keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | mpes-kit/fuller | figures/extra/E03_Band_path.ipynb | .ipynb | 4,605 | 155 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Slice the band mapping or band structure data along certain high-symmetry lines\n",
"The following demo relates to the software package [mpes](https://github.com/mpes-kit/mpes/), which contains the functionality for making band ... | Unknown |
3D | mpes-kit/fuller | figures/extra/E02_Brillouin_zoning.ipynb | .ipynb | 4,761 | 223 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Cutting band structure or band mapping data to the first Brillouin zone"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import warnings as wn\n",
"wn.fi... | Unknown |
3D | mpes-kit/fuller | figures/extra/E01_Hexagonal_tiling.ipynb | .ipynb | 2,209 | 106 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Construct large patches of the Brillouin zones (from DFT calculations) using symmetry operations"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import warn... | Unknown |
3D | mpes-kit/fuller | figures/recon/R02_Example_reconstruction_synthetic_multiband_3D_data.ipynb | .ipynb | 5,729 | 199 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Reconstruction of synthetic 3D multiband photoemission data"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import warnings as wn\n",
"wn.filterwarnings... | Unknown |
3D | mpes-kit/fuller | figures/recon/R01_Example_reconstruction_wse2_3D_data.ipynb | .ipynb | 5,592 | 172 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Reconstruction of photoemission band structure using Markov Random Field model\n",
"### Model setup"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"impo... | Unknown |
3D | mpes-kit/fuller | examples/synthetic_mpes_data_generation_I (from calculation).ipynb | .ipynb | 4,958 | 242 | {
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import fuller\n",
"from fuller import generator\n",
"import scipy.io as sio\n",
"from mpes import analysis as aly\n",
"from symmetrize import pointop... | Unknown |
3D | mpes-kit/fuller | examples/05_synthetic_data_and_initial_conditions.ipynb | .ipynb | 11,861 | 398 | {
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import fuller\n",
"from mpes import analysis as aly\n",
"import matplotlib.pyplot as plt\n",
"from tqdm import tqdm_notebook as tqdm\n",
"import tiff... | Unknown |
3D | mpes-kit/fuller | examples/01_Hexagonal_tiling.ipynb | .ipynb | 2,556 | 122 | {
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from mpes import visualization as vis\n",
"import fuller\n",
"import matplotlib.pyplot as plt\n",
"import os"
]
},
{
"cell_type": "code",
"e... | Unknown |
3D | mpes-kit/fuller | examples/02_Brillouin_zoning.ipynb | .ipynb | 6,441 | 300 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Cutting band structure or band mapping data to the first Brillouin zone"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import fu... | Unknown |
3D | mpes-kit/fuller | examples/04_mpes_reconstruction_mrf.ipynb | .ipynb | 4,360 | 186 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Reconstruction of band using Markov Random Field Model"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Model setup"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata":... | Unknown |
3D | mpes-kit/fuller | examples/interpolation_cutter.ipynb | .ipynb | 4,555 | 203 | {
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import fuller\n",
"import scipy.io as sio\n",
"from mpes import fprocessing as fp, analysis as aly\n",
"import matplotlib.pyplot as plt"
]
},
{
... | Unknown |
3D | mpes-kit/fuller | examples/03_preprocessing.ipynb | .ipynb | 5,321 | 242 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"source": [
"# Illustration of the preprocessing steps"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Import packages\n",
"import numpy as ... | Unknown |
3D | mpes-kit/fuller | docs/conf.py | .py | 8,956 | 276 | # 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... | Python |
