├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin └── environmentfinder ├── environmentfinder ├── App.ipynb ├── __init__.py ├── environmentfinder.py ├── examples │ ├── Ga_II.vasp │ ├── IceIh.pdb │ └── urea2.pdb ├── logo-notext.png └── logo.png ├── postBuild ├── requirements.txt ├── setup.py └── tests ├── test_basic.py └── with-max-neighbors.py /.github/workflows/python-package.yml: -------------------------------------------------------------------------------- 1 | # This workflow will install Python dependencies, run tests and lint with a variety of Python versions 2 | # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python 3 | 4 | name: Python package 5 | 6 | on: 7 | push: 8 | branches: [ "master" ] 9 | pull_request: 10 | branches: [ "master" ] 11 | 12 | jobs: 13 | build: 14 | 15 | runs-on: ubuntu-latest 16 | strategy: 17 | fail-fast: false 18 | matrix: 19 | python-version: ["3.8", "3.9", "3.10", "3.11"] 20 | 21 | steps: 22 | - uses: actions/checkout@v3 23 | - name: Set up Python ${{ matrix.python-version }} 24 | uses: actions/setup-python@v3 25 | with: 26 | python-version: ${{ matrix.python-version }} 27 | - name: Install dependencies 28 | run: | 29 | python -m pip install --upgrade pip 30 | python -m pip install flake8 pytest 31 | if [ -f requirements.txt ]; then pip install -r requirements.txt; fi 32 | pip install . 33 | - name: Lint with flake8 34 | run: | 35 | # stop the build if there are Python syntax errors or undefined names 36 | flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics 37 | # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide 38 | flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 39 | - name: Test with pytest 40 | run: | 41 | pytest 42 | -------------------------------------------------------------------------------- /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- 1 | # This workflow will upload a Python Package using Twine when a release is created 2 | # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries 3 | 4 | # This workflow uses actions that are not certified by GitHub. 5 | # They are provided by a third-party and are governed by 6 | # separate terms of service, privacy policy, and support 7 | # documentation. 8 | 9 | name: Upload Python Package 10 | 11 | on: 12 | release: 13 | types: [published] 14 | 15 | permissions: 16 | contents: read 17 | 18 | jobs: 19 | deploy: 20 | 21 | runs-on: ubuntu-latest 22 | 23 | steps: 24 | - uses: actions/checkout@v3 25 | - name: Set up Python 26 | uses: actions/setup-python@v3 27 | with: 28 | python-version: '3.x' 29 | - name: Install dependencies 30 | run: | 31 | python -m pip install --upgrade pip 32 | pip install build 33 | - name: Build package 34 | run: python -m build 35 | - name: Publish package 36 | uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 37 | with: 38 | user: __token__ 39 | password: ${{ secrets.PYPI_API_TOKEN }} 40 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include environmentfinder/logo*.png 2 | include environmentfinder/examples/* 3 | include environmentfinder/App.ipynb 4 | include requirements.txt 5 | include README.md 6 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # EnviornmentFinder Environment finder 2 | 3 | A tool for finding and analyzing atomic environments in crystal structures. 4 | 5 | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4746325.svg)](https://doi.org/10.5281/zenodo.4746325) 6 | ![example workflow](https://github.com/PabloPiaggi/EnvironmentFinder/actions/workflows/python-package.yml/badge.svg) 7 | 8 | ## Instructions 9 | 10 | We recommend using Google Chrome. This software has not been tested on other browsers. 11 | 12 | ### Simple instructions 13 | 14 | On linux, execute the commands: 15 | 16 | ``` 17 | pip install environmentfinder 18 | environmentfinder 19 | ``` 20 | 21 | Voila! A browser tab should now be open with the environment finder app. 22 | 23 | ### Installation 24 | 25 | The simplest way to install environment finder is to use [pip](https://pip.pypa.io/en/stable/) with the command, 26 | ``` 27 | pip install environmentfinder 28 | ``` 29 | This will automatically get the source code from [PyPI](https://pypi.org/project/environmentfinder/). 30 | 31 | However, I suggest that you encapsulate the installation using a [conda](https://docs.conda.io/en/latest/) environment, for example, 32 | 33 | ``` 34 | conda create --name env_finder python=3.8 35 | conda activate env_finder 36 | pip install environmentfinder 37 | ``` 38 | 39 | ### Execution 40 | 41 | To execute the app just type, 42 | 43 | ``` 44 | environmentfinder 45 | ``` 46 | and a browser tab should now be open with the environment finder app 47 | 48 | ## Purpose 49 | 50 | The purpose of this tool is to find atomic environments in crystal structures. 51 | These environments can then be used to define measures of similarity and collective variables for enhanced sampling simulations. 52 | The output from this tool can be used directly to create reference environments for the [EnvironmentSimilarity](https://www.plumed.org/doc-master/user-doc/html/_e_n_v_i_r_o_n_m_e_n_t_s_i_m_i_l_a_r_i_t_y.html) collective variable in [PLUMED](https://www.plumed.org/doc-master/user-doc/html/index.html). 53 | The tool can also be used to visualize chemical environments around an atom for general purposes. 54 | 55 | ## Features 56 | 57 | * Choose from the examples or upload your own configuration. 58 | * Determine unique environments in crystal structures. Generally, these environments correspond to the *basis* of the crystal structure. 59 | * An algorithm to find unique environments is used. 60 | * Visualize the environments. 61 | * Output the environments in Protein Data Bank (pdb) format. 62 | 63 | ## Usage 64 | 65 | The app has four tabs: 66 | * Choose configuration 67 | * Define environments 68 | * Analyze environments 69 | * Output environments 70 | 71 | that should be used sequentially. 72 | 73 | ### Choose configuration 74 | The *Choose configuration* tab has a dropdown menu and an *Upload* button. 75 | By default the user can select a configuration from some examples that are useful to play with and get a grasp of the tool. 76 | The *Upload* button should be used to analyze a configuration stored in the user's hard drive. 77 | Once a configuration file has been uploaded the file should appear in the dropdown choices. 78 | Any file format supported by the ASE library can be used. 79 | A complete list can be found [here](https://wiki.fysik.dtu.dk/ase/ase/io/io.html). 80 | ASE determines the file format by its extension so be sure to name the file properly! 81 | 82 | ### Define environments 83 | The *Define environments* tab is where the user defines the environments. 84 | There are three different ways to define the environments, *Type*, *String*, and *Step* that can be selected with the toggle buttons. 85 | Typically the most useful one is the *Type* option. 86 | In this case one chooses the atom type of the central atom, the atom type of the neighboring atoms, and a cutoff. 87 | These parameters are set using the *Central atoms type:*, *Neighbor atoms type:*, and *Cutoff (Å):* boxes. 88 | The app will find all environments with atoms of the second type around atoms of the first type inside the specified cutoff. 89 | 90 | The tool then calculates the unique environments. 91 | For this purpose it compares all environments and keeps only the ones that are different from each other. 92 | Two environments are considered equal if the distance of every neighboring atom differs by less than some tolerance. 93 | The tolerance is specified in the *Tolerance (Å):* box. 94 | In order to compare environments, all permutations of the atoms have to be considered and that calculation can be slow. 95 | 96 | When the calculation has finished the app prints the number of environments that have been found and the average number of neighbors in the environments. 97 | 98 | #### Units 99 | * Cutoff should be given in angstrom 100 | * Tolerance should be given in angstrom 101 | 102 | ### Analyze environments 103 | The *Analyze environments* tab allows to visualize the calculated environments. 104 | One can toggle between the *Unique* environments and *All* of them. 105 | There is a slide bar to select the environment to visualize. 