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Python
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############################################################################## # pymbar: A Python Library for MBAR # # Copyright 2017-2022 University of Colorado Boulder # Copyright 2010-2017 Memorial Sloan-Kettering Cancer Center # Portions of this software are Copyright (c) 2010-2016 University of Virginia # Portions...
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Python
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############################################################################## # pymbar: A Python Library for MBAR # # Copyright 2017-2022 University of Colorado Boulder # Copyright 2010-2017 Memorial Sloan-Kettering Cancer Center # Portions of this software are Copyright (c) 2010-2016 University of Virginia # Portions...
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import base64 import io import json import logging import math import multiprocessing import platform import random import re import subprocess from datetime import datetime from functools import lru_cache from pathlib import Path from typing import ( Any, Dict, Generic, List, Mapping, Optional,...
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import numpy as np import pandas as pd import glob, os import scipy.stats as st import matplotlib.pyplot as plt import seaborn as sns from functools import reduce from sklearn.preprocessing import StandardScaler import lifelines, itertools from sklearn.model_selection import KFold log_metadata_cols = ['F2', 'TTP_basel...
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# Version: 0.29 """The Versioneer - like a rocketeer, but for versions. The Versioneer ============== * like a rocketeer, but for versions! * https://github.com/python-versioneer/python-versioneer * Brian Warner * License: Public Domain (Unlicense) * Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3 * [![L...
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import datetime import os from pathlib import Path import numpy as np import pandas as pd import plotly.express as px import plotly.graph_objects as go import plotly.io as pio import statsmodels.formula.api as smf from hrpqct_database.dataclasses_hrpqct import HRpQCT_Dataset from PIL import Image from plotly.subplots...
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# Version: 0.29+8.gf9bbd1b """The Versioneer - like a rocketeer, but for versions. The Versioneer ============== * like a rocketeer, but for versions! * https://github.com/python-versioneer/python-versioneer * Brian Warner * License: Public Domain (Unlicense) * Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and ...
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""" @package forcebalance.gmxio GROMACS input/output. @todo Even more stuff from forcefield.py needs to go into here. @author Lee-Ping Wang @date 12/2011 """ from __future__ import division from __future__ import print_function from builtins import zip from builtins import str from builtins import range import os, s...
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# Task Class definitions # March 2021: First version: Ladan Shahshahani - Maedbh King - Suzanne Witt, # Revised 2023: Bassel Arafat, Jorn Diedrichsen, Incé Husain # Revised 2024: Caroline Nettekoven from pathlib import Path import pandas as pd import numpy as np import random from psychopy import prefs prefs.hardware...
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""" @package forcebalance.amberio AMBER force field input/output. This serves as a good template for writing future force matching I/O modules for other programs because it's so simple. @author Lee-Ping Wang @date 01/2012 """ from __future__ import division from __future__ import print_function from builtins import ...
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import numpy as np import copy import inspect from scipy import signal #import matplotlib.pyplot as plt import logging import os.path as path # define activation functions def linear(x, slope=1.0, offset=0.0): x = x-offset return np.array(x*slope) def d_linear(x, slope=1.0, offset=0.0): x = x-offset return np.ones...
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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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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ Multistatereporter ================== Master multi-thermodynamic state reporter module. Handles all Disk...
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# This code is part of OpenFE and is licensed under the MIT license. # For details, see https://github.com/OpenFreeEnergy/openfe """OpenMM Equilibrium SepTop RBFE Protocol --- :mod:`openfe.protocols.openmm_septop.equil_septop_method` ======================================================================================...
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import shutil import subprocess from pathlib import Path import numpy import pandas from openff.toolkit import Topology from openff.units import unit from pymbar import timeseries from proteinbenchmark.analysis_parameters import * from proteinbenchmark.benchmark_targets import benchmark_targets, experimental_datasets...
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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ MultistateSampler ================= Base multi-thermodynamic state multistate class COPYRIGHT Current ...
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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ MultistateSampler ================= Base multi-thermodynamic state multistate class COPYRIGHT Current ...