3D | Autodesk/molecular-design-toolkit | setup.py | .py | 3,184 | 94 | # Copyright 2017 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | versioneer.py | .py | 68,587 | 1,818 |
# Version: 0.17
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, and pypy
* [![Latest Version]
(http... | Python |
3D | Autodesk/molecular-design-toolkit | nb-output-filter.sh | .sh | 137 | 6 | #!/bin/bash
git config filter.notebooks.clean moldesign/_notebooks/nbscripts/strip_nb_output.py
git config filter.notebooks.smudge cat
| Shell |
3D | Autodesk/molecular-design-toolkit | DEVELOPMENT.md | .md | 6,110 | 113 | # DEVELOPING MDT
### Setting up a dev environment
(still under construction)
### Install prequisites (first time only)
You need to install docker, and an environment manager for Python 3 (Miniconda 3). Here's one way to do that:
1. Install docker: [link]
2. Install pyenv and pyenv-venv: [link]
3. Install miniconda3 b... | Markdown |
3D | Autodesk/molecular-design-toolkit | CONTRIBUTING.md | .md | 6,484 | 119 | # Contributing to Molecular Design Toolkit
<!-- START doctoc generated TOC please keep comment here to allow auto update -->
<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
**Table of Contents** *generated with [DocToc](https://github.com/thlorenz/doctoc)*
- [Contributing to Molecular Design Toolk... | Markdown |
3D | Autodesk/molecular-design-toolkit | DockerMakefiles/buildfiles/notebook/run_notebook.sh | .sh | 84 | 4 | #!/bin/bash
jupyter notebook --ip=0.0.0.0 --no-browser --port=8888 --allow-root $@
| Shell |
3D | Autodesk/molecular-design-toolkit | DockerMakefiles/buildfiles/ambertools/runsander.py | .py | 7,026 | 255 | #!/usr/bin/env python
"""
This script drives an NWChem calculation given a generic QM specification
"""
import json
import os
import pint
ureg = pint.UnitRegistry()
ureg.define('bohr = a0 = hbar/(m_e * c * fine_structure_constant')
"""
&cntrl
ntb=1, ! use PBC
imin=1, ! run minimization
ntmin=5 ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/parameters.py | .py | 9,802 | 238 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/HISTORY.md | .md | 6,854 | 116 | ## Changelog
### 0.8.0 - September 9, 2017
MDT 0.8 represents a substantial refinement of the core MDT code, offering Python 2/3 support
and increased stability and robustness.
##### NEW MODELING FEATURES
- Initial **NWChem** integration and pre-compiled docker image ([\#120](https://github.com/autodesk/molecular-... | Markdown |
3D | Autodesk/molecular-design-toolkit | moldesign/fileio.py | .py | 16,197 | 501 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/__init__.py | .py | 2,506 | 89 | # Copyright 2017 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/widgets.py | .py | 2,933 | 90 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/exceptions.py | .py | 1,736 | 57 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_version.py | .py | 18,450 | 521 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/__main__.py | .py | 10,065 | 303 | """
This file collects the various command line tasks accessed via
``python -m moldesign [command]``
The functions here are intended help users set up their environment.
Note that MDT routines will NOT be importable from this module when it runs as a script -- you
won't be working with molecules or atoms in this modu... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/method.py | .py | 4,182 | 135 | """
This module contains abstract base classes for potential models, integrators, and various
associated data types (force fields, orbitals, basis sets, etc.).
"""
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/helpers/qmmm.py | .py | 3,277 | 93 | # Copyright 2016 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/helpers/__init__.py | .py | 82 | 5 | from .helpers import *
from .pdb import *
from .qmmm import *
from .logs import *
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/helpers/helpers.py | .py | 4,375 | 133 | """
This module contains various helper functions used by MDT internally.