106 | 107 | ### Output environments 108 | The *Output environments* tab prints the environments in Protein Data Bank (PDB) format. 109 | One can toggle between the *Unique* environments and *All* of them. 110 | The environments can be downloaded in a zip file. 111 | 112 | ## Acknowledgments 113 | 114 | * The app uses several python libraries, for instance [ASE](https://wiki.fysik.dtu.dk/ase/), [NGLVIEW](https://github.com/arose/nglview), and [ipywidgets](https://ipywidgets.readthedocs.io/en/latest/index.html). 115 | * I am grateful to Giovanni Pizzi and Dou Du for suggestions on how to deploy the tool. 116 | * This tool was developed with support of the Swiss National Science Foundation (SNSF) through an Early Postdoc.Mobility fellowship. 117 | * I also acknowledge funding from the NCCR MARVEL funded by the SNSF and from the CSI Computational Science Center funded by the Department of Energy of the USA. 118 | 119 | ## How to cite 120 | 121 | If you are using this tool to find environments for enhanced sampling simulations please read and cite: 122 | * [Pablo Piaggi, *Environment finder: A tool for finding and analyzing atomic environments in crystal structures*, Zenodo (2021)](https://doi.org/10.5281/zenodo.4746324) 123 | * [Pablo Piaggi and Michele Parrinello, *Calculation of phase diagrams in the multithermal-multibaric ensemble*, J. Chem. Phys. 150, 244119 (2019)](https://aip.scitation.org/doi/full/10.1063/1.5102104) 124 | -------------------------------------------------------------------------------- /bin/environmentfinder: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | location=`pip show environmentfinder | grep "Location" | awk '{print $2}'` 4 | 5 | voila $location/environmentfinder/App.ipynb --VoilaConfiguration.file_whitelist="['.*download.zip']" 6 | -------------------------------------------------------------------------------- /environmentfinder/App.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "\n", 8 | "\n", 9 | "# Environment Finder\n", 10 | "A tool for finding and analyzing atomic environments in crystal structures" 11 | ] 12 | }, 13 | { 14 | "cell_type": "code", 15 | "execution_count": 1, 16 | "metadata": {}, 17 | "outputs": [], 18 | "source": [ 19 | "import numpy as np\n", 20 | "from ipywidgets import interactive, widgets, HTML\n", 21 | "import warnings\n", 22 | "import os\n", 23 | "import markdown\n", 24 | "\n", 25 | "warnings.simplefilter('ignore')" 26 | ] 27 | }, 28 | { 29 | "cell_type": "code", 30 | "execution_count": 2, 31 | "metadata": {}, 32 | "outputs": [ 33 | { 34 | "data": { 35 | "application/vnd.jupyter.widget-view+json": { 36 | "model_id": "c328bf3b301f40b6b95b1349b71a3d87", 37 | "version_major": 2, 38 | "version_minor": 0 39 | }, 40 | "text/plain": [ 41 | "Accordion(children=(HTML(value='

The purpose of this tool is to find atomic environments in crystal structur…" 42 | ] 43 | }, 44 | "metadata": {}, 45 | "output_type": "display_data" 46 | } 47 | ], 48 | "source": [ 49 | "html_description = markdown.markdown(\"\"\"\n", 50 | "The purpose of this tool is to find atomic environments in crystal structures. These environments can then be used to define measures of similarity and collective variables for enhanced sampling simulations. The output from this tool can be used directly to create reference environments for the [EnvironmentSimilarity](https://www.plumed.org/doc-master/user-doc/html/_e_n_v_i_r_o_n_m_e_n_t_s_i_m_i_l_a_r_i_t_y.html) collective variable in [PLUMED](https://www.plumed.org/doc-master/user-doc/html/index.html). The tool can also be used to visualize chemical environments around an atom for general purposes.\n", 51 | "\"\"\")\n", 52 | "description=HTML(html_description)\n", 53 | "\n", 54 | "pre_accordion = widgets.Accordion()\n", 55 | "pre_accordion.children = [description]\n", 56 | "pre_accordion.set_title(0, 'Description')\n", 57 | "pre_accordion.selected_index = None\n", 58 | "pre_accordion" 59 | ] 60 | }, 61 | { 62 | "cell_type": "markdown", 63 | "metadata": {}, 64 | "source": [ 65 | "Proceed through the four tabs sequentially." 66 | ] 67 | }, 68 | { 69 | "cell_type": "code", 70 | "execution_count": 3, 71 | "metadata": {}, 72 | "outputs": [ 73 | { 74 | "data": { 75 | "application/vnd.jupyter.widget-view+json": { 76 | "model_id": "8e4a41d60b8b4350a0ec467ac5e3403d", 77 | "version_major": 2, 78 | "version_minor": 0 79 | }, 80 | "text/plain": [ 81 | "_ColormakerRegistry()" 82 | ] 83 | }, 84 | "metadata": {}, 85 | "output_type": "display_data" 86 | } 87 | ], 88 | "source": [ 89 | "from environmentfinder import EnvironmentFinder\n", 90 | "# Define instance of class EnvironmentFinder\n", 91 | "MyEnvironmentFinder = EnvironmentFinder()" 92 | ] 93 | }, 94 | { 95 | "cell_type": "code", 96 | "execution_count": 4, 97 | "metadata": {}, 98 | "outputs": [], 99 | "source": [ 100 | "#############################\n", 101 | "# WIDGET 1: Choose and upload\n", 102 | "#############################\n", 103 | "\n", 104 | "# Define upload widget\n", 105 | "Widget1UploadConfiguration = widgets.FileUpload(\n", 106 | " accept='', # Accepted file extension e.g. '.txt', '.pdf', 'image/*', 'image/*,.pdf'\n", 107 | " multiple=False, # True to accept multiple files upload else False\n", 108 | " wait=True\n", 109 | ")\n", 110 | "\n", 111 | "examples = ('Ice Ih', 'examples/IceIh.pdb'),('Urea', 'examples/urea2.pdb'), ('Ga II', 'examples/Ga_II.vasp')\n", 112 | "widget_choose_filename = widgets.Dropdown(options=examples,description='Structure:')\n", 113 | "\n", 114 | "Widget1Out = widgets.Output()\n", 115 | "def chooseAndPlotConfigurationAltOutput(filename):\n", 116 | " Widget1Out.clear_output()\n", 117 | " with Widget1Out:\n", 118 | " MyEnvironmentFinder.chooseAndPlotConfiguration(filename)\n", 119 | " \n", 120 | "Widget1ExampleConfiguration = interactive(chooseAndPlotConfigurationAltOutput, filename=widget_choose_filename)\n", 121 | "\n", 122 | "# This function updates the dropdown list when a new file is uploaded\n", 123 | "def updateWidget1ExampleConfiguration(*args):\n", 124 | " uploaded_filename = Widget1UploadConfiguration.value[-1]['name']\n", 125 | " content = Widget1UploadConfiguration.value[-1]['content']\n", 126 | " upload_directory=\"upload\"\n", 127 | " if not os.path.exists(upload_directory):\n", 128 | " os.mkdir(upload_directory)\n", 129 | " with open(upload_directory + \"/\" + uploaded_filename, 'wb') as f: f.write(content)\n", 130 | " mypath=upload_directory + \"/\"\n", 131 | " found_files=[]\n", 132 | " for f in os.listdir(mypath):\n", 133 | " found_files += [(f , mypath + f)]\n", 134 | " found_files = tuple(found_files)\n", 135 | " #found_files = tuple([(f , mypath + f) for f in os.listdir(mypath)])\n", 136 | " examples = ('Ice Ih', 'examples/IceIh.pdb'),('Urea', 'examples/urea2.pdb'), ('Ga II', 'examples/Ga_II.vasp')\n", 137 | " all_files = found_files+examples\n", 138 | " widget_choose_filename.options = all_files\n", 139 | " \n", 140 | "Widget1UploadConfiguration.observe(updateWidget1ExampleConfiguration,names='value')\n", 141 | "\n", 142 | "Widget1ExamplesAndUpload = widgets.HBox([Widget1ExampleConfiguration,Widget1UploadConfiguration])\n", 143 | "Widget1Text = HTML(markdown.markdown(\"\"\"\n", 144 | "Choose a structure from the examples or upload your own in xyz, pdb, vasp, lammps-data, or [other formats](https://wiki.fysik.dtu.dk/ase/ase/io/io.html).