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# region ======================================== Imports ============================================================== import os import random import mplcursors import numpy as np import pandas as pd import statsmodels.formula.api as smf import statsmodels.api as sm import pingouin as pg from imblearn.under_sampling...
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# Copyright 2022 Google LLC. # # 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,...
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from collections import defaultdict import gc import numpy as np import pyamg import scipy from scipy import sparse from scipy.sparse.linalg import LinearOperator from scipy.spatial import KDTree import time from feabas import config, spatial, common, caching, storage import feabas.constant as const from feabas.mesh i...
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import datetime from truesight.db.models import DbEvaluation, DbLLM from truesight.db.session import get_session from truesight.evaluation import evals, services as evaluation_services import numpy as np from truesight import stats_utils, plot_utils from loguru import logger ANIMAL_RANKING_PROMPT_TEMPLATES = [ "On...
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import shutil from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QVBoxLayout, QGridLayout, QDialog, QDialogButtonBox,\ QComboBox, QPushButton, QScrollArea, QLineEdit, QFileDialog, QMessageBox, QSpinBox, QCheckBox, QStackedWidget, QGroupBox from PySide6.QtCore import Qt, QSize, Signal from PySide6.QtGui im...
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import cv2 from collections import defaultdict, namedtuple from functools import partial import gc import json import matplotlib.tri import numpy as np import os from rtree import index from scipy.interpolate import interp1d from scipy.ndimage import gaussian_filter, binary_dilation, distance_transform_cdt from scipy i...
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""" @package forcebalance.openmmio OpenMM input/output. @author Lee-Ping Wang @date 04/2012 """ from __future__ import division from builtins import zip from builtins import range import os from forcebalance import BaseReader from forcebalance.abinitio import AbInitio from forcebalance.binding import BindingEnergy fr...
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############################################################################## # pymbar: A Python Library for MBAR (FES module) # # Copyright 2019 University of Colorado Boulder # # Authors: Michael Shirts # # pymbar is free software: you can redistribute it and/or modify # it under the terms of the MIT License as # # ...
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import pytest import datetime from time import sleep import os from pathlib import Path from itertools import chain import json from gufe import AlchemicalNetwork from gufe.tokenization import TOKENIZABLE_REGISTRY, GufeKey, JSON_HANDLER from gufe.protocols.protocoldag import execute_DAG import networkx as nx from alc...
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import copy import re from itertools import chain import openmm import pytest from openff.units import unit as offunit from openff.units.openmm import ensure_quantity, from_openmm, to_openmm from openmm import app, unit from openmmforcefields.generators import SystemGenerator from openfe.protocols.openmm_rfe import R...
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############################################################################## # pymbar: A Python Library for MBAR (FES module) # # Copyright 2019 University of Colorado Boulder # # Authors: Michael Shirts # # pymbar is free software: you can redistribute it and/or modify # it under the terms of the MIT License as # # ...
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############################################################################## # pymbar: A Python Library for MBAR (FES module) # # Copyright 2019 University of Colorado Boulder # # Authors: Michael Shirts # # pymbar is free software: you can redistribute it and/or modify # it under the terms of the MIT License as # # ...
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"""Tests for custom image data generators""" import numpy as np import skimage as sk from PIL import Image from tensorflow.keras import backend as K from tensorflow.keras.preprocessing.image import img_to_array from tensorflow.python.platform import test from deepcell import image_generators def all_test_images(...
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""" Enhanced Multi-Class and Binary Brain Segmentation with K-Fold Cross-Validation Journal Paper Implementation with K-Fold Strategy Scenarios: Multi-class (4 classes) and Binary (Abnormal WMH, Ventricles) K-Fold Cross-Validation (k=5, 80/20 split) Author: Mahdi Bashiri Bawil """ ###################### Libraries ###...
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# This code is part of OpenFE and is licensed under the MIT license. # For details, see https://github.com/OpenFreeEnergy/openfe import copy import json import logging import sys import xml.etree.ElementTree as ET from importlib import resources from math import sqrt from pathlib import Path from unittest import mock ...
