Merge pull request #102 from dprada/main

Make biossemblies and merge fixed. Function names changed.
uibcdf · Apr 6, 2023 · da8dabd · da8dabd
2 parents 1bffaf6 + a4d0bbd
commit da8dabd
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diff --git a/.github/workflows/sphinx_docs_to_gh_pages.yaml b/.github/workflows/sphinx_docs_to_gh_pages.yaml
@@ -27,45 +27,27 @@ jobs:
       - name: Setup GNU Fortran
         uses: modflowpy/install-gfortran-action@v1 # https://github.com/modflowpy/install-gfortran-action
 
-      - name: Make conda environment
-        uses: conda-incubator/setup-miniconda@v2    # https://github.com/conda-incubator/setup-miniconda
+      - name: Setup conda env
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          python-version: 3.9
           environment-file: devtools/conda-envs/docs_env.yaml
-          #mamba-version: "*"
-          #use-mamba: true
-          auto-update-conda: false
-          auto-activate-base: false
-          show-channel-urls: true
-          activate-environment: test
+          environment-name: docs
+          channels: uibcdf, conda-forge, ambermd, defaults
 
-          #- name: Setup conda env
-          #  uses: mamba-org/provision-with-micromamba@main
-          #  with:
-          #    environment-file: devtools/conda-envs/docs_env.yaml
-          #    environment-name: docs
-          #    channels: uibcdf, conda-forge, ambermd, defaults
-
-          #    extra-specs: |
-          #      python=="3.9"
+          extra-specs: |
+            python=="3.9"
 
       - name: Install package
 
         shell: bash -l {0}
         run: |
           python setup.py develop
 
-          #- name: Info conda
-          #  shell: bash -l {0}
-          #  run: |
-          #    micromamba info
-          #    micromamba list
-
-      - name: Info conda
-        shell: bash -l {0}
-        run: |
-          conda info
-          conda list
+        - name: Info conda
+          shell: bash -l {0}
+          run: |
+            micromamba info
+            micromamba list
 
       - name: Test import module
         shell: bash -l {0}

diff --git a/...s/about/showcase/Polyglot_selection.ipynb → docs/contents/about/showcase/Selection.ipynb b/...s/about/showcase/Polyglot_selection.ipynb → docs/contents/about/showcase/Selection.ipynb
@@ -5,7 +5,7 @@
    "id": "4486ce37-5967-47a7-84eb-3493a59fb55b",
    "metadata": {},
    "source": [
-    "# Polyglot Selection"
+    "# Atoms Selection"
    ]
   },
   {
@@ -41,7 +41,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,

diff --git a/docs/contents/about/showcase/Thirds.ipynb b/docs/contents/about/showcase/Thirds.ipynb
@@ -0,0 +1,254 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import molsysmt as msm\n",
+    "import nglview as nv\n",
+    "import warnings\n",
+    "warnings.filterwarnings('ignore')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Working with thirds"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Working with NGLView"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.convert([nv.datafiles.GRO, nv.datafiles.XTC], to_form='molsysmt.MolSys')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view = nv.show_molsysmt(molsys, standardize=True, viewer='NGLView')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.info(view)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.get(view, element='group', indices=[81, 82, 83], name=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.get(view, element='system', n_structures=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.get(view, element='atom', selection='atom_name==\"CA\"', coordinates=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.get(view, element='system', box=True) # Warning: only 1 frame"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.is_composed_of(view, proteins=1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.select(view, selection='atom_name==\"CA\" and group_name==\"LYS\"')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.select(view, selection='atom_name==\"CA\" and group_name==\"LYS\"', to_syntax='nglview')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.select(view, element='group', selection='group_name==\"LYS\"', to_syntax='nglview')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "contact_map = msm.structure.get_contacts(view, selection='molecule_type==\"protein\" and atom_name==\"CA\"', threshold='12 angstroms')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from matplotlib import pyplot as plt\n",
+    "plt.imshow(contact_map[10], cmap='Greys', origin='lower')\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.convert(view, to_form='string:aminoacids1')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys_A = msm.build.build_peptide(['AceAlaNME',{'forcefield':'AMBER14', 'implicit_solvent':'OBC1'}])\n",
+    "molsys_B = msm.structure.translate(molsys_A, translation='[0.5, 0.0, 0.0] nm')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view1 = msm.convert(molsys_A, to_form='nglview.NGLWidget')\n",
+    "view2 = msm.view(molsys_B)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view = msm.merge([view1, view2])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.info(view)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view = msm.concatenate_frames([view1, view2])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.info(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": "3.9.15"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/docs/contents/about/showcase/index.md b/docs/contents/about/showcase/index.md
@@ -6,7 +6,6 @@
 
    Quickstart_guide.ipynb
    Barnase_Barstar.ipynb
-   Polyglot_selection.ipynb
-   OpenMM.ipynb
-   NGLView.ipynb
+   Selection.ipynb
+   Thirds.ipynb
 ```
diff --git a/docs/contents/user/demo/index.md b/docs/contents/user/demo/index.md
@@ -0,0 +1,7 @@
+# Demo Systems
+
+```{eval-rst}
+.. toctree::
+   :maxdepth: 2
+
+```