\n", 145 | "\"\"\"))\n", 146 | "Widget1 = widgets.VBox([Widget1Text,Widget1ExamplesAndUpload,Widget1Out])" 147 | ] 148 | }, 149 | { 150 | "cell_type": "code", 151 | "execution_count": 5, 152 | "metadata": {}, 153 | "outputs": [ 154 | { 155 | "name": "stderr", 156 | "output_type": "stream", 157 | "text": [ 158 | "/home/local/PRINCETON/ppiaggi/miniconda3/lib/python3.8/site-packages/traitlets/traitlets.py:714: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison\n", 159 | " silent = bool(old_value == new_value)\n" 160 | ] 161 | } 162 | ], 163 | "source": [ 164 | "#############################\n", 165 | "# WIDGET 2: Define\n", 166 | "#############################\n", 167 | "\n", 168 | "MyEnvironmentFinder.chooseConfiguration('examples/IceIh.pdb') # Have to load the first example\n", 169 | "widget_atom_type_1 = widgets.Dropdown(options=MyEnvironmentFinder.atom_types, value=MyEnvironmentFinder.atom_types[1], description='Central atoms type:', style = {'description_width': 'initial'})\n", 170 | "widget_atom_type_2 = widgets.Dropdown(options=MyEnvironmentFinder.atom_types, value=MyEnvironmentFinder.atom_types[0], description='Neighbor atoms type:', style = {'description_width': 'initial'})\n", 171 | "\n", 172 | "def update_atom_types(*args):\n", 173 | " widget_atom_type_1.options = MyEnvironmentFinder.atom_types\n", 174 | " widget_atom_type_1.value = MyEnvironmentFinder.atom_types[0]\n", 175 | " widget_atom_type_2.options = MyEnvironmentFinder.atom_types\n", 176 | " widget_atom_type_2.value = MyEnvironmentFinder.atom_types[0]\n", 177 | "\n", 178 | "widget_choose_filename.observe(update_atom_types, names='value')\n", 179 | "\n", 180 | "def toggleTypeAndIndex(value):\n", 181 | " if (value=='Type'):\n", 182 | " # Call function with widgets\n", 183 | " widget_define_type_pre = interactive(MyEnvironmentFinder.calculateEnvironmentsType, \n", 184 | " atom_type_1 = widget_atom_type_1,\n", 185 | " atom_type_2 = widget_atom_type_2,\n", 186 | " cutoff = widgets.FloatText(value=2,description='Cutoff (Å):',disabled=False),\n", 187 | " tolerance = widgets.FloatText(value=0.02,description='Tolerance (Å):',disabled=False, style = {'description_width': 'initial'}) \n", 188 | " )\n", 189 | " widget_define_type_text = widgets.Label(value=\"Choose the atom type of the central and neighbor atoms, the cutoff, and the similarity tolerance.\")\n", 190 | " widget_define_type = widgets.VBox([widget_define_type_text,widget_define_type_pre]) \n", 191 | " display(widget_define_type)\n", 192 | " elif (value=='String'):\n", 193 | " # Call function with widgets\n", 194 | " widget_define_string_pre = interactive(MyEnvironmentFinder.calculateEnvironmentsString, \n", 195 | " listastring = widgets.Text(value=\"1,2,3\", description='List central atoms:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 196 | " listbstring = widgets.Text(value=\"1,2\", description='List neighbor atoms:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 197 | " cutoff = widgets.FloatText(value=2,description='Cutoff (Å):',disabled=False, style = {'description_width': 'initial'}),\n", 198 | " tolerance = widgets.FloatText(value=0.02,description='Tolerance (Å):',disabled=False, style = {'description_width': 'initial'}) \n", 199 | " )\n", 200 | " widget_define_string_text = widgets.Label(value=\"Choose central and neighbor atoms using lists, then choose the cutoff and the similarity tolerance.\")\n", 201 | " widget_define_string = widgets.VBox([widget_define_string_text,widget_define_string_pre])\n", 202 | " display(widget_define_string)\n", 203 | " elif (value=='Step'):\n", 204 | " # Call function with widgets\n", 205 | " widget_define_step_pre = interactive(MyEnvironmentFinder.calculateEnvironmentsMinMaxStride,\n", 206 | " mina = widgets.Text(value=\"1\", description='Central atoms min:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 207 | " maxa = widgets.Text(value=\"2\", description='Central atoms max:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 208 | " stridea = widgets.Text(value=\"1\", description='Central atoms step:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 209 | " minb = widgets.Text(value=\"1\", description='Neighbor atoms min:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 210 | " maxb = widgets.Text(value=\"2\", description='Neighbor atoms max:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 211 | " strideb = widgets.Text(value=\"1\", description='Neighbor atoms step:',placeholder='Type something',disabled=False, style = {'description_width': 'initial'}),\n", 212 | " cutoff = widgets.FloatText(value=2,description='Cutoff (Å):',disabled=False, style = {'description_width': 'initial'}),\n", 213 | " tolerance = widgets.FloatText(value=0.02,description='Tolerance (Å):',disabled=False, style = {'description_width': 'initial'}) \n", 214 | " )\n", 215 | " widget_define_step_text = widgets.Label(value=\"Choose central and neighbor atoms using minimum and maximum indeces and a step. Then choose the cutoff and the similarity tolerance.\")\n", 216 | " widget_define_step = widgets.VBox([widget_define_step_text,widget_define_step_pre])\n", 217 | " display(widget_define_step)\n", 218 | " else:\n", 219 | " print(\"Error\")\n", 220 | "\n", 221 | "Widget2Pre = interactive(toggleTypeAndIndex, value=widgets.ToggleButtons(options=['Type','String','Step'], description='Choose based on:', style = {'description_width': 'initial'}, disabled=False))\n", 222 | "\n", 223 | "Widget2Text = widgets.Label(value=\"Define the environments. The tool will then find the unique environments in the configuration using your definition.\")\n", 224 | "Widget2 = widgets.VBox([Widget2Text,Widget2Pre])" 225 | ] 226 | }, 227 | { 228 | "cell_type": "code", 229 | "execution_count": null, 230 | "metadata": {}, 231 | "outputs": [], 232 | "source": [ 233 | "#############################\n", 234 | "# WIDGET 3: Analyze\n", 235 | "#############################\n", 236 | "\n", 237 | "Widget3Out = widgets.Output()\n", 238 | "\n", 239 | "def update3(*args):\n", 240 | " toggleAllVsUnique('Unique')\n", 241 | " \n", 242 | "def toggleAllVsUnique(value):\n", 243 | " Widget3Out.clear_output()\n", 244 | " if (value=='Unique' and MyEnvironmentFinder.uniqueEnvs.shape[0]>0 and MyEnvironmentFinder.uniqueFlag):\n", 245 | " plotMyEnv = interactive(MyEnvironmentFinder.chooseEnvPlotUnique, number=widgets.IntSlider(description='Environment:',min=1,max=MyEnvironmentFinder.uniqueEnvs.shape[0],step=1,value=0)) #, anglex=widgets.IntSlider(description='Angle x:',min=-90,max=90,step=5,value=0), angley=widgets.IntSlider(description='Angle y:',min=-90,max=90,step=5,value=0), anglez=widgets.IntSlider(description='Angle z:',min=-90,max=90,step=5,value=0))\n", 246 | " with Widget3Out:\n", 247 | " display(plotMyEnv)\n", 248 | " elif (value=='All' and MyEnvironmentFinder.allEnvs.shape[0]>0):\n", 249 | " plotMyEnv = interactive(MyEnvironmentFinder.chooseEnvPlotAll, number=widgets.IntSlider(description='Environment:',min=1,max=MyEnvironmentFinder.allEnvs.shape[0],step=1,value=0, style = {'description_width': 'initial'})) #, anglex=widgets.IntSlider(description='Angle x:',min=-90,max=90,step=5,value=0), angley=widgets.IntSlider(description='Angle y:',min=-90,max=90,step=5,value=0), anglez=widgets.IntSlider(description='Angle z:',min=-90,max=90,step=5,value=0))\n", 250 | " with Widget3Out:\n", 251 | " display(plotMyEnv)\n", 252 | " elif (value!='All' and value!='Unique'):\n", 253 | " with Widget3Out:\n", 254 | " print(\"Error: keyword \" + str(value) + \" not recognized!\")\n", 255 | " elif (not(MyEnvironmentFinder.uniqueFlag)):\n", 256 | " with Widget3Out:\n", 257 | " print(\"Error: unique environments not requested!\")\n", 258 | " elif (MyEnvironmentFinder.allEnvs.shape[0]==0 or MyEnvironmentFinder.uniqueEnvs.shape[0]==0):\n", 259 | " with Widget3Out:\n", 260 | " print(\"Error: empty environments!\")\n", 261 | " else:\n", 262 | " with Widget3Out:\n", 263 | " print(\"Error\")\n", 264 | " \n", 265 | "Widget3AnalyzeEnvironmentsToggle = interactive(toggleAllVsUnique, value=widgets.ToggleButtons(options=['Unique','All'], description='Choose:', disabled=False))\n", 266 | "\n", 267 | "Widget3Text = widgets.Label(value='Visualize the calculated environments. Toggle between the unique environments or all, and slide to choose environment.')\n", 268 | "\n", 269 | "Widget3AnalyzeEnvironments = widgets.VBox([Widget3Text,Widget3AnalyzeEnvironmentsToggle,Widget3Out])" 270 | ] 271 | }, 272 | { 273 | "cell_type": "code", 274 | "execution_count": null, 275 | "metadata": {}, 276 | "outputs": [], 277 | "source": [ 278 | "#############################\n", 279 | "# WIDGET 4: Output\n", 280 | "#############################\n", 281 | "\n", 282 | "Widget4Out = widgets.Output()\n", 283 | "\n", 284 | "def update4(*args):\n", 285 | " toggleAllVsUniqueForOutput('Unique')\n", 286 | " \n", 287 | "def toggleAllVsUniqueForOutput(value):\n", 288 | " Widget4Out.clear_output()\n", 289 | " if (value=='Unique' and MyEnvironmentFinder.uniqueEnvs.shape[0]>0 and MyEnvironmentFinder.uniqueFlag):\n", 290 | " with Widget4Out:\n", 291 | " MyEnvironmentFinder.printEnvironments(MyEnvironmentFinder.uniqueEnvs)\n", 292 | " MyEnvironmentFinder.printEnvironmentsToZipFile(MyEnvironmentFinder.uniqueEnvs)\n", 293 | " elif (value=='All' and MyEnvironmentFinder.allEnvs.shape[0]>0):\n", 294 | " with Widget4Out:\n", 295 | " MyEnvironmentFinder.printEnvironments(MyEnvironmentFinder.allEnvs)\n", 296 | " MyEnvironmentFinder.printEnvironmentsToZipFile(MyEnvironmentFinder.allEnvs)\n", 297 | " elif (value!