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import sys import math import pickle from datetime import datetime import torch import torch.nn as nn import torch.nn.functional as F from torch import Tensor from dataclasses import dataclass, field from typing import Dict, Tuple, Optional, NamedTuple, List import numpy as np import matplotlib.pyplot as plt from scipy...
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""" Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import sys from pathlib import Path import h5py import matplotlib.pyplot as plt import numpy as np import pyqtgraph as pg import torch from matplotlib import cm from qtpy import QtCore, QtWidgets, QtGui from...
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# ============================================================================================ # MODULE DOCSTRING # ============================================================================================ """ Custom integrators for molecular simulation. DESCRIPTION This module provides various custom integrators...
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# -*- coding: UTF-8 -*- # ============================================================================================ # MODULE DOCSTRING # ============================================================================================ """ Custom integrators for molecular simulation. DESCRIPTION This module provides va...
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# region ======================================== Imports ============================================================== import os import numpy as np import pandas as pd import pingouin as pg import scipy.stats as ss from multiprocessing import cpu_count, pool from matplotlib import pyplot as plt from scipy.signal impo...
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""" PDB parsing class This module parses PDBs in accordance to PDB Format Description Version 2.2 (1996); it is not very forgiving. Each class in this module corresponds to a record in the PDB Format Description. Much of the documentation for the classes is taken directly from the above PDB Format D...
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import pytest import datetime from time import sleep import os from pathlib import Path from itertools import chain import json from gufe import AlchemicalNetwork from gufe.archival import AlchemicalArchive from gufe.tokenization import TOKENIZABLE_REGISTRY, GufeKey, JSON_HANDLER from gufe.protocols import ProtocolRes...
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import os import torch import pandas as pd import numpy as np import networkx as nx from tqdm import tqdm from sklearn.model_selection import GridSearchCV from sklearn.cluster import AgglomerativeClustering import seaborn as sns import matplotlib.pyplot as plt import matplotlib.ticker as mticker from sksurv.util import...
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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ MultiStateAnalyzers =================== Analysis tools and module for MultiStateSampler simulations. Pro...
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#!/usr/local/bin/env python # ============================================================================== # MODULE DOCSTRING # ============================================================================== """ MultiStateAnalyzers =================== Analysis tools and module for MultiStateSampler simulations. Pro...
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from __future__ import absolute_import, division, unicode_literals from pip._vendor.six import with_metaclass, viewkeys import types from . import _inputstream from . import _tokenizer from . import treebuilders from .treebuilders.base import Marker from . import _utils from .constants import ( spaceCharacters,...
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# This code is a slightly modified version of the HybridTopologyFactory code # from https://github.com/choderalab/perses # The eventual goal is to move a version of this towards openmmtools # LICENSE: MIT import logging import openmm from openmm import unit, app import numpy as np import copy import itertools # OpenMM...
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import warnings from collections import Counter, defaultdict, deque, abc from collections.abc import Sequence from concurrent.futures import ThreadPoolExecutor from functools import partial, reduce, wraps from heapq import merge, heapify, heapreplace, heappop from itertools import ( chain, compress, count,...
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#!/usr/bin/env python # -*- coding: utf-8 -*- from __future__ import print_function, division, absolute_import, unicode_literals import sys, os, glob, shutil, shlex, re, subprocess, multiprocessing, warnings, time import json from os import path from collections import OrderedDict import numpy as np from numpy.polynomi...
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#!/usr/bin/env python # ============================================================================= # MODULE DOCSTRING # ============================================================================= """ Test State classes in states.py. """ # ========================================================================...
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from copy import deepcopy import warnings import logging import numpy as np from scipy.spatial.distance import pdist, squareform from scipy.stats import norm as normal import scipy.stats from scipy import sparse import matplotlib import matplotlib.pyplot as plt from sklearn.svm import SVR from sklearn.decomposition imp...
