From cdb3d53690ee10bccd4e861c0ffac9a43f169a7d Mon Sep 17 00:00:00 2001 From: Diego Prada Date: Wed, 22 May 2024 16:32:42 -0600 Subject: [PATCH] Module user/tools/basic in the documentation was fixed --- docs/contents/user/tools/basic/iterator.ipynb | 2 +- docs/contents/user/tools/basic/merge.ipynb | 48 +- docs/contents/user/tools/basic/remove.ipynb | 279 ++++++- docs/contents/user/tools/basic/select.ipynb | 34 +- docs/contents/user/tools/basic/set.ipynb | 684 +++++++++--------- docs/contents/user/tools/basic/view.ipynb | 229 +++++- .../user/tools/basic/where_is_attribute.ipynb | 72 +- molsysmt/basic/convert.py | 6 +- molsysmt/basic/get.py | 20 +- molsysmt/basic/get_attributes.py | 2 +- molsysmt/build/get_missing_bonds.py | 7 +- molsysmt/data/h5msm/alanine_dipeptide.h5msm | Bin 84984 -> 84984 bytes molsysmt/data/h5msm/lysine_dipeptide.h5msm | Bin 84984 -> 84984 bytes molsysmt/data/h5msm/proline_dipeptide.h5msm | Bin 84984 -> 84984 bytes molsysmt/data/h5msm/valine_dipeptide.h5msm | Bin 84984 -> 84984 bytes .../element/component/get_component_type.py | 5 +- molsysmt/element/entity/get_entity_index.py | 9 +- molsysmt/form/file_inpcrd/__init__.py | 4 +- .../form/openmm_Topology/has_attribute.py | 2 +- .../test_view_molsysmt_MolSys_with_NGLView.py | 3 +- sandbox/Tests.ipynb | 155 +--- 21 files changed, 918 insertions(+), 643 deletions(-) diff --git a/docs/contents/user/tools/basic/iterator.ipynb b/docs/contents/user/tools/basic/iterator.ipynb index 8351969f9..0ede55763 100644 --- a/docs/contents/user/tools/basic/iterator.ipynb +++ b/docs/contents/user/tools/basic/iterator.ipynb @@ -68,7 +68,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "f710a3d37d3644e5ad2f18ee7ab42dc6", + "model_id": "9e23f16870f449d887ab208316501631", "version_major": 2, "version_minor": 0 }, diff --git a/docs/contents/user/tools/basic/merge.ipynb b/docs/contents/user/tools/basic/merge.ipynb index a189f2552..c4e80cf74 100644 --- a/docs/contents/user/tools/basic/merge.ipynb +++ b/docs/contents/user/tools/basic/merge.ipynb @@ -45,7 +45,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "3901d160dd23485992e32bc34cd47e36", + "model_id": "cec0845488d4439c93f49653ba211077", "version_major": 2, "version_minor": 0 }, @@ -122,37 +122,37 @@ "text/html": [ "\n", - "\n", + "
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formn_atomsn_groupsn_componentsn_chainsn_moleculesn_entitiesn_peptidesn_structuresformn_atomsn_groupsn_componentsn_chainsn_moleculesn_entitiesn_peptidesn_structures
molsysmt.MolSys889333131molsysmt.MolSys889333131
\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, @@ -192,7 +192,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "af3cee061f264a69afdf00f3c47e7ec2", + "model_id": "e3f829f9407441469c336be8b090b1a4", "version_major": 2, "version_minor": 0 }, @@ -210,7 +210,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 9, "metadata": { "editable": true, "slideshow": { @@ -260,7 +260,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.11" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/contents/user/tools/basic/remove.ipynb b/docs/contents/user/tools/basic/remove.ipynb index 27d26a142..0a4634a19 100644 --- a/docs/contents/user/tools/basic/remove.ipynb +++ b/docs/contents/user/tools/basic/remove.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "editable": true, "slideshow": { @@ -50,16 +50,29 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "83d0d1cddacd4aaf989ae1a28c8d6e4e", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "import molsysmt as msm" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -68,16 +81,121 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
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\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "msm.info(molecular_system, element='chain')" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -95,9 +213,54 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
indexidnamen atomsn groupsn componentsmolecule indexmolecule typeentity indexentity name
00A128916210protein0T4 LYSOZYME