='All' and value!='Unique'):\n", 298 | " with Widget4Out:\n", 299 | " print(\"Error: keyword \" + str(value) + \" not recognized!\")\n", 300 | " elif (not(MyEnvironmentFinder.uniqueFlag)):\n", 301 | " with Widget4Out:\n", 302 | " print(\"Error: unique environments not requested!\")\n", 303 | " elif (MyEnvironmentFinder.allEnvs.shape[0]==0 or MyEnvironmentFinder.uniqueEnvs.shape[0]==0):\n", 304 | " with Widget4Out:\n", 305 | " print(\"Error: empty environments!\")\n", 306 | " else:\n", 307 | " with Widget4Out:\n", 308 | " print(\"Error\")\n", 309 | " \n", 310 | "Widget4OutputEnvironmentsToggle = interactive(toggleAllVsUniqueForOutput, value=widgets.ToggleButtons(options=['Unique','All'], description='Choose:', disabled=False))\n", 311 | "\n", 312 | "Widget4Text = widgets.Label(value='Print the environments in Protein Data Bank (PDB) format. Toggle between the unique environments or all.')\n", 313 | "\n", 314 | "Widget4TextPost = HTML(markdown.markdown(\"\"\"\n", 315 | "These environments can be used in an enhanced sampling simulation using the [EnvironmentSimilarity](https://www.plumed.org/doc-master/user-doc/html/_e_n_v_i_r_o_n_m_e_n_t_s_i_m_i_l_a_r_i_t_y.html) collective variable in [PLUMED](https://www.plumed.org/doc-master/user-doc/html/index.html).\n", 316 | "\"\"\"))\n", 317 | "\n", 318 | "#Widget4Button = widgets.Button(\n", 319 | "# description='Download',\n", 320 | "# disabled=False,\n", 321 | "# button_style='', # 'success', 'info', 'warning', 'danger' or ''\n", 322 | "# tooltip='Download',\n", 323 | "# icon='download' # (FontAwesome names without the `fa-` prefix)\n", 324 | "#)\n", 325 | "#\n", 326 | "#def zip_and_download(dummy):\n", 327 | "# MyEnvironmentFinder.printEnvironmentsToFile(MyEnvironmentFinder.uniqueEnvs)\n", 328 | "#\n", 329 | "#Widget4Button.on_click(zip_and_download)\n", 330 | "\n", 331 | "Widget4OutputEnvironments = widgets.VBox([Widget4Text,Widget4OutputEnvironmentsToggle,Widget4Out,Widget4TextPost])" 332 | ] 333 | }, 334 | { 335 | "cell_type": "code", 336 | "execution_count": null, 337 | "metadata": {}, 338 | "outputs": [], 339 | "source": [ 340 | "#############################\n", 341 | "# Combine widgets into tabs\n", 342 | "#############################\n", 343 | "\n", 344 | "children = [Widget1,Widget2,Widget3AnalyzeEnvironments,Widget4OutputEnvironments]\n", 345 | "tab = widgets.Tab() #layout=widgets.Layout(width='800px', height='800px'))\n", 346 | "tab.children = children\n", 347 | "tab.set_title(0, 'Choose configuration')\n", 348 | "tab.set_title(1, 'Define environments')\n", 349 | "tab.set_title(2, 'Analyze environments')\n", 350 | "tab.set_title(3, 'Output environments')\n", 351 | "\n", 352 | "\n", 353 | "tab.observe(update3, names='selected_index')\n", 354 | "tab.observe(update4, names='selected_index')" 355 | ] 356 | }, 357 | { 358 | "cell_type": "code", 359 | "execution_count": null, 360 | "metadata": {}, 361 | "outputs": [], 362 | "source": [ 363 | "display(tab)" 364 | ] 365 | }, 366 | { 367 | "cell_type": "code", 368 | "execution_count": null, 369 | "metadata": {}, 370 | "outputs": [], 371 | "source": [ 372 | "html_acknowledgments = markdown.markdown(\"\"\"\n", 373 | "* The app uses several python libraries, for instance [ASE](https://wiki.fysik.dtu.dk/ase/), [NGLVIEW](https://github.com/arose/nglview), and [ipywidgets](https://ipywidgets.readthedocs.io/en/latest/index.html).\n", 374 | "* I am grateful to Giovanni Pizzi and Dou Du for suggesting to deploy the tool using [Binder](https://mybinder.org/)+[appmode](https://github.com/oschuett/appmode).\n", 375 | "* This tool was mainly developed with support of the Swiss National Science Foundation (SNSF) through an Early Postdoc.Mobility fellowship.\n", 376 | "* I also acknowledge funding from the NCCR MARVEL funded by the SNSF and from the CSI Computational Science Center funded by the Department of Energy of the USA.\n", 377 | "\"\"\")\n", 378 | "acknowledgments=widgets.VBox([\n", 379 | " HTML(html_acknowledgments)\n", 380 | "])\n", 381 | "\n", 382 | "html_howtocite = markdown.markdown(\"\"\"\n", 383 | "If you are using this tool to find environments for enhanced sampling simulations please read and cite:\n", 384 | "\n", 385 | "* [Pablo Piaggi and Michele Parrinello, *Calculation of phase diagrams in the multithermal-multibaric ensemble*, J. Chem. Phys. 150, 244119 (2019)](https://aip.scitation.org/doi/full/10.1063/1.5102104)\n", 386 | "\"\"\")\n", 387 | "howtocite=widgets.VBox([\n", 388 | " HTML(html_howtocite)\n", 389 | "])\n", 390 | "\n", 391 | "post_children=[acknowledgments,howtocite]\n", 392 | "post_accordion = widgets.Accordion(layout=widgets.Layout())\n", 393 | "#print(post_accordion.layout.keys)\n", 394 | "post_accordion.children = post_children\n", 395 | "post_accordion.set_title(0, 'Acknowledgments')\n", 396 | "post_accordion.set_title(1, 'How to cite')\n", 397 | "post_accordion.selected_index = None\n", 398 | "post_accordion" 399 | ] 400 | }, 401 | { 402 | "cell_type": "markdown", 403 | "metadata": {}, 404 | "source": [ 405 | "See the project on [GitHub](https://github.com/PabloPiaggi/EnvironmentFinder)" 406 | ] 407 | }, 408 | { 409 | "cell_type": "markdown", 410 | "metadata": {}, 411 | "source": [ 412 | "Environment Finder, Copyright © 2020-2023, Pablo Piaggi" 413 | ] 414 | }, 415 | { 416 | "cell_type": "code", 417 | "execution_count": null, 418 | "metadata": {}, 419 | "outputs": [], 420 | "source": [] 421 | } 422 | ], 423 | "metadata": { 424 | "kernelspec": { 425 | "display_name": "Python 3 (ipykernel)", 426 | "language": "python", 427 | "name": "python3" 428 | }, 429 | "language_info": { 430 | "codemirror_mode": { 431 | "name": "ipython", 432 | "version": 3 433 | }, 434 | "file_extension": ".py", 435 | "mimetype": "text/x-python", 436 | "name": "python", 437 | "nbconvert_exporter": "python", 438 | "pygments_lexer": "ipython3", 439 | "version": "3.8.17" 440 | } 441 | }, 442 | "nbformat": 4, 443 | "nbformat_minor": 2 444 | } 445 | -------------------------------------------------------------------------------- /environmentfinder/__init__.py: -------------------------------------------------------------------------------- 1 | from .environmentfinder import * 2 | -------------------------------------------------------------------------------- /environmentfinder/environmentfinder.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from ipywidgets import widgets 3 | import ase 4 | import ase.io 5 | import ase.neighborlist 6 | from itertools import permutations 7 | from tqdm.notebook import tqdm, trange 8 | import nglview 9 | from IPython.display import display, FileLink 10 | from zipfile import ZipFile 11 | import os 12 | import glob 13 | 14 | import warnings 15 | warnings.simplefilter('ignore') 16 | 17 | # Class to define and operate on environments 18 | class Environments: 19 | def __init__(self): 20 | self.myindex = -1 21 | self.indeces = np.array([],dtype=int) 22 | self.delta = np.array([]) 23 | self.distance = np.array([]) 24 | # degeneracy defaults to 1 and is different from 1 for unique environments 25 | self.degeneracy = 1 26 | 27 | 28 | # Class to find environments 29 | class EnvironmentFinder: 30 | 31 | def __init__(self): 32 | # self.fractionalFlag is True if the coordinates are fractional 33 | self.fractionalFlag=False 34 | # uniqueFlags is True if unique environments are to be calculated 35 | self.uniqueFlag=True 36 | # self.verboseFlag is True if verbose mode is on 37 | self.verboseFlag=True 38 | # self.allEnvs stores all calculated environments 39 | self.allEnvs=np.ndarray((0,),dtype=object) 40 | # self.uniqueEnvs stores the unique environments 41 | self.uniqueEnvs = np.ndarray((0,),dtype=object) 42 | # self.tolerance is the tolerance to determine if two elements of the 43 | # distance vectors are