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# This code is a slightly modified version of the HybridTopologyFactory code # from https://github.com/choderalab/perses # The eventual goal is to move a version of this towards openmmtools # LICENSE: MIT # turn off formatting since this is mostly vendored code # fmt: off import copy import itertools import logging ...
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#!/usr/bin/python # ============================================================================= # MODULE DOCSTRING # ============================================================================= """ Tests for alchemical factory in `alchemy.py`. """ # ==============================================================...
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#!/usr/bin/env python3 """ Dentate Gyrus Circuit Visualization Module Visualization tools for spatial organization, connectivity patterns, and circuit dynamics in the dentate gyrus model. """ import numpy as np import matplotlib.pyplot as plt from matplotlib.patches import Circle, Rectangle from mpl_toolkits.mplot3d ...
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#!/usr/bin/env python3 """ Optimization framework including optogenetic stimulation effects - Circuits are recreated for each trial with different seeds - Seed strategy: base_seed + trial_index ensures reproducibility - Maintains batch parallelism within each trial EvaluationStrategy pattern for automatic device-appr...
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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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#!/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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""" Nested Weights Distributional Analysis Extends nested weights analysis to compare log-normal weight distributions using: 1. Geometric mean ratios (parametric, assumes log-normal) 2. Mann-Whitney U / CLES (non-parametric, distribution-free) 3. Quantile differences (robust, reveals mechanism) All analyses maintain ...
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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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# Copyright 2022 Google LLC. # # 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,...
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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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from collections import defaultdict import copy import cv2 import gc import h5py import inspect import matplotlib.tri import numpy as np from rtree import index from scipy.interpolate import interp1d from scipy import sparse import scipy.sparse.csgraph as csgraph from scipy.spatial import KDTree import shapely import s...
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""" :mod:`alchemiscale.storage.statestore` --- state store interface ================================================================ """ import abc import bisect import datetime from contextlib import contextmanager import json import re from functools import lru_cache, update_wrapper from collections import default...
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import datetime from datetime import timedelta import random from pathlib import Path from functools import reduce from itertools import chain import operator from collections import defaultdict import uuid import pytest from gufe import AlchemicalNetwork from gufe.tokenization import TOKENIZABLE_REGISTRY from gufe.pr...
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import datetime from datetime import timedelta import random from pathlib import Path from functools import reduce from itertools import chain import operator from collections import defaultdict import uuid import pytest from gufe import AlchemicalNetwork from gufe.tokenization import TOKENIZABLE_REGISTRY from gufe.pr...
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""" :mod:`alchemiscale.storage.statestore` --- state store interface ================================================================ """ import abc import bisect import datetime from contextlib import contextmanager import json import re from functools import lru_cache, update_wrapper from collections import default...
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""" Nested Experimental Framework for Dentate Gyrus Circuit: Core nested simulation loop and aggregation functions This framework enables hierarchical variance decomposition to investigate whether paradoxical excitation is driven by specific synaptic weight patterns (connectivity-driven) or population-level dynamics (...
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import sys import math import pickle from datetime import datetime import torch import torch.nn as nn import torch.nn.functional as F from torch import Tensor from dataclasses import dataclass, field from typing import Dict, Tuple, Optional, NamedTuple, List import numpy as np import matplotlib.pyplot as plt from scipy...
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#!/usr/bin/env python3 """DG Analysis Script - Offline analysis of dentate gyrus experiments This script provides analysis and visualization capabilities for results from DG optogenetic experiments. Available Commands: plot-comparative Plot PV vs SST comparative results plot-ablations Plot a...
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#!/usr/bin/env python # ============================================================================= # MODULE DOCSTRING # ============================================================================= """ Classes that represent a portion of the state of an OpenMM context. """ # ====================================...
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#!/usr/bin/env python # ============================================================================= # MODULE DOCSTRING # ============================================================================= """ Classes that represent a portion of the state of an OpenMM context. """ # ====================================...
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""" Module to generate Systems and positions for simple reference molecular systems for testing. DESCRIPTION This module provides functions for building a number of test systems of varying complexity, useful for testing both OpenMM and various codes based on pyopenmm. Note that the PYOPENMM_SOURCE_DIR must be set to...