"""
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Versi... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/helpers/pdb.py | .py | 10,837 | 323 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/helpers/logs.py | .py | 3,405 | 93 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with t... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/descriptors.py | .py | 2,890 | 95 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/classes.py | .py | 6,291 | 226 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/__init__.py | .py | 844 | 25 | # Copyright 2017 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/databases.py | .py | 2,281 | 82 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/numerical.py | .py | 3,902 | 107 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/exportutils.py | .py | 1,476 | 50 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/utils.py | .py | 9,726 | 329 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
import future.utils
from functools import reduce
import fractions
import operator
import os
import re
import sys
import tempfile
from html.parser import... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/json_extension.py | .py | 1,405 | 42 | # Copyright 2016 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/apply_copyright.sh | .sh | 729 | 22 | #!/bin/bash
for file in `grep -L "Copyright 2016 Autodesk Inc." *.py`; do
mv $file{.bak}
cat > $file <<EOF
# Copyright 2016 Autodesk 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... | Shell |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/callsigs.py | .py | 9,122 | 259 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/docparsers/__init__.py | .py | 46 | 2 | from .google import GoogleDocArgumentInjector
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/utils/docparsers/google.py | .py | 22,562 | 649 | """
Routines for runtime docstring argument injection
This file contains HEAVILY modified routines from sphinx.ext.napoleon, from version 1.4.4
This has been vendored into MDT because the modification makes use of
private functions which have already changed in the dev branch.
~~~~~~~~~~~~~~~~~~~... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/ambertools.py | .py | 6,291 | 161 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/opsin_interface.py | .py | 1,509 | 44 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/symmol_interface.py | .py | 10,144 | 260 | from __future__ import print_function, absolute_import, division
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk 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 obtai... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/pdbfixer_interface.py | .py | 11,774 | 312 | from __future__ import print_function, absolute_import, division
import string
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/biopython_interface.py | .py | 5,289 | 151 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/tleap_interface.py | .py | 12,300 | 321 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/__init__.py | .py | 571 | 20 | from . import ambertools
from . import biopython_interface
from . import nbo_interface
from . import openbabel
from . import openmm
from . import opsin_interface
from . import parmed_interface
from . import pdbfixer_interface
from . import pyscf_interface
from . import symmol_interface
from . import tleap_interface
# ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/nbo_interface.py | .py | 9,611 | 265 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/openbabel.py | .py | 10,502 | 321 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/pyscf_interface.py | .py | 4,498 | 127 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/parmed_interface.py | .py | 9,298 | 302 | from __future__ import print_function, absolute_import, division
import io
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in comp... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/interfaces/openmm.py | .py | 12,178 | 349 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/units/tools.py | .py | 7,651 | 245 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/units/quantity.py | .py | 11,689 | 361 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/units/__init__.py | .py | 95 | 4 | from .quantity import *
from .constants import *
from .tools import *
from .unitsystem import * | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/units/constants.py | .py | 1,972 | 69 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/units/unitsystem.py | .py | 6,681 | 190 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/tools/__init__.py | .py | 120 | 8 | def toplevel(o):
__all__.append(o.__name__)
return o
__all__ = []
from .topology import *
from .build import *
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/tools/topology.py | .py | 7,884 | 223 | """
This module contains various utility functions that are exposed to API users
"""
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/tools/build.py | .py | 3,448 | 86 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb | .ipynb | 6,849 | 264 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Example 4. HIV Protease bound to an inhibitor.ipynb | .ipynb | 10,729 | 350 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Getting Started.ipynb | .ipynb | 2,498 | 80 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"<br>\n",
"\n",
"# Get started \n",
"\n",
"Get started with these step-by-step demonstration notebooks. Check out the accompanying [video tutorials](https://... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Tutorial 3. Quantum Chemistry.ipynb | .ipynb | 10,473 | 415 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb | .ipynb | 9,215 | 330 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Tutorial 1. Making a molecule.ipynb | .ipynb | 7,813 | 289 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Example 5. Enthalpic barriers.ipynb | .ipynb | 9,049 | 308 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Example 3. Simulating a crystal structure.ipynb | .ipynb | 10,039 | 382 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/Example 2. UV-vis absorption spectra.ipynb | .ipynb | 7,656 | 243 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a> <a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" targe... | Unknown |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/nbscripts/strip_nb_output.py | .py | 1,747 | 55 | #!/usr/bin/env python
"""strip outputs from an IPython Notebook
Opens a notebook, strips its output, and writes the outputless version to the original file.
