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docs/contents/user/tools/thirds/nglview/add_arrows.ipynb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,202 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "076f5fb3-fdc5-4cad-a0f2-2dd0dc0173a6", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Add arrows" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "id": "ce3cebe7-4369-4d23-a8ba-4b1ed7758c9f", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "application/vnd.jupyter.widget-view+json": { | ||
| "model_id": "651d53ded2944d8fb32196b30d0a8dc8", | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| }, | ||
| "text/plain": [] | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "import molsysmt as msm\n", | ||
| "from molsysmt import pyunitwizard as puw\n", | ||
| "import numpy as np" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "id": "7f117f22-46e0-4928-a192-dc68f7e9d9e3", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "molecular_system = msm.convert('181L', selection='molecule_type==\"protein\"')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "id": "9ede7e3b-1de2-4414-9c5a-513866826718", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "n_CAs, coordinates_CAs = msm.get(molecular_system, selection='atom_name==\"CA\"', n_atoms=True, coordinates=True)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "id": "ec81e187-2f2a-4399-9192-1940a1dd1c37", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "arrows = puw.quantity(2.0*np.ones([n_CAs,3]), 'angstroms')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "id": "9ef8c575-e40d-451b-a2e5-93192433a005", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "view = msm.view(molecular_system)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "id": "1c3ab7aa-d99a-4ace-838b-225c2040ca0a", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "msm.thirds.nglview.add_arrows(view, arrows, origin=coordinates_CAs)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "id": "4b119c2b-4f60-440e-9964-5979a32a380a", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "msm.thirds.nglview.add_arrows(view, puw.quantity([[10,0,0],[0,10,0],[0,0,10]], 'angstroms'),\n", | ||
| " origin=puw.quantity([[0,0,0],[0,0,0],[0,0,0]], 'angstroms'),\n", | ||
| " color=['#FF0000', '#00FF00', '#0000FF'], radius='0.2 angstroms')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "id": "929d66d7-d205-434b-b5e8-47fb27705f61", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "application/vnd.jupyter.widget-view+json": { | ||
| "model_id": "5ef73157669947c0b4f4f9c1f63dca2a", | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| }, | ||
| "text/plain": [ | ||
| "NGLWidget()" | ||
| ] | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "view\n", | ||
| "\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 54, | ||
| "id": "105bad4e-7ee2-43de-9a80-68544a9ff2e8", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "view = msm.view(molecular_system)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 55, | ||
| "id": "a7f9cb89-6fa5-4f76-a570-a6d0faf46e38", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "arrows = puw.quantity([[9,0,0],[0,6,0],[0,0,-12], [0,5,5]], 'angstroms')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 56, | ||
| "id": "44bb51fc-d81d-47bb-9a6d-9db96a95cd04", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "msm.thirds.nglview.add_arrows(view, arrows, selection='atom_name==\"CA\" and group_index in [10,30,60,90]', color='#0B6E4F', \n", | ||
| " radius='0.5 angstroms')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 57, | ||
| "id": "5fab1a62-1800-4e6d-b968-2e0777171375", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "application/vnd.jupyter.widget-view+json": { | ||
| "model_id": "cb126cd2594746e79e6e993663cfd850", | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| }, | ||
| "text/plain": [ | ||
| "NGLWidget()" | ||
| ] | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "view" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.11.9" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -4,6 +4,7 @@ | |
| .. toctree:: | ||
| :maxdepth: 2 | ||
| add_arrows.ipynb | ||
| add_hbonds.ipynb | ||
| color_by_value.ipynb | ||
| ``` | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| from ...exceptions import ArgumentError | ||
| import numpy as np | ||
| from molsysmt import pyunitwizard as puw | ||
|
|
||
| methods_where_bool = [ | ||
| ] | ||
|
|
||
| def digest_origin(origin, caller=None): | ||
|
|
||
| if caller in methods_where_bool: | ||
| if isinstance(origin, bool): | ||
| return origin | ||
|
|
||
| if caller.endswith('add_arrows'): | ||
| if origin is None: | ||
| return None | ||
|
|
||
| value = puw.get_value(origin) | ||
| unit = puw.get_unit(origin) | ||
|
|
||
| if not puw.check(unit, dimensionality={'[L]':1}): | ||
| raise ArgumentError('origin', value=origin, caller=caller, message=None) | ||
|
|
||
| if not isinstance(value, np.ndarray): | ||
| value = np.array(value) | ||
|
|
||
| shape = value.shape | ||
|
|
||
| if len(shape) == 1: | ||
| if shape[0] == 3: | ||
| return puw.quantity(value[np.newaxis, np.newaxis, :], unit, standardized=True) | ||
| elif len(shape) == 2: | ||
| if shape[1] == 3: | ||
| return puw.quantity(value[np.newaxis, :, :], unit, standardized=True) | ||
| elif len(shape) == 3: | ||
| if shape[2] == 3: | ||
| return puw.quantity(value, unit, standardized=True) | ||
|
|
||
| raise ArgumentError('origin', value=origin, caller=caller, message=None) | ||
|
|
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