.toolkit import ForceFi...
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'''mapping.py - Utility functions for mapping short reads ============================================================== Mapping reads is a common task in pipelines. Different pipelines combine different sources of input (:term:`fastq` files, :term:`sra` files) of different data (single end, paired end) with differen...
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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ MultiStateAnalyzers =================== Analysis tools and module for MultiStateSampler simulations. Pro...
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Python
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from __future__ import print_function """ Test systems for perses automated design. Examples -------- Alanine dipeptide in various environments (vacuum, implicit, explicit): >>> from perses.tests.testsystems import AlaninDipeptideSAMS >>> testsystem = AlanineDipeptideTestSystem() >>> system_generator = testsystem.sy...
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from __future__ import print_function """ Test systems for perses automated design. Examples -------- Alanine dipeptide in various environments (vacuum, implicit, explicit): >>> from perses.tests.testsystems import AlaninDipeptideSAMS >>> testsystem = AlanineDipeptideTestSystem() >>> system_generator = testsystem.sy...
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from math import sin, cos, radians from OCC.Core.BRepPrimAPI import BRepPrimAPI_MakePrism, BRepPrimAPI_MakeRevol from OCC.Core.BRepAlgoAPI import BRepAlgoAPI_Cut, BRepAlgoAPI_Fuse, BRepAlgoAPI_Common from OCC.Display.SimpleGui import init_display from OCC.Core.gp import gp_Pnt, gp_Ax1, gp_Ax2, gp_Dir, gp_Circ, gp_Vec f...
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Python
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"""=========================== Pipeline GWAS =========================== .. Replace the documentation below with your own description of the pipeline's purpose Overview ======== This pipeline computes the word frequencies in the configuration files :file:``pipeline.yml` and :file:`conf.py`. Usage ===== See :re...
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Python
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import logging import os import shutil import tempfile import warnings from collections import OrderedDict from pathlib import Path from typing import Callable, List, Literal, Tuple, Union import czifile import dask import dask.array as da import dask_image.imread import h5py import numpy as np import pandas as pd imp...
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#################################################################################### # # STEPS - STochastic Engine for Pathway Simulation # Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan. # Copyright (C) 2003-2006 University of Antwerp, Belgium. # # See the file AUTHORS for d...
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Python
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#!/usr/bin/python # ============================================================================= # MODULE DOCSTRING # ============================================================================= """ Tests for alchemical factory in `alchemy.py`. """ # ==============================================================...
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Python
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import matplotlib from tqdm import trange from bernn.utils.pool_metrics import log_pool_metrics import pandas as pd import numpy as np import random import torch from torch import nn from torch import nn from sklearn import metrics import contextlib import copy from bernn.utils.ax_compat import optimize, AX_AVAILABLE ...
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Python
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""" This file contains the base classes for topology proposals """ from simtk.openmm import app import copy import logging import itertools import os import numpy as np import networkx as nx import openmoltools.forcefield_generators as forcefield_generators from perses.storage import NetCDFStorageView from perses.rjm...
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# Copyright 2024 DeepMind Technologies Limited # # AlphaFold 3 source code is 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...
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""" A modified version of the original Scholar implementation by Dallas Card to support survival analysis supervision (Cox and several parametric AFT losses), and where we explicitly support two underlying topic models (LDA and SAGE) The original Scholar code that this file is modified from can be found at: https...
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Python
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""" This file contains the base classes for topology proposals """ from simtk.openmm import app import copy import logging import itertools import os import numpy as np import networkx as nx import openmoltools.forcefield_generators as forcefield_generators from perses.storage import NetCDFStorageView from perses.rjm...
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Python
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import torch from torch import nn from torch.utils.data import TensorDataset import torch.nn.functional as F import numpy as np import math import copy from net_helpers import BaseNetwork from net_helpers import rand_weight_init, linear_fn from net_helpers import relu_fn, sigmoid, tanh_re, tukey_fn from net_helpers i...
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Python
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from __future__ import absolute_import from perses.dispersed import feptasks from perses.utils.openeye import createOEMolFromSDF, createSystemFromSMILES, extractPositionsFromOEMol, generate_unique_atom_names from perses.utils.data import load_smi from perses.annihilation.lambda_protocol import RelativeAlchemicalState,...
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#!/usr/bin/python # ============================================================================= # MODULE DOCSTRING # ============================================================================= """ Alchemical factory for free energy calculations that operates directly on OpenMM System objects. DESCRIPTION This m...
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Python
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from __future__ import absolute_import from perses.dispersed import feptasks from perses.utils.openeye import createOEMolFromSDF, createSystemFromSMILES, extractPositionsFromOEMol, generate_unique_atom_names from perses.utils.data import load_smi from perses.annihilation.lambda_protocol import RelativeAlchemicalState,...
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# mypy: ignore-errors """ Wrapper class providing a minimal consistent interface to the `RDKit <http://www.rdkit.org/>`. """ __all__ = ("RDKitToolkitWrapper",) import copy import functools import importlib import itertools import logging import pathlib import tempfile import warnings from collections import defaultdi...
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Python
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""" This contains the base class for the geometry engine, which proposes new positions for each additional atom that must be added. """ from simtk import unit import numpy as np import networkx as nx from perses.storage import NetCDFStorageView ########################################################################...
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""" This contains the base class for the geometry engine, which proposes new positions for each additional atom that must be added. """ from simtk import unit import numpy as np import networkx as nx from perses.storage import NetCDFStorageView ########################################################################...
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# -*- coding: utf-8 -*- """ Created on Sun Aug 9 22:18:39 2020 @author: Shencong Ni """ import numpy as np from scipy.sparse import csc_matrix from scipy.sparse import csr_matrix from scipy.stats import sem import matplotlib as mpl import matplotlib.pyplot as plt import matplotlib.animation as animation import connec...
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""" Parameter handlers for the SMIRNOFF force field engine This file contains standard parameter handlers for the SMIRNOFF force field engine. These classes implement the object model for self-contained parameter assignment. New pluggable handlers can be created by creating subclasses of :class:`ParameterHandler`. ""...
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''' Expression.py - wrap various differential expression tools =========================================================== :Tags: Python Purpose ------- This module provides tools for differential expression analysis for a variety of methods. Methods implemented are: DESeq EdgeR ttest The aim of this mod...
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#################################################################################### # # STEPS - STochastic Engine for Pathway Simulation # Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan. # Copyright (C) 2003-2006 University of Antwerp, Belgium. # # See the file AUTHORS for detai...
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"""Test the base tool implementation.""" import inspect import json import logging import pickle import sys import textwrap import threading import warnings from collections.abc import Callable from dataclasses import dataclass from datetime import datetime from enum import Enum from functools import partial from typi...
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# -- coding: utf-8 -- # @Time : 2022/10/17 14:28 # @Author : Biao Zhang # @Email : littlebiao@outlook.com # @File : analysis.py import pickle import numpy as np import scanpy as sc, anndata as ad import scipy.sparse as sp import pandas as pd import sys import matplotlib.pyplot as plt import re, seaborn as sns from coll...