\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "msm.info(molecular_system_trimmed, element='chain')" ] @@ -113,26 +276,67 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ - "pdbfile = msm.systems.demo['Trp-Cage']['1l2y.pdb']\n", + "pdbfile = msm.systems['Trp-Cage']['1l2y.pdb']\n", "molecular_system = msm.convert(pdbfile, to_form='molsysmt.Structures')" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
formn_atomsn_groupsn_componentsn_chainsn_moleculesn_entitiesn_structures
molsysmt.Structures304NoneNoneNoneNoneNone38
\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "msm.info(molecular_system)" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -150,9 +354,50 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
formn_atomsn_groupsn_componentsn_chainsn_moleculesn_entitiesn_structures
molsysmt.Structures304NoneNoneNoneNoneNone1
\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "msm.info(molecular_system_trimmed)" ] @@ -192,7 +437,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.11" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/contents/user/tools/basic/select.ipynb b/docs/contents/user/tools/basic/select.ipynb index 6202378af..1e2363cdd 100644 --- a/docs/contents/user/tools/basic/select.ipynb +++ b/docs/contents/user/tools/basic/select.ipynb @@ -239,7 +239,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "731a9befc8bb479b8b7e90df0c099219", + "model_id": "7174190f95964d919eaacf9cbd9fe139", "version_major": 2, "version_minor": 0 }, @@ -6391,7 +6391,7 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": 39, "metadata": {}, "outputs": [], "source": [ @@ -6404,7 +6404,7 @@ }, { "cell_type": "code", - "execution_count": 46, + "execution_count": 40, "metadata": {}, "outputs": [ { @@ -6449,7 +6449,7 @@ }, { "cell_type": "code", - "execution_count": 47, + "execution_count": 41, "metadata": {}, "outputs": [ { @@ -6493,7 +6493,7 @@ " [64, 661, 1183, 1276, 1458, 1976, 2573, 3095, 3188, 3370]]" ] }, - "execution_count": 47, + "execution_count": 41, "metadata": {}, "output_type": "execute_result" } @@ -6513,7 +6513,7 @@ }, { "cell_type": "code", - "execution_count": 48, + "execution_count": 42, "metadata": {}, "outputs": [ { @@ -6525,7 +6525,7 @@ " [4, 5, 6]]" ] }, - "execution_count": 48, + "execution_count": 42, "metadata": {}, "output_type": "execute_result" } @@ -6549,7 +6549,7 @@ }, { "cell_type": "code", - "execution_count": 49, + "execution_count": 43, "metadata": {}, "outputs": [ { @@ -6558,7 +6558,7 @@ "array([10, 13, 17, 20, 26, 29])" ] }, - "execution_count": 49, + "execution_count": 43, "metadata": {}, "output_type": "execute_result" } @@ -6578,7 +6578,7 @@ }, { "cell_type": "code", - "execution_count": 50, + "execution_count": 44, "metadata": {}, "outputs": [ { @@ -6587,7 +6587,7 @@ "'@25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44'" ] }, - "execution_count": 50, + "execution_count": 44, "metadata": {}, "output_type": "execute_result" } @@ -6598,7 +6598,7 @@ }, { "cell_type": "code", - "execution_count": 51, + "execution_count": 45, "metadata": {}, "outputs": [ { @@ -6607,7 +6607,7 @@ "'index 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44'" ] }, - "execution_count": 51, + "execution_count": 45, "metadata": {}, "output_type": "execute_result" } @@ -6625,7 +6625,7 @@ }, { "cell_type": "code", - "execution_count": 52, + "execution_count": 46, "metadata": {}, "outputs": [ { @@ -6634,7 +6634,7 @@ "'7:A 8:A 9:A'" ] }, - "execution_count": 52, + "execution_count": 46, "metadata": {}, "output_type": "execute_result" } @@ -6645,7 +6645,7 @@ }, { "cell_type": "code", - "execution_count": 53, + "execution_count": 47, "metadata": {}, "outputs": [ { @@ -6654,7 +6654,7 @@ "'resid 3 4 5'" ] }, - "execution_count": 53, + "execution_count": 47, "metadata": {}, "output_type": "execute_result" } diff --git a/docs/contents/user/tools/basic/set.ipynb b/docs/contents/user/tools/basic/set.ipynb index 04d8adee0..9f0351f31 100644 --- a/docs/contents/user/tools/basic/set.ipynb +++ b/docs/contents/user/tools/basic/set.ipynb @@ -56,7 +56,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d1eb5aba80c345c1a625ff96dfd76b32", + "model_id": "6e9e97634bb3444dba7687a0ef6d4c92", "version_major": 2, "version_minor": 0 }, @@ -95,43 +95,43 @@ "text/html": [ "\n", - "\n", + "