the same 44 | self.tolerance=0 45 | # self.atom_types contains the unique atom types 46 | self.atom_types = np.empty(1) 47 | # Max number of neighbors in environment 48 | self.max_neighbors=1 49 | self.max_neighbors_flag=False 50 | #env=Environments() 51 | #env.delta.shape = (0,3) 52 | #uniqueEnvs = np.append(uniqueEnvs,env) 53 | # self.box_layout contains options to display a box 54 | self.box_layout = widgets.Layout(display='flex', 55 | flex_flow='column', 56 | align_items='stretch', 57 | border='solid', 58 | width='90%') 59 | 60 | def plotConf(self): 61 | """ Plot configuration using nglview """ 62 | 63 | v = nglview.show_ase(self.conf) 64 | v.add_representation("unitcell") 65 | boxy=widgets.Box([v],layout=self.box_layout) 66 | display(boxy) 67 | 68 | def chooseConfiguration(self,filename): 69 | """ Choose configuration by filename 70 | 71 | Args: 72 | filename (string): the file name 73 | 74 | Returns: 75 | no value 76 | """ 77 | 78 | self.conf = ase.io.read(filename) 79 | self.atom_types = np.unique(self.conf.get_chemical_symbols()) 80 | self.atom_types = np.append(self.atom_types,"Any") 81 | 82 | def chooseAndPlotConfiguration(self,filename): 83 | """ Choose and plot configuration by filename 84 | 85 | Args: 86 | filename (string): the file name 87 | 88 | Returns: 89 | no value 90 | """ 91 | 92 | self.chooseConfiguration(filename) 93 | self.plotConf() 94 | 95 | def setMaximumNumberOfNeighbors(self,max_neighbors): 96 | self.max_neighbors_flag = True 97 | self.max_neighbors = max_neighbors 98 | 99 | def calculateEnvironments(self,lista,listb,cutoff): 100 | """ Find environments 101 | 102 | This function calculates all environments centered at the atom in 103 | lista using atoms in listb as neighbors if they are within the cutoff. 104 | 105 | Args: 106 | lista (numpy vector): list of central atoms 107 | listb (numpy vector): list of neighboring atoms 108 | cutoff (float): cut off for the calculation of neighbors 109 | 110 | Returns: 111 | no value 112 | """ 113 | 114 | self.allEnvs = np.ndarray((0,),dtype=object) 115 | # Find all environments 116 | # Loop over input particles of type atom_type_1: 117 | myindeces=lista 118 | nl = ase.neighborlist.NeighborList((cutoff/2.0)*np.ones(self.conf.get_number_of_atoms()),skin=0.1,bothways=True) 119 | nl.update(self.conf) 120 | mat = self.conf.get_cell() 121 | for index in myindeces: 122 | neighbors, offsets = nl.get_neighbors(index) 123 | # Iterate over the neighbors of the current particle: 124 | Environment = Environments() 125 | Environment.myindex = index 126 | Environment.delta.shape = (0,3) 127 | for neigh, offset in zip(neighbors, offsets): 128 | if (neigh in listb): # Only if neighbor is in listb 129 | delta = self.conf.positions[neigh] + np.dot(offset, mat) - self.conf.positions[index] 130 | distance=np.linalg.norm(delta) 131 | if (distance>1.e-10): 132 | if (not self.fractionalFlag): 133 | Environment.delta = np.append(Environment.delta,np.array([[delta[0], delta[1], delta[2]]])*0.1,axis=0) 134 | else: 135 | Environment.delta = np.append(Environment.delta,np.array([[delta[0]/mat[0][0], delta[1]/mat[1][1], delta[2]/mat[2][2]]]),axis=0) 136 | Environment.distance = np.append(Environment.distance,distance) 137 | Environment.indeces = np.append(Environment.indeces,neigh) 138 | # Use maximum number of neighbors 139 | if (self.max_neighbors_flag==True): 140 | # Sort 141 | sortindeces=np.argsort(Environment.distance,kind='stable') 142 | Environment.delta = Environment.delta[sortindeces,:] 143 | Environment.distance = Environment.distance[sortindeces] 144 | Environment.indeces = Environment.indeces[sortindeces] 145 | # Choose first max_neighbors 146 | Environment.delta = Environment.delta[:self.max_neighbors,:] 147 | Environment.distance = Environment.distance[:self.max_neighbors] 148 | Environment.indeces = Environment.indeces[:self.max_neighbors] 149 | self.allEnvs = np.append(self.allEnvs,Environment) 150 | 151 | 152 | def CalculateUniqueEnvironments(self): 153 | """ Calculate unique Environments 154 | 155 | This algorithm calculates unique environments by comparing all possible 156 | permutations of the environments. However, it discards entire sets of 157 | permutations if it is found that there is no possibility of match. 158 | 159 | The number of operations scales roughly as as N^2*(\sum_{i=1}^M M+1-i) 160 | where N is the total number of environments and M is the number of i 161 | atoms in the environments. 162 | 163 | Args: 164 | none 165 | 166 | Returns: 167 | no value 168 | """ 169 | 170 | num_of_templates=self.allEnvs.shape[0] 171 | flag_unique=np.ones(num_of_templates) 172 | same_as=np.linspace(0,num_of_templates-1,num_of_templates) 173 | # Disregard empty environments 174 | for i in range(num_of_templates): 175 | if (self.allEnvs[i].indeces.shape[0]==0): 176 | flag_unique[i]=0 177 | for i in trange(num_of_templates,desc="Progress", leave=False): 178 | if ( self.allEnvs[i].indeces.shape[0]>0 and flag_unique[i]==1): 179 | for j in range(i+1,num_of_templates): 180 | # Not empty, unique, and same number of neighbors 181 | if ( self.allEnvs[j].indeces.shape[0]>0 and flag_unique[j]==1 and self.allEnvs[i].indeces.shape[0]==self.allEnvs[j].indeces.shape[0]): 182 | atom_match = np.zeros(self.allEnvs[j].indeces.shape[0]) 183 | for k1 in range(self.allEnvs[i].indeces.shape[0]): 184 | for k2 in range(self.allEnvs[j].indeces.shape[0]): 185 | if (np.count_nonzero(np.isclose(self.allEnvs[i].delta[k1,:],self.allEnvs[j].delta[k2,:],atol=self.tolerance))==3 ): 186 | #print(i,j,self.allEnvs[i].delta[k1,:],self.allEnvs[j].delta[k2,:],np.isclose(self.allEnvs[i].delta[k1,:],self.allEnvs[j].delta[k2,:],atol=self.tolerance)) 187 | atom_match[k1] = 1 188 | break 189 | # If no match was found for a given atom the whole self.allEnvs[j] must be discarded 190 | if (atom_match[k1]==0): 191 | break 192 | # If a match was found for every atom in self.allEnvs[i] 193 | #print(i,j,atom_match) 194 | if np.all(atom_match==np.ones(atom_match.shape[0])): 195 | flag_unique[j]=0 196 | same_as[j] = i 197 | #break 198 | self.uniqueEnvs = np.ndarray((0,),dtype=object) 199 | for i in range(num_of_templates): 200 | if (flag_unique[i]==1): 201 | self.uniqueEnvs = np.append(self.uniqueEnvs,self.allEnvs[i]) 202 | self.uniqueEnvs[-1].degeneracy = np.sum(np.ones(num_of_templates)[same_as==i]) 203 | 204 | def printEnvironmentSummaryInfo(self,Environments): 205 | if (self.verboseFlag): 206 | num_of_templates=Environments.shape[0] 207 | if (num_of_templates>0): 208 | avg_num_neighbors = 0.0 209 | for i in range(num_of_templates): 210 | avg_num_neighbors += Environments[i].indeces.shape[0] 211 | avg_num_neighbors /= num_of_templates 212 | else: 213 | avg_num_neighbors = 0 214 | print("Found " + str(num_of_templates) + " environments each with " + str(int(avg_num_neighbors)) + " neighbors on average") 215 | if (num_of_templates>0): 216 | for i in range(num_of_templates): 217 | print("Environment " + str(int(i+1)) + ": degeneracy = " + str(int(Environments[i].degeneracy)) + " - number of neighbors = ", str(int(Environments[i].indeces.shape[0])) ) 218 | 219 | def printEnvironments(self,Environments): 220 | num_of_templates=Environments.shape[0] 221 | for i in range(num_of_templates): 222 | env_atom_types = np.asarray(self.conf.get_chemical_symbols())[Environments[i].indeces.astype(int)] 223 | env_positions = Environments[i].delta*10 224 | env = ase.Atoms(env_atom_types,env_positions) 225 | ase.io.write('-', env, format='proteindatabank') 226 | 227 | 228 | def printEnvironmentsToFile(self,Environments): 229 | num_of_templates=Environments.shape[0] 230 | for i in range(num_of_templates): 231 | env_atom_types = np.asarray(self.conf.get_chemical_symbols())[Environments[i].indeces.astype(int)] 232 | env_positions = Environments[i].delta*10 233 | env = ase.Atoms(env_atom_types,env_positions) 234 | fileName="env" + str(i+1) + ".pdb" 235 | ase.io.write(fileName, env, format='proteindatabank') 236 | 237 | def printEnvironmentsToZipFile(self,Environments): 238 | num_of_templates=Environments.shape[0] 239 | download_directory="Download" 240 | if not os.path.exists(download_directory): 241 | os.mkdir(download_directory) 242 | zipObj = ZipFile(download_directory + '/download.zip', 'w') 