Useful mainly as a git pre-commit hook for users who don't want to track output in VCS.
This does mostly the same thing as the `Clear All Output` command in the... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/nbscripts/gen_example_md.py | .py | 237 | 13 | #!/usr/bin/env python
from __future__ import print_function
import glob
for f in glob.glob('Example*.ipynb'):
print('* [%s](%s)' % (f[:-6], f))
print()
for f in glob.glob('Tutorial*.ipynb'):
print('* [%s](%s)' % (f[:-6], f))
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_notebooks/nbscripts/gen_toc.py | .py | 817 | 42 | #!/usr/bin/env python
from __future__ import print_function
import sys, os
from nbformat import v4
def parse_line(line):
if not line.startswith('#'):
return None
ilevel = 0
for char in line:
if char == '#': ilevel += 1
else: break
name = line[ilevel:].strip()
return ileve... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/external/__init__.py | .py | 29 | 1 | from . import transformations | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/external/pathlib.py | .py | 1,191 | 40 | # Copyright 2017 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/external/transformations.py | .py | 66,070 | 1,922 | # -*- coding: utf-8 -*-
# transformations.py
# Copyright (c) 2006-2015, Christoph Gohlke
# Copyright (c) 2006-2015, The Regents of the University of California
# Produced at the Laboratory for Fluorescence Dynamics
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modifica... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/external/pyquante2/__init__.py | .py | 0 | 0 | null | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/external/pyquante2/utils.py | .py | 6,283 | 243 | """
utils.py - Simple utilility funtions used in pyquante2.
"""
import numpy as np
from math import factorial,lgamma
from itertools import combinations_with_replacement,combinations
from functools import reduce
def pairs(it): return combinations_with_replacement(it,2)
def upairs(it): return combinations(it,2)
def fac... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/external/pyquante2/one.py | .py | 7,343 | 254 | """
One electron integrals.
"""
from numpy import pi,exp,floor,array,isclose
from math import factorial
## BEGIN MODIFIED CODE:
#from pyquante2.utils import binomial, fact2, Fgamma, norm2
from .utils import binomial, fact2, Fgamma, norm2
#END MODIFIED CODE
# Notes:
# The versions S,T,V include the normalization con... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/mathutils/__init__.py | .py | 67 | 3 | from .vectormath import *
from .eigen import *
from .grids import * | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/mathutils/spherical_harmonics.py | .py | 6,809 | 199 | from __future__ import print_function, absolute_import, division
from future import standard_library
standard_library.install_aliases()
from future.builtins import *
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/mathutils/vectormath.py | .py | 5,770 | 191 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/mathutils/grids.py | .py | 5,650 | 164 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/mathutils/eigen.py | .py | 3,708 | 101 | from __future__ import print_function, absolute_import, division
from future import standard_library
standard_library.install_aliases()
from future.builtins import *
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/min/scipy.py | .py | 5,685 | 159 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/min/descent.py | .py | 5,961 | 153 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/min/__init__.py | .py | 159 | 10 | def toplevel(o):
__all__.append(o.__name__)
return o
__all__ = []
from . import base
from .scipy import *
from .descent import *
from .smart import *
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/min/smart.py | .py | 4,412 | 129 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/min/base.py | .py | 8,600 | 227 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/amber.py | .py | 2,282 | 63 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/models.py | .py | 2,349 | 80 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/nwchem.py | .py | 6,978 | 175 | # Copyright 2016 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/jsonmodel.py | .py | 6,004 | 167 | # Copyright 2016 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/qmmm.py | .py | 8,032 | 208 | # Copyright 2016 Autodesk 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 in writing... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/__init__.py | .py | 172 | 8 | from .openmm import *
from .pyscf import *
from .models import *
from .toys import *
from .amber import *
from .openbabel import *
from .nwchem import *
from .qmmm import * | Python |
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