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252253CBC3031HISaminoacid000protein0T4 lysozyme252253CBC3031HISamino acid000protein0T4 LYSOZYME
253254CGC3031HISaminoacid000protein0T4 lysozyme253254CGC3031HISamino acid000protein0T4 LYSOZYME
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Magnitude
[[[0.0 0.0 0.0]]]
Unitsnanometer
" ], "text/latex": [ - "$arr[,0,:,:] = \\begin{pmatrix}0.0 & 0.0 & 0.0\\end{pmatrix}\\ \\mathrm{nanometer}$" + "$arr[,0,:,:] = \\begin{pmatrix} & & \\end{pmatrix}\\ \\mathrm{nanometer}$" ], "text/plain": [ "array([[[0., 0., 0.]]]) " @@ -718,7 +718,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.11" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/contents/user/tools/basic/view.ipynb b/docs/contents/user/tools/basic/view.ipynb index 23bb5f461..9299f6d45 100644 --- a/docs/contents/user/tools/basic/view.ipynb +++ b/docs/contents/user/tools/basic/view.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "tags": [ "remove-input" @@ -48,16 +48,29 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "0f4230d372c5478cb1309ae32a07e2e4", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "import molsysmt as msm" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": { "editable": true, "slideshow": { @@ -77,16 +90,31 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "701d031cf96541b7a979b333972e77d8", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "NGLWidget()" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "msm.view('181L', standard=True, with_water_as='licorice', viewer='NGLView')" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": { "editable": true, "slideshow": { @@ -125,7 +153,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": { "tags": [ "remove-input" @@ -141,16 +169,31 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "1fdb3ac30cf74434af6622da361369b5", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "NGLWidget()" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ - "msm.view('181L', selection='molecule_name==\"Benzene\"', standard=True, viewer='NGLView')" + "msm.view('181L', selection='molecule_name==\"BENZENE\"', standard=True, viewer='NGLView')" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": { "editable": true, "slideshow": { @@ -179,16 +222,16 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ - "molecular_system = msm.convert('181L', selection='molecule_type==\"protein\" or molecule_name==\"Benzene\"', to_form='openmm.Modeller')" + "molecular_system = msm.convert('181L', selection='molecule_type==\"protein\" or molecule_name==\"BENZENE\"', to_form='openmm.Modeller')" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "metadata": { "editable": true, "slideshow": { @@ -208,16 +251,31 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "ccc681f7c68040edbc7a90a331249c14", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "NGLWidget()" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "msm.view(molecular_system, selection='all within 7.0 angstroms of molecule_type==\"small molecule\"', standard=True)" ] }, { "cell_type": "code", - 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Magnitude
[[[0.9586227516599011]]]
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" + ], + "text/latex": [ + "$arr[,0,:,:] = \\begin{pmatrix}\\end{pmatrix}\\ \\mathrm{nanometer}$" + ], + "text/plain": [ + "array([[[0.95862275]]]) " + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "msm.structure.get_distances(view, selection='atom_index==0', selection_2='atom_index==20')" ] @@ -367,7 +534,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.11" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/docs/contents/user/tools/basic/where_is_attribute.ipynb b/docs/contents/user/tools/basic/where_is_attribute.ipynb index 7d07913f4..2e7e1576b 100644 --- a/docs/contents/user/tools/basic/where_is_attribute.ipynb +++ b/docs/contents/user/tools/basic/where_is_attribute.ipynb @@ -45,14 +45,14 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "id": "bbecf5a9-b8d3-49ac-85e3-e7cea880c231", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "e2557f2620a54d84bcbcfaf98b02c4d6", + "model_id": "560c647d5b434346adfa25914efe605c", "version_major": 