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""" Module to generate Systems and positions for simple reference molecular systems for testing. DESCRIPTION This module provides functions for building a number of test systems of varying complexity, useful for testing both OpenMM and various codes based on pyopenmm. Note that the PYOPENMM_SOURCE_DIR must be set to...
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#!/usr/bin/env python3 """ Statistical testing framework for disinhibition hypothesis in DG circuit Compatible with DG_circuit_dendritic_somatic_transfer.py and DG_protocol.py Supports batch GPU evaluation for efficient parallel trial execution. """ import sys import torch import numpy as np import scipy.stats as stat...
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# Copyright 2022 Google LLC. # # 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,...
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#!/usr/bin/python2 # # Copyright (c) 2009 Google Inc. All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are # met: # # * Redistributions of source code must retain the above copyright # notice, this list of...
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# This file is automatically generated by tools/idna-data """IDNA Mapping Table from UTS46.""" __version__ = '13.0.0' def _seg_0(): return [ (0x0, '3'), (0x1, '3'), (0x2, '3'), (0x3, '3'), (0x4, '3'), (0x5, '3'), (0x6, '3'), (0x7, '3'), (0x8, '3'), (0x9, '3'), (0xA, '3...
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import os, sys, pickle import requests import random import time import operator import math import ast import numpy as np import pandas as pd import multiprocessing as mp import difflib import matplotlib.pyplot as plt from decimal import Decimal from tqdm import tqdm from rdkit import Chem, DataStructs from rdkit.Chem...
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from __future__ import absolute_import from __future__ import division from __future__ import print_function import copy import itertools import os import re import sys import sysconfig import json from collections import OrderedDict, namedtuple, Counter from ctypes import * from datetime import date from warnings imp...
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# region ======================================== Imports ============================================================== import os import numpy as np import pandas as pd import scipy.stats as ss from matplotlib import pyplot as plt from multiprocessing import cpu_count, pool from scipy.stats import linregress from skl...
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{{< include README.md >}}
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--- title: How-To listing: type: table --- How-To Guides
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--- title: Explanations listing: type: table --- Pages that help you understand the inner workings of KIMMDY
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--- title: Tutorials listing: type: default categories: true --- Tutorials to help you get familiar with KIMMDY.
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# parsing.TopologyDict { #kimmdy.parsing.TopologyDict } `parsing.TopologyDict` A raw representation of a topology file returned by [](`~kimmdy.parsing.read_top`).
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# dummyreaction.reaction.DummyReaction { #dummyreaction.reaction.DummyReaction } ```python reaction.DummyReaction(name, runmng) ``` Dummy reaction, returns empty RecipeCollection
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# hat_naive.reaction.NaiveHAT { #hat_naive.reaction.NaiveHAT } ```python reaction.NaiveHAT(name, runmng) ``` Naive HAT reaction, selects all neighboring hydrogens and assigns random rates.
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# homolysis.reaction.Homolysis { #homolysis.reaction.Homolysis } ```python reaction.Homolysis(name, runmng) ``` Homolytic bond breaking leading to 2 radicals. Implementation for time-varying rates
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# topology.ff { #kimmdy.topology.ff } `topology.ff` ## Classes | Name | Description | | --- | --- | | [FF](#kimmdy.topology.ff.FF) | Container for parsed forcefield data. | ### FF { #kimmdy.topology.ff.FF } ```python topology.ff.FF(top, residuetypes_path=None, gromacs_alias='gmx') ``` Container for parsed force...
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# constants { #kimmdy.constants } `constants` Constants used throughout KIMMDY ## Attributes | Name | Description | | --- | --- | | [ATOMTYPE_BONDORDER](#kimmdy.constants.ATOMTYPE_BONDORDER) | To determin if an atom is a radical. | | [ATOMTYPE_BONDORDER_FLAT](#kimmdy.constants.ATOMTYPE_BONDORDER_FLAT) | To determin...