243 | for i in range(num_of_templates): 244 | env_atom_types = np.asarray(self.conf.get_chemical_symbols())[Environments[i].indeces.astype(int)] 245 | env_positions = Environments[i].delta*10 246 | env = ase.Atoms(env_atom_types,env_positions) 247 | fileName=download_directory + "/env" + str(i+1) + ".pdb" 248 | ase.io.write(fileName, env, format='proteindatabank') 249 | zipObj.write(fileName) 250 | zipObj.close() 251 | local_file = FileLink(download_directory + '/download.zip', result_html_prefix="Click here to download the environments in PDB format: ") 252 | display(local_file) 253 | fileList = glob.glob(download_directory + '/env*') 254 | for filePath in fileList: 255 | os.remove(filePath) 256 | 257 | 258 | def plotEnv(self,myEnvironment): 259 | env_atom_types = np.asarray(self.conf.get_chemical_symbols())[myEnvironment.indeces.astype(int)] #,np.array('C')] #Template[env_number].myindex)] 260 | env_atom_types = np.append(env_atom_types,np.asarray(self.conf.get_chemical_symbols())[myEnvironment.myindex]) 261 | env_positions = np.vstack((myEnvironment.delta*10,np.array([0,0,0]) ) ) 262 | env = ase.Atoms(env_atom_types,env_positions) 263 | v = nglview.show_ase(env) 264 | boxy=widgets.Box([v],layout=self.box_layout) 265 | display(boxy) 266 | 267 | def chooseEnvPlotAll(self,number): 268 | if (self.allEnvs.shape[0]>0 and ((number-1)0): 275 | self.plotEnv(self.uniqueEnvs[number-1]) 276 | if (self.verboseFlag): 277 | print("Degeneracy of the environment is " + str(int(self.uniqueEnvs[number-1].degeneracy)) ) 278 | print("Number of neighbors in the environment is " + str(int(self.uniqueEnvs[number-1].indeces.shape[0])) ) 279 | 280 | def chooseEnvPlot(self,number): 281 | if (self.uniqueFlag and self.uniqueEnvs.shape[0]>0): 282 | self.chooseEnvPlotUnique(number) 283 | elif (not(self.uniqueFlag) and self.allEnvs.shape[0]>0): 284 | self.chooseEnvPlotAll(number) 285 | else: 286 | print("Error") 287 | 288 | def calculateEnvironmentsType(self,atom_type_1,atom_type_2,cutoff,tolerance): 289 | self.tolerance=tolerance 290 | chemical_symbols = np.asarray(self.conf.get_chemical_symbols()) 291 | lista=np.argwhere(chemical_symbols == atom_type_1).flatten() 292 | listb=np.argwhere(chemical_symbols == atom_type_2).flatten() 293 | if (atom_type_1=="Any"): 294 | lista=np.linspace(0,chemical_symbols.shape[0]-1,chemical_symbols.shape[0]).astype(int) 295 | if (atom_type_2=="Any"): 296 | listb=np.linspace(0,chemical_symbols.shape[0]-1,chemical_symbols.shape[0]).astype(int) 297 | self.calculateEnvironments(lista,listb,cutoff) 298 | if (self.uniqueFlag): 299 | self.CalculateUniqueEnvironments() 300 | self.printEnvironmentSummaryInfo(self.uniqueEnvs) 301 | else: 302 | self.printEnvironmentSummaryInfo(self.globalTemplate) 303 | 304 | def calculateEnvironmentsString(self,listastring,listbstring,cutoff,tolerance): 305 | self.tolerance=tolerance 306 | lista=np.fromstring(listastring, dtype=int, sep=',')-1 307 | listb=np.fromstring(listbstring, dtype=int, sep=',')-1 308 | self.calculateEnvironments(lista,listb,cutoff) 309 | if (self.uniqueFlag): 310 | self.CalculateUniqueEnvironments() 311 | self.printEnvironmentSummaryInfo(self.uniqueEnvs) 312 | else: 313 | self.printEnvironmentSummaryInfo(self.allEnvs) 314 | 315 | def calculateEnvironmentsMinMaxStride(self,mina,maxa,stridea,minb,maxb,strideb,cutoff,tolerance): 316 | self.tolerance=tolerance 317 | lista=np.arange(int(mina),int(maxa)+1,int(stridea))-1 318 | listb=np.arange(int(minb),int(maxb)+1,int(strideb))-1 319 | self.calculateEnvironments(lista,listb,cutoff) 320 | if (self.uniqueFlag): 321 | self.CalculateUniqueEnvironments() 322 | self.printEnvironmentSummaryInfo(self.uniqueEnvs) 323 | else: 324 | self.printEnvironmentSummaryInfo(self.allEnvs) 325 | -------------------------------------------------------------------------------- /environmentfinder/examples/Ga_II.vasp: -------------------------------------------------------------------------------- 1 | ga 2 | 1.0 3 | 5.9510002136 0.0000000000 0.0000000000 4 | 0.0000000000 5.9510002136 0.0000000000 5 | 0.0000000000 0.0000000000 5.9510002136 6 | Ga 7 | 12 8 | Cartesian 9 | 2.231625080 0.000000000 1.487750053 10 | 0.743875027 0.000000000 4.463250160 11 | 3.719375134 2.975500107 1.487750053 12 | 5.207125187 2.975500107 4.463250160 13 | 1.487750053 2.231625080 0.000000000 14 | 4.463250160 0.743875027 0.000000000 15 | 1.487750053 3.719375134 2.975500107 16 | 4.463250160 5.207125187 2.975500107 17 | 0.000000000 1.487750053 2.231625080 18 | 0.000000000 4.463250160 0.743875027 19 | 2.975500107 1.487750053 3.719375134 20 | 2.975500107 4.463250160 5.207125187 21 | -------------------------------------------------------------------------------- /environmentfinder/examples/IceIh.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 13.470 15.562 14.672 90.00 90.00 90.00 P 1 1 2 | ATOM 1 O X 1 0.000 2.593 4.126 0.00 0.00 O 3 | ATOM 2 H X 1 0.000 3.509 3.847 0.00 0.00 H 4 | ATOM 3 H X 1 0.000 2.635 5.083 0.00 0.00 H 5 | ATOM 4 O X 1 0.000 2.593 11.462 0.00 0.00 O 6 | ATOM 5 H X 1 0.000 3.509 11.183 0.00 0.00 H 7 | ATOM 6 H X 1 0.000 2.635 12.419 0.00 0.00 H 8 | ATOM 7 O X 1 0.000 10.374 4.126 0.00 0.00 O 9 | ATOM 8 H X 1 0.000 11.290 3.847 0.00 0.00 H 10 | ATOM 9 H X 1 0.000 10.415 5.083 0.00 0.00 H 11 | ATOM 10 O X 1 0.000 10.374 11.462 0.00 0.00 O 12 | ATOM 11 H X 1 0.000 11.290 11.183 0.00 0.00 H 13 | ATOM 12 H X 1 0.000 10.415 12.419 0.00 0.00 H 14 | ATOM 13 O X 1 4.492 2.593 4.126 0.00 0.00 O 15 | ATOM 14 H X 1 4.492 3.509 3.847 0.00 0.00 H 16 | ATOM 15 H X 1 4.492 2.635 5.083 0.00 0.00 H 17 | ATOM 16 O X 1 4.492 2.593 11.462 0.00 0.00 O 18 | ATOM 17 H X 1 4.492 3.509 11.183 0.00 0.00 H 19 | ATOM 18 H X 1 4.492 2.635 12.419 0.00 0.00 H 20 | ATOM 19 O X 1 4.492 10.374 4.126 0.00 0.00 O 21 | ATOM 20 H X 1 4.492 11.290 3.847 0.00 0.00 H 22 | ATOM 21 H X 1 4.492 10.415 5.083 0.00 0.00 H 23 | ATOM 22 O X 1 4.492 10.374 11.462 0.00 0.00 O 24 | ATOM 23 H X 1 4.492 11.290 11.183 0.00 0.00 H 25 | ATOM 24 H X 1 4.492 10.415 12.419 0.00 0.00 H 26 | ATOM 25 O X 1 8.984 2.593 4.126 0.00 0.00 O 27 | ATOM 26 H X 1 8.984 3.509 3.847 0.00 0.00 H 28 | ATOM 27 H X 1 8.984 2.635 5.083 0.00 0.00 H 29 | ATOM 28 O X 1 8.984 2.593 11.462 0.00 0.00 O 30 | ATOM 29 H X 1 8.984 3.509 11.183 0.00 0.00 H 31 | ATOM 30 H X 1 8.984 2.635 12.419 0.00 0.00 H 32 | ATOM 31 O X 1 8.984 10.374 4.126 0.00 0.00 O 33 | ATOM 32 H X 1 8.984 11.290 3.847 0.00 0.00 H 34 | ATOM 33 H X 1 8.984 10.415 5.083 0.00 0.00 H 35 | ATOM 34 O X 1 8.984 10.374 11.462 0.00 0.00 O 36 | ATOM 35 H X 1 8.984 11.290 11.183 0.00 0.00 H 37 | ATOM 36 H X 1 8.984 10.415 12.419 0.00 0.00 H 38 | ATOM 37 O X 1 2.246 6.484 4.126 0.00 0.00 O 39 | ATOM 38 H X 1 2.246 7.400 3.847 0.00 0.00 H 40 | ATOM 39 H X 1 2.246 6.525 5.083 0.00 0.00 H 41 | ATOM 40 O X 1 2.246 6.484 11.462 0.00 0.00 O 42 | ATOM 41 H X 1 2.246 7.400 11.183 0.00 0.00 H 43 | ATOM 42 H X 1 2.246 6.525 12.419 0.00 0.00 H 44 | ATOM 43 O X 1 2.246 14.265 4.126 0.00 0.00 O 45 | ATOM 44 H X 1 2.246 15.180 3.847 0.00 0.00 H 46 | ATOM 45 H X 1 2.246 14.306 5.083 0.00 0.00 H 47 | ATOM 46 O X 1 2.246 14.265 11.462 0.00 0.00 O 48 | ATOM 47 H X 1 2.246 15.180 11.183 0.00 0.00 H 49 | ATOM 48 H X 1 2.246 14.306 12.419 0.00 0.00 H 50 | ATOM 49 O X 1 6.738 6.484 4.126 0.00 0.00 O 51 | ATOM 50 H X 1 6.738 7.400 3.847 0.00 0.00 H 52 | ATOM 51 H X 1 6.738 6.525 5.083 0.00 0.00 H 53 | ATOM 52 O X 1 6.738 6.484 11.462 0.00 0.00 O 54 | ATOM 53 H X 1 6.738 7.400 11.183 0.00 0.00 H 55 | ATOM 54 H X 1 6.738 6.525 12.419 0.00 0.00 H 56 | ATOM 55 O X 1 6.738 14.265 4.126 0.00 0.00 O 57 | ATOM 56 H X 1 6.738 15.180 3.847 0.00 0.00 H 58 | ATOM 57 H X 1 6.738 14.306 5.083 0.00 0.00 H 59 | ATOM 58 O X 1 6.738 14.265 11.462 0.00 0.00 O 60 | ATOM 59 H X 1 6.738 15.180 11.183 0.00 0.00 H 61 | ATOM 60 H X 1 6.738 14.306 12.419 0.00 0.00 H 62 | ATOM 61 O X 1 11.231 6.484 4.126 0.00 0.00 O 63 | ATOM 62 H X 1 11.231 7.400 3.847 0.00 0.00 H 64 | ATOM 63 H X 1 11.231 6.525 5.083 0.00 0.00 H 65 | ATOM 64 O X 1 11.231 6.484 11.462 0.00 0.00 O 66 | ATOM 65 H X 1 11.231 7.400 11.183 0.00 0.00 H 67 | ATOM 66 H X 1 11.231 6.525 12.419 0.00 0.00 H 68 | ATOM 67 O X 1 11.231 14.265 4.126 0.00 0.00 O 69 | ATOM 68 H X 1 11.231 15.180 3.847 0.00 0.00 H 70 | ATOM 69 H X 