2, "version_minor": 0 }, @@ -68,18 +68,18 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "id": "83ecdd1d-aa92-443d-9fa7-dfe3adac50c2", "metadata": {}, "outputs": [], "source": [ - "structure = msm.systems.demo['pentalanine']['pentalanine.inpcrd']\n", - "topology = msm.systems.demo['pentalanine']['pentalanine.prmtop']" + "structure = msm.systems['pentalanine']['pentalanine.inpcrd']\n", + "topology = msm.systems['pentalanine']['pentalanine.prmtop']" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "id": "f4242553-453a-4f9c-9f07-64ce7c0da8d6", "metadata": {}, "outputs": [ @@ -88,42 +88,42 @@ "text/html": [ "\n", - "\n", + "
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\n" ], "text/plain": [ - "" + "" ] }, - "execution_count": 3, + "execution_count": 4, "metadata": {}, "output_type": "execute_result" } @@ -142,18 +142,18 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "id": "b6813e3b-50c6-4624-bb65-3a76d3cd77dc", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "(PosixPath('/home/diego/projects@uibcdf/MolSysMT/molsysmt/data/inpcrd/pentalanine.inpcrd'),\n", + "('/home/diego/repos@uibcdf/MolSysMT/molsysmt/data/inpcrd/pentalanine.inpcrd',\n", " 'file:inpcrd')" ] }, - "execution_count": 4, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -164,18 +164,18 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "id": "c1f3bf93-9107-42e3-937f-57ddc5e5c9e2", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "(PosixPath('/home/diego/projects@uibcdf/MolSysMT/molsysmt/data/prmtop/pentalanine.prmtop'),\n", + "('/home/diego/repos@uibcdf/MolSysMT/molsysmt/data/prmtop/pentalanine.prmtop',\n", " 'file:prmtop')" ] }, - "execution_count": 5, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } @@ -225,7 +225,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.11" + "version": "3.10.14" } }, "nbformat": 4, diff --git a/molsysmt/basic/convert.py b/molsysmt/basic/convert.py index 401208bce..56f7b14b9 100644 --- a/molsysmt/basic/convert.py +++ b/molsysmt/basic/convert.py @@ -140,6 +140,9 @@ def _convert_multiple_to_one_with_shortcuts(molecular_system, if 'structure_indices' in input_arguments: conversion_arguments['structure_indices']=structure_indices + if 'get_missing_bonds' in kwargs and 'get_missing_bonds' not in input_arguments: + del kwargs['get_missing_bonds'] + for element, element_index in _element_index.items(): if _element_indices[element] in input_arguments: if not is_all(selection): @@ -175,8 +178,6 @@ def _convert_multiple_to_one(molecular_system, from molsysmt.basic import has_attribute from molsysmt.attribute import attributes as _attributes - output = None - n_items = len(from_forms) # Conversion arguments @@ -502,7 +503,6 @@ def convert(molecular_system, """ - from . import get_form from molsysmt._private import _multiple_conversion_shortcuts diff --git a/molsysmt/basic/get.py b/molsysmt/basic/get.py index c2c5f0dde..14268e4b6 100644 --- a/molsysmt/basic/get.py +++ b/molsysmt/basic/get.py @@ -258,17 +258,21 @@ def _piped_molecular_system(molecular_system, element, in_attributes): if is_topological_attribute(in_attribute, skip_digestion=True): _, aux_form = where_is_attribute(molecular_system, in_attribute, skip_digestion=True) if aux_form is not None: - if piped_topological_attribute[aux_form] not in aux_piped_topological_attribute: - aux_piped_topological_attribute.append(piped_topological_attribute[aux_form]) - if piped_any_attribute[aux_form] not in aux_piped_any_attribute: - aux_piped_any_attribute.append(piped_any_attribute[aux_form]) + if piped_topological_attribute[aux_form] is not None: + if piped_topological_attribute[aux_form] not in aux_piped_topological_attribute: + aux_piped_topological_attribute.append(piped_topological_attribute[aux_form]) + if piped_any_attribute[aux_form] is not None: + if piped_any_attribute[aux_form] not in aux_piped_any_attribute: + aux_piped_any_attribute.append(piped_any_attribute[aux_form]) elif is_structural_attribute(in_attribute, skip_digestion=True): _, aux_form = where_is_attribute(molecular_system, in_attribute) if aux_form is not None: - if piped_structural_attribute[aux_form] not in