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--- execute: echo: true --- # CLI Arguments The prefered method of starting a KIMMDY run is via the command line, though [Python entry points](../../_reference/cmd.qmd) are supported as well. ## KIMMDY ```{python} !kimmdy --help ``` ## Analysis ```{python} !kimmdy-analysis --help ``` ## Create plumed input Th...
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--- title: "High Performance Computing" subtitle: "Run KIMMDY on HPC clusters" --- ## Setup You need an installation of python (`>= 3.10`) and (possibly PLUMED patched) GROMACS in your HPC environment. Example setup: ```bash srun -t 1400:00 --mem=16000 -n20 --pty /bin/bash ml EasyBuild eb ./assets/Python-3.10.8.eb ...
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--- title: "Examples" subtitle: "Examples for running KIMMDY with different options for various systems" --- ## Further Examples KIMMDY contains examples generated from our internal test systems. Those examples don't currently have extensive documentation, but they can be used as a starting point for your own simulat...
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--- title: Reaction only subtitle: Perform reactions on precomputed Trajectory author: Kai Riedmiller --- You might want to apply a KIMMDY reaction to an already existing simulation. Here are some important points for doing so. ## KIMMDY yaml If you want to start your sequence of tasks with a reaction, you have to g...
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--- title: "Common Issues" author: "Kai Riedmiller" --- ## Submodules Clone with added `--recurse-submodules`. Update submodules with `git submodule update --init --recursive`. See [Project Structure](../how-to/install-kimmdy.qmd#notes-on-the-project-strucure). ## Plumed Plumed is required for the homolysis plu...
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Functional outcome after acute ischemic stroke (AIS) varies widely, and existing prognostic scores may not capture complex relationships. We evaluated a diverse set of clinical characteristics and blood biomarkers with multiple machine learning models to predict 3-month functional outcome after AIS, and used explainabl...
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--- title: "Install KIMMDY with Plugins" author: "Kai Riedmiller" --- ## Complete Installation with ML Plugins ### Prerequisites - `uv`: recommended package manager to install kimmdy. [Get it here](https://docs.astral.sh/uv/getting-started/installation/) - `gromacs>=2023.2` - Version 2021.4 works with everything ...
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--- title: "Input File" execute: echo: false --- ## Autocompletion KIMMDY comes with autocompletion and tooltips inside your editor for its configuration file `kimmdy.yml`. All you need to do is activate a [yaml-language-server](https://github.com/redhat-developer/yaml-language-server) in your editor (e.g. [VS Co...
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# References {.doc .doc-index} ## Input file [Options of the main KIMMDY input file](/guide/references/input.qmd) ## Command Line Interface [Arguments of all KIMMDY parts.](../guide/references/cmd_ref.qmd) ## Python API Start KIMMDY from a python script or the command line | | | | --- | --- | | [cmd](cmd.qmd#kim...
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# config { #kimmdy.config } `config` Read and validate kimmdy.yml configuration files and package into a parsed format for internal use. ## Classes | Name | Description | | --- | --- | | [Config](#kimmdy.config.Config) | Internal representation of the configuration generated | ### Config { #kimmdy.config.Config } ...
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--- title: Analyze a KIMMDY run author: Kai Riedmiller lightbox: true --- Through [`kimmdy-analysis`](/guide/references/cmd_ref.html#analysis), several tools are provided to analyze various aspects of KIMMDY runs. ## Energy `kimmdy-analysis energy` sets the usual energy analysis by gmx energy into the context of KI...
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--- title: Visualize Topologies mermaid-format: svg --- ## Capped Alanine with a radical ```{python} from kimmdy.parsing import read_top from kimmdy.topology.topology import Topology from pathlib import Path from kimmdy.tools import write_top_as_dot import copy ``` This is the same reaction that would occur in the n...
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# schema { #kimmdy.schema } `schema` Handle the schema for the config file. To be used by the config module to validate the config file and set defaults for the Config object. Reserved keywords: - pytype - default - description - type - required ## Classes | Name | Description | | --- | --- | ...