1 11.231 14.306 5.083 0.00 0.00 H 71 | ATOM 70 O X 1 11.231 14.265 11.462 0.00 0.00 O 72 | ATOM 71 H X 1 11.231 15.180 11.183 0.00 0.00 H 73 | ATOM 72 H X 1 11.231 14.306 12.419 0.00 0.00 H 74 | ATOM 73 O X 1 0.000 5.187 7.794 0.00 0.00 O 75 | ATOM 74 H X 1 0.000 4.272 7.515 0.00 0.00 H 76 | ATOM 75 H X 1 0.000 5.146 8.751 0.00 0.00 H 77 | ATOM 76 O X 1 0.000 5.187 15.130 0.00 0.00 O 78 | ATOM 77 H X 1 0.000 4.272 14.851 0.00 0.00 H 79 | ATOM 78 H X 1 0.000 5.146 16.087 0.00 0.00 H 80 | ATOM 79 O X 1 0.000 12.968 7.794 0.00 0.00 O 81 | ATOM 80 H X 1 0.000 12.052 7.515 0.00 0.00 H 82 | ATOM 81 H X 1 0.000 12.927 8.751 0.00 0.00 H 83 | ATOM 82 O X 1 0.000 12.968 15.130 0.00 0.00 O 84 | ATOM 83 H X 1 0.000 12.052 14.851 0.00 0.00 H 85 | ATOM 84 H X 1 0.000 12.927 16.087 0.00 0.00 H 86 | ATOM 85 O X 1 4.492 5.187 7.794 0.00 0.00 O 87 | ATOM 86 H X 1 4.492 4.272 7.515 0.00 0.00 H 88 | ATOM 87 H X 1 4.492 5.146 8.751 0.00 0.00 H 89 | ATOM 88 O X 1 4.492 5.187 15.130 0.00 0.00 O 90 | ATOM 89 H X 1 4.492 4.272 14.851 0.00 0.00 H 91 | ATOM 90 H X 1 4.492 5.146 16.087 0.00 0.00 H 92 | ATOM 91 O X 1 4.492 12.968 7.794 0.00 0.00 O 93 | ATOM 92 H X 1 4.492 12.052 7.515 0.00 0.00 H 94 | ATOM 93 H X 1 4.492 12.927 8.751 0.00 0.00 H 95 | ATOM 94 O X 1 4.492 12.968 15.130 0.00 0.00 O 96 | ATOM 95 H X 1 4.492 12.052 14.851 0.00 0.00 H 97 | ATOM 96 H X 1 4.492 12.927 16.087 0.00 0.00 H 98 | ATOM 97 O X 1 8.984 5.187 7.794 0.00 0.00 O 99 | ATOM 98 H X 1 8.984 4.272 7.515 0.00 0.00 H 100 | ATOM 99 H X 1 8.984 5.146 8.751 0.00 0.00 H 101 | ATOM 100 O X 1 8.984 5.187 15.130 0.00 0.00 O 102 | ATOM 101 H X 1 8.984 4.272 14.851 0.00 0.00 H 103 | ATOM 102 H X 1 8.984 5.146 16.087 0.00 0.00 H 104 | ATOM 103 O X 1 8.984 12.968 7.794 0.00 0.00 O 105 | ATOM 104 H X 1 8.984 12.052 7.515 0.00 0.00 H 106 | ATOM 105 H X 1 8.984 12.927 8.751 0.00 0.00 H 107 | ATOM 106 O X 1 8.984 12.968 15.130 0.00 0.00 O 108 | ATOM 107 H X 1 8.984 12.052 14.851 0.00 0.00 H 109 | ATOM 108 H X 1 8.984 12.927 16.087 0.00 0.00 H 110 | ATOM 109 O X 1 2.246 1.297 7.794 0.00 0.00 O 111 | ATOM 110 H X 1 2.246 0.381 7.515 0.00 0.00 H 112 | ATOM 111 H X 1 2.246 1.256 8.751 0.00 0.00 H 113 | ATOM 112 O X 1 2.246 1.297 15.130 0.00 0.00 O 114 | ATOM 113 H X 1 2.246 0.381 14.851 0.00 0.00 H 115 | ATOM 114 H X 1 2.246 1.256 16.087 0.00 0.00 H 116 | ATOM 115 O X 1 2.246 9.078 7.794 0.00 0.00 O 117 | ATOM 116 H X 1 2.246 8.162 7.515 0.00 0.00 H 118 | ATOM 117 H X 1 2.246 9.037 8.751 0.00 0.00 H 119 | ATOM 118 O X 1 2.246 9.078 15.130 0.00 0.00 O 120 | ATOM 119 H X 1 2.246 8.162 14.851 0.00 0.00 H 121 | ATOM 120 H X 1 2.246 9.037 16.087 0.00 0.00 H 122 | ATOM 121 O X 1 6.738 1.297 7.794 0.00 0.00 O 123 | ATOM 122 H X 1 6.738 0.381 7.515 0.00 0.00 H 124 | ATOM 123 H X 1 6.738 1.256 8.751 0.00 0.00 H 125 | ATOM 124 O X 1 6.738 1.297 15.130 0.00 0.00 O 126 | ATOM 125 H X 1 6.738 0.381 14.851 0.00 0.00 H 127 | ATOM 126 H X 1 6.738 1.256 16.087 0.00 0.00 H 128 | ATOM 127 O X 1 6.738 9.078 7.794 0.00 0.00 O 129 | ATOM 128 H X 1 6.738 8.162 7.515 0.00 0.00 H 130 | ATOM 129 H X 1 6.738 9.037 8.751 0.00 0.00 H 131 | ATOM 130 O X 1 6.738 9.078 15.130 0.00 0.00 O 132 | ATOM 131 H X 1 6.738 8.162 14.851 0.00 0.00 H 133 | ATOM 132 H X 1 6.738 9.037 16.087 0.00 0.00 H 134 | ATOM 133 O X 1 11.231 1.297 7.794 0.00 0.00 O 135 | ATOM 134 H X 1 11.231 0.381 7.515 0.00 0.00 H 136 | ATOM 135 H X 1 11.231 1.256 8.751 0.00 0.00 H 137 | ATOM 136 O X 1 11.231 1.297 15.130 0.00 0.00 O 138 | ATOM 137 H X 1 11.231 0.381 14.851 0.00 0.00 H 139 | ATOM 138 H X 1 11.231 1.256 16.087 0.00 0.00 H 140 | ATOM 139 O X 1 11.231 9.078 7.794 0.00 0.00 O 141 | ATOM 140 H X 1 11.231 8.162 7.515 0.00 0.00 H 142 | ATOM 141 H X 1 11.231 9.037 8.751 0.00 0.00 H 143 | ATOM 142 O X 1 11.231 9.078 15.130 0.00 0.00 O 144 | ATOM 143 H X 1 11.231 8.162 14.851 0.00 0.00 H 145 | ATOM 144 H X 1 11.231 9.037 16.087 0.00 0.00 H 146 | ATOM 145 O X 1 2.246 1.297 3.209 0.00 0.00 O 147 | ATOM 146 H X 1 3.003 1.776 3.548 0.00 0.00 H 148 | ATOM 147 H X 1 1.489 1.776 3.548 0.00 0.00 H 149 | ATOM 148 O X 1 2.246 1.297 10.545 0.00 0.00 O 150 | ATOM 149 H X 1 3.003 1.776 10.883 0.00 0.00 H 151 | ATOM 150 H X 1 1.489 1.776 10.883 0.00 0.00 H 152 | ATOM 151 O X 1 2.246 9.078 3.209 0.00 0.00 O 153 | ATOM 152 H X 1 3.003 9.556 3.548 0.00 0.00 H 154 | ATOM 153 H X 1 1.489 9.556 3.548 0.00 0.00 H 155 | ATOM 154 O X 1 2.246 9.078 10.545 0.00 0.00 O 156 | ATOM 155 H X 1 3.003 9.556 10.883 0.00 0.00 H 157 | ATOM 156 H X 1 1.489 9.556 10.883 0.00 0.00 H 158 | ATOM 157 O X 1 6.738 1.297 3.209 0.00 0.00 O 159 | ATOM 158 H X 1 7.495 1.776 3.548 0.00 0.00 H 160 | ATOM 159 H X 1 5.981 1.776 3.548 0.00 0.00 H 161 | ATOM 160 O X 1 6.738 1.297 10.545 0.00 0.00 O 162 | ATOM 161 H X 1 7.495 1.776 10.883 0.00 0.00 H 163 | ATOM 162 H X 1 5.981 1.776 10.883 0.00 0.00 H 164 | ATOM 163 O X 1 6.738 9.078 3.209 0.00 0.00 O 165 | ATOM 164 H X 1 7.495 9.556 3.548 0.00 0.00 H 166 | ATOM 165 H X 1 5.981 9.556 3.548 0.00 0.00 H 167 | ATOM 166 O X 1 6.738 9.078 10.545 0.00 0.00 O 168 | ATOM 167 H X 1 7.495 9.556 10.883 0.00 0.00 H 169 | ATOM 168 H X 1 5.981 9.556 10.883 0.00 0.00 H 170 | ATOM 169 O X 1 11.231 1.297 3.209 0.00 0.00 O 171 | ATOM 170 H X 1 11.988 1.776 3.548 0.00 0.00 H 172 | ATOM 171 H X 1 10.474 1.776 3.548 0.00 0.00 H 173 | ATOM 172 O X 1 11.231 1.297 10.545 0.00 0.00 O 174 | ATOM 173 H X 1 11.988 1.776 10.883 0.00 0.00 H 175 | ATOM 174 H X 1 10.474 1.776 10.883 0.00 0.00 H 176 | ATOM 175 O X 1 11.231 9.078 3.209 0.00 0.00 O 177 | ATOM 176 H X 1 11.988 9.556 3.548 0.00 0.00 H 178 | ATOM 177 H X 1 10.474 9.556 3.548 0.00 0.00 H 179 | ATOM 178 O X 1 11.231 9.078 10.545 0.00 0.00 O 180 | ATOM 179 H X 1 11.988 9.556 10.883 0.00 0.00 H 181 | ATOM 180 H X 1 10.474 9.556 10.883 0.00 0.00 H 182 | ATOM 181 O X 1 0.000 5.187 3.209 0.00 0.00 O 183 | ATOM 182 H X 1 0.757 5.666 3.548 0.00 0.00 H 184 | ATOM 183 H X 1 -0.757 5.666 3.548 0.00 0.00 H 185 | ATOM 184 O X 1 0.000 5.187 10.545 0.00 0.00 O 186 | ATOM 185 H X 1 0.757 5.666 10.883 0.00 0.00 H 187 | ATOM 186 H X 1 -0.757 5.666 10.883 0.00 0.00 H 188 | ATOM 187 O X 1 0.000 12.968 3.209 0.00 0.00 O 189 | ATOM 188 H X 1 0.757 13.447 3.548 0.00 0.00 H 190 | ATOM 189 H X 1 -0.757 13.447 3.548 0.00 0.00 H 191 | ATOM 190 O X 1 0.000 12.968 10.545 0.00 0.00 O 192 | ATOM 191 H X 1 0.757 13.447 10.883 0.00 0.00 H 193 | ATOM 192 H X 1 -0.757 13.447 10.883 0.00 0.00 H 194 | ATOM 193 O X 1 4.492 5.187 3.209 0.00 0.00 O 195 | ATOM 194 H X 1 5.249 5.666 3.548 0.00 0.00 H 196 | ATOM 195 H X 1 3.735 5.666 3.548 0.00 0.00 H 197 | ATOM 196 O X 1 4.492 5.187 10.545 0.00 0.00 O 198 | ATOM 197 H X 1 5.249 5.666 10.883 0.00 0.00 H 199 | ATOM 198 H X 1 3.735 5.666 10.883 0.00 0.00 H 200 | ATOM 199 O X 1 4.492 12.968 3.209 0.00 0.00 O 201 | ATOM 200 H X 1 5.249 13.447 3.548 0.00 0.00 H 202 | ATOM 201 H X 1 3.735 13.447 3.548 0.00 0.00 H 203 | ATOM 202 O X 1 4.492 12.968 10.545 0.00 0.00 O 204 | ATOM 203 H X 1 5.249 13.447 10.883 0.00 0.00 H 205 | ATOM 204 H X 1 3.735 13.447 10.883 0.00 0.00 H 206 | ATOM 205 O X 1 8.984 5.187 3.209 0.00 0.00 O 207 | ATOM 206 H X 1 9.741 5.666 3.548 0.00 0.00 H 208 | ATOM 207 H X 1 8.228 5.666 3.548 0.00 0.00 H 209 | ATOM 208 O X 1 8.984 5.187 10.545 0.00 0.00 O 210 | ATOM 209 H X 1 9.741 5.666 10.883 0.00 0.00 H 211 | ATOM 210 H X 1 8.228 5.666 10.883 0.00 0.00 H 212 | ATOM 211 O X 1 8.984 12.968 3.209 0.00 0.00 O 213 | ATOM 212 H X 1 9.741 13.447 3.548 0.00 0.00 H 214 | ATOM 213 H X 1 8.228 13.447 3.548 0.00 0.00 H 215 | ATOM 214 O X 1 8.984 12.968 10.545 0.00 0.00 O 216 | ATOM 215 H X 1 9.741 13.447 10.883 0.00 0.00 H 217 | ATOM 216 H X 1 8.228 13.447 10.883 0.00 0.00 H 218 | ATOM 217 O X 1 2.246 6.484 6.877 0.00 0.00 O 219 | ATOM 218 H X 1 1.489 6.005 7.215 0.00 0.00 H 220 | ATOM 219 H X 1 3.003 6.005 7.215 0.00 0.00 H 221 | ATOM 220 O X 1 2.246 6.484 14.213 0.00 0.00 O 222 | ATOM 221 H X 1 1.489 6.005 14.551 0.00 0.00 H 223 | ATOM 222 H X 1 3.003 6.005 14.551 0.00 0.00 H 224 | ATOM 223 O X 1 2.246 14.265 6.877 0.00 0.00 O 225 | ATOM 224 H X 1 1.489 13.786 7.215 0.00 0.00 H 226 | ATOM 225 H X 1 3.003 13.786 7.215 0.00 0.00 H 227 | ATOM 226 O X 1 2.246 14.265 14.213 0.00 0.00 O 228 | ATOM 227 H X 1 1.489 13.786 14.551 0.00 0.00 H 229 | ATOM 228 H X 1 3.003 13.786 14.551 