aux_piped_structural_attribute: - aux_piped_structural_attribute.append(piped_structural_attribute[aux_form]) - if piped_any_attribute[aux_form] not in aux_piped_any_attribute: - aux_piped_any_attribute.append(piped_any_attribute[aux_form]) + if piped_structural_attribute[aux_form] is not None: + if piped_structural_attribute[aux_form] not in aux_piped_structural_attribute: + aux_piped_structural_attribute.append(piped_structural_attribute[aux_form]) + if piped_any_attribute[aux_form] is not None: + if piped_any_attribute[aux_form] not in aux_piped_any_attribute: + aux_piped_any_attribute.append(piped_any_attribute[aux_form]) n_top = len(aux_piped_topological_attribute) n_str = len(aux_piped_structural_attribute) diff --git a/molsysmt/basic/get_attributes.py b/molsysmt/basic/get_attributes.py index fcf671aaa..49057c730 100644 --- a/molsysmt/basic/get_attributes.py +++ b/molsysmt/basic/get_attributes.py @@ -82,7 +82,7 @@ def get_attributes(molecular_system, output_type='dictionary'): for form_in, item in zip(forms_in, molecular_system): for key, value in _dict_modules[form_in].attributes.items(): if value: - if _dict_modules[form_in].has_attribute(item, key): + if _dict_modules[form_in].has_attribute(item, key, skip_digestion=True): output[key]=value if output_type=='dictionary': diff --git a/molsysmt/build/get_missing_bonds.py b/molsysmt/build/get_missing_bonds.py index 7b25e156f..a8140eee7 100644 --- a/molsysmt/build/get_missing_bonds.py +++ b/molsysmt/build/get_missing_bonds.py @@ -88,9 +88,12 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all' sorted=False) bonds += aux_bonds + + if 'C' in atom_names: + aux_peptidic_bonds_C[group_index]=atom_indices[atom_names.index('C')] - aux_peptidic_bonds_C[group_index]=atom_indices[atom_names.index('C')] - aux_peptidic_bonds_N[group_index]=atom_indices[atom_names.index('N')] + if 'N' in atom_names: + aux_peptidic_bonds_N[group_index]=atom_indices[atom_names.index('N')] case 'terminal capping': diff --git a/molsysmt/data/h5msm/alanine_dipeptide.h5msm b/molsysmt/data/h5msm/alanine_dipeptide.h5msm index 02fbae9c405700d26bee76686b1439045e6ca832..677bfd4fa61b841d4d07c8264788e4916f61b7b6 100644 GIT binary patch delta 20 ccmew{o%P3b)(sc<7#*80@@>D!$Ea=#0A)=GRsaA1 delta 20 ccmew{o%P3b)(sc<7!8{*@@>D!$Ea=#0A#HQMgRZ+ diff --git a/molsysmt/data/h5msm/lysine_dipeptide.h5msm b/molsysmt/data/h5msm/lysine_dipeptide.h5msm index 89902eb03e6a303c1effc2c3e7368b1dad4e9a14..8a39c024b4bbf29845cf78992655f09986913d19 100644 GIT binary patch delta 20 ccmew{o%P3b)(rxJjE>EMg4+cJ8J}AL08@_!+yDRo delta 20 ccmew{o%P3b)(rxJjE2pEg4+cJ8J}AL08;M;%m4rY diff --git a/molsysmt/data/h5msm/proline_dipeptide.h5msm b/molsysmt/data/h5msm/proline_dipeptide.h5msm index 37f731641f25f9e53c2c58e0d56017a73c46271d..55f897477ac5c30e68fdffec909d47c3d18e012b 100644 GIT binary patch delta 20 ccmew{o%P3b)(sQ*86BG^@^7EW&zNol0AFJV*Z=?k delta 20 ccmew{o%P3b)(sQ*84a5!@^7EW&zNol0A9lf$N&HU diff --git a/molsysmt/data/h5msm/valine_dipeptide.h5msm b/molsysmt/data/h5msm/valine_dipeptide.h5msm index ecf59be2848ac60d3cfd7dc2f0a9145418aa4492..2b9acaabcde98dcd1bb63044ed95ccb449fc44eb 100644 GIT binary patch delta 20 ccmew{o%P3b)(s!{86BHH@^Amh&&X~A0BB\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
entity_identity_nameentity_type
00T4 LYSOZYMEprotein
11CHLORIDE IONion
222-HYDROXYETHYL DISULFIDEsmall molecule
33BENZENEsmall molecule
44waterwater
\n", - "" - ], - "text/plain": [ - " entity_id entity_name entity_type\n", - "0 0 T4 LYSOZYME protein\n", - "1 1 CHLORIDE ION ion\n", - "2 2 2-HYDROXYETHYL DISULFIDE small molecule\n", - "3 3 BENZENE small molecule\n", - "4 4 water water" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "molsys.topology.entities" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4cdc4f01-cba8-494c-b029-e3cb4e801786", - "metadata": {}, - "outputs": [], - "source": [ - "item = msm.convert('181L','mmcif.PdbxContainers.DataContainer')" - ] - }, { "cell_type": "code", "execution_count": null, - "id": "c9b7fe10-d644-4d8d-b26c-fbcfc5d8136d", + "id": "89627ab5-532e-4815-ac94-3c3295fb685c", "metadata": {}, "outputs": [], "source": [ - "item.getObj('chem_comp_bond')" + "import molsysmt as msm\n