0.00 0.00 H 230 | ATOM 229 O X 1 6.738 6.484 6.877 0.00 0.00 O 231 | ATOM 230 H X 1 5.981 6.005 7.215 0.00 0.00 H 232 | ATOM 231 H X 1 7.495 6.005 7.215 0.00 0.00 H 233 | ATOM 232 O X 1 6.738 6.484 14.213 0.00 0.00 O 234 | ATOM 233 H X 1 5.981 6.005 14.551 0.00 0.00 H 235 | ATOM 234 H X 1 7.495 6.005 14.551 0.00 0.00 H 236 | ATOM 235 O X 1 6.738 14.265 6.877 0.00 0.00 O 237 | ATOM 236 H X 1 5.981 13.786 7.215 0.00 0.00 H 238 | ATOM 237 H X 1 7.495 13.786 7.215 0.00 0.00 H 239 | ATOM 238 O X 1 6.738 14.265 14.213 0.00 0.00 O 240 | ATOM 239 H X 1 5.981 13.786 14.551 0.00 0.00 H 241 | ATOM 240 H X 1 7.495 13.786 14.551 0.00 0.00 H 242 | ATOM 241 O X 1 11.231 6.484 6.877 0.00 0.00 O 243 | ATOM 242 H X 1 10.474 6.005 7.215 0.00 0.00 H 244 | ATOM 243 H X 1 11.988 6.005 7.215 0.00 0.00 H 245 | ATOM 244 O X 1 11.231 6.484 14.213 0.00 0.00 O 246 | ATOM 245 H X 1 10.474 6.005 14.551 0.00 0.00 H 247 | ATOM 246 H X 1 11.988 6.005 14.551 0.00 0.00 H 248 | ATOM 247 O X 1 11.231 14.265 6.877 0.00 0.00 O 249 | ATOM 248 H X 1 10.474 13.786 7.215 0.00 0.00 H 250 | ATOM 249 H X 1 11.988 13.786 7.215 0.00 0.00 H 251 | ATOM 250 O X 1 11.231 14.265 14.213 0.00 0.00 O 252 | ATOM 251 H X 1 10.474 13.786 14.551 0.00 0.00 H 253 | ATOM 252 H X 1 11.988 13.786 14.551 0.00 0.00 H 254 | ATOM 253 O X 1 0.000 2.593 6.877 0.00 0.00 O 255 | ATOM 254 H X 1 -0.757 2.115 7.215 0.00 0.00 H 256 | ATOM 255 H X 1 0.757 2.115 7.215 0.00 0.00 H 257 | ATOM 256 O X 1 0.000 2.593 14.213 0.00 0.00 O 258 | ATOM 257 H X 1 -0.757 2.115 14.551 0.00 0.00 H 259 | ATOM 258 H X 1 0.757 2.115 14.551 0.00 0.00 H 260 | ATOM 259 O X 1 0.000 10.374 6.877 0.00 0.00 O 261 | ATOM 260 H X 1 -0.757 9.896 7.215 0.00 0.00 H 262 | ATOM 261 H X 1 0.757 9.896 7.215 0.00 0.00 H 263 | ATOM 262 O X 1 0.000 10.374 14.213 0.00 0.00 O 264 | ATOM 263 H X 1 -0.757 9.896 14.551 0.00 0.00 H 265 | ATOM 264 H X 1 0.757 9.896 14.551 0.00 0.00 H 266 | ATOM 265 O X 1 4.492 2.593 6.877 0.00 0.00 O 267 | ATOM 266 H X 1 3.735 2.115 7.215 0.00 0.00 H 268 | ATOM 267 H X 1 5.249 2.115 7.215 0.00 0.00 H 269 | ATOM 268 O X 1 4.492 2.593 14.213 0.00 0.00 O 270 | ATOM 269 H X 1 3.735 2.115 14.551 0.00 0.00 H 271 | ATOM 270 H X 1 5.249 2.115 14.551 0.00 0.00 H 272 | ATOM 271 O X 1 4.492 10.374 6.877 0.00 0.00 O 273 | ATOM 272 H X 1 3.735 9.896 7.215 0.00 0.00 H 274 | ATOM 273 H X 1 5.249 9.896 7.215 0.00 0.00 H 275 | ATOM 274 O X 1 4.492 10.374 14.213 0.00 0.00 O 276 | ATOM 275 H X 1 3.735 9.896 14.551 0.00 0.00 H 277 | ATOM 276 H X 1 5.249 9.896 14.551 0.00 0.00 H 278 | ATOM 277 O X 1 8.984 2.593 6.877 0.00 0.00 O 279 | ATOM 278 H X 1 8.228 2.115 7.215 0.00 0.00 H 280 | ATOM 279 H X 1 9.741 2.115 7.215 0.00 0.00 H 281 | ATOM 280 O X 1 8.984 2.593 14.213 0.00 0.00 O 282 | ATOM 281 H X 1 8.228 2.115 14.551 0.00 0.00 H 283 | ATOM 282 H X 1 9.741 2.115 14.551 0.00 0.00 H 284 | ATOM 283 O X 1 8.984 10.374 6.877 0.00 0.00 O 285 | ATOM 284 H X 1 8.228 9.896 7.215 0.00 0.00 H 286 | ATOM 285 H X 1 9.741 9.896 7.215 0.00 0.00 H 287 | ATOM 286 O X 1 8.984 10.374 14.213 0.00 0.00 O 288 | ATOM 287 H X 1 8.228 9.896 14.551 0.00 0.00 H 289 | ATOM 288 H X 1 9.741 9.896 14.551 0.00 0.00 H 290 | END 291 | -------------------------------------------------------------------------------- /environmentfinder/examples/urea2.pdb: -------------------------------------------------------------------------------- 1 | HEADER CSD ENTRY UREAXX 2 | CRYST1 5.6620 5.6620 4.7160 90.00 90.00 90.00 P-421m 3 | SCALE1 0.176616 0.000000 0.000000 0.000000 4 | SCALE2 0.000000 0.176616 0.000000 0.000000 5 | SCALE3 0.000000 0.000000 0.212044 0.000000 6 | HETATM 1 C1 UNK 1 0.000 2.831 1.556 1.00 0.00 C 7 | HETATM 2 H1 UNK 1 1.376 4.207 1.325 1.00 0.00 H 8 | HETATM 3 H2 UNK 1 0.804 3.635 0.132 1.00 0.00 H 9 | HETATM 4 N1 UNK 1 0.811 3.642 0.871 1.00 0.00 N 10 | HETATM 5 O1 UNK 1 0.000 2.831 2.820 1.00 0.00 O 11 | HETATM 6 N1B UNK 1 -0.811 2.020 0.871 1.00 0.00 N 12 | HETATM 7 H1B UNK 1 -1.376 1.455 1.325 1.00 0.00 H 13 | HETATM 8 H2B UNK 1 -0.804 2.027 0.132 1.00 0.00 H 14 | HETATM 9 C1 UNK 1 2.831 0.000 3.160 1.00 0.00 C 15 | HETATM 10 H1 UNK 1 1.455 1.376 3.391 1.00 0.00 H 16 | HETATM 11 H2 UNK 1 2.027 0.804 4.584 1.00 0.00 H 17 | HETATM 12 N1 UNK 1 2.020 0.811 3.845 1.00 0.00 N 18 | HETATM 13 O1 UNK 1 2.831 0.000 1.896 1.00 0.00 O 19 | HETATM 14 N1B UNK 1 3.642 -0.811 3.845 1.00 0.00 N 20 | HETATM 15 H1B UNK 1 4.207 -1.376 3.391 1.00 0.00 H 21 | HETATM 16 H2B UNK 1 3.635 -0.804 4.584 1.00 0.00 H 22 | CONECT 1 4 5 6 23 | CONECT 2 4 24 | CONECT 3 4 25 | CONECT 4 1 2 3 26 | CONECT 5 1 27 | CONECT 6 1 7 8 28 | CONECT 7 6 29 | CONECT 8 6 30 | CONECT 9 12 13 14 31 | CONECT 10 12 32 | CONECT 11 12 33 | CONECT 12 9 10 11 34 | CONECT 13 9 35 | CONECT 14 9 15 16 36 | CONECT 15 14 37 | CONECT 16 14 38 | MASTER 0 0 0 0 0 0 0 3 16 0 16 0 39 | END 40 | -------------------------------------------------------------------------------- /environmentfinder/logo-notext.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PabloPiaggi/EnvironmentFinder/6a312958fdf03101d38b431785bc2d136b9a0fae/environmentfinder/logo-notext.png -------------------------------------------------------------------------------- /environmentfinder/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PabloPiaggi/EnvironmentFinder/6a312958fdf03101d38b431785bc2d136b9a0fae/environmentfinder/logo.png -------------------------------------------------------------------------------- /postBuild: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | jupyter nbextension enable --py widgetsnbextension 3 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy==1.24.2 2 | ase==3.22.1 3 | ipywidgets==8.1.3 4 | voila==0.5.7 5 | tqdm==4.66.4 6 | nglview==3.1.2 7 | markdown==3.6 8 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | from pathlib import Path 3 | 4 | TOP_DIR = Path(__file__).parent.resolve() 5 | 6 | with open(TOP_DIR.joinpath("requirements.txt")) as handle: 7 | REQUIREMENTS = [f"{_.strip()}" for _ in handle.readlines() if " " not in _] 8 | 9 | with open(TOP_DIR.joinpath("README.md")) as fd: 10 | long_description = fd.read() 11 | 12 | setup(name='environmentfinder', 13 | version='1.1.6', 14 | description='Tool for finding atomic environments in crystal structures', 15 | long_description=long_description, 16 | long_description_content_type='text/markdown', 17 | url='http://github.com/PabloPiaggi/EnvironmentFinder', 18 | author='Pablo Piaggi', 19 | author_email='ppiaggi@princeton.edu', 20 | license='GNU General Public License v3.0', 21 | packages=['environmentfinder'], 22 | #packages=find_packages(), 23 | install_requires=REQUIREMENTS, 24 | scripts=['bin/environmentfinder'], 25 | include_package_data=True 26 | #package_data={"environmentfinder": ["App.ipynb", "logo*.png"]} 27 | ) 28 | -------------------------------------------------------------------------------- /tests/test_basic.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import os 3 | 4 | from environmentfinder import EnvironmentFinder 5 | # Define instance of class EnvironmentFinder 6 | ef = EnvironmentFinder() 7 | ef.verboseFlag=False 8 | filename='environmentfinder/examples/IceIh.pdb' 9 | ef.chooseConfiguration(filename) 10 | ef.calculateEnvironmentsType('O','O',3.0,0.02) 11 | 12 | # Test number of unique environments 13 | def test_env_num(): 14 | assert ef.uniqueEnvs.shape[0] == 4, "Should be 4" 15 | 16 | def test_env_num_neighbors(): 17 | assert ef.uniqueEnvs[0].indeces.shape[0] == 4, "Should be 4" 18 | assert ef.uniqueEnvs[1].indeces.shape[0] == 4, "Should be 4" 19 | assert ef.uniqueEnvs[2].indeces.shape[0] == 4, "Should be 4" 20 | assert ef.uniqueEnvs[3].indeces.shape[0] == 4, "Should be 4" 21 | -------------------------------------------------------------------------------- /tests/with-max-neighbors.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import os 3 | 4 | from environmentfinder import EnvironmentFinder 5 | # Define instance of class EnvironmentFinder 6 | ef = EnvironmentFinder() 7 | filename='../Examples/IceIh.pdb' 8 | ef.chooseConfiguration(filename) 9 | ef.setMaximumNumberOfNeighbors(16) 10 | ef.calculateEnvironmentsType('O','O',5.5,0.25) 11 | ef.printEnvironmentsToFile(ef.uniqueEnvs) 12 | 13 | --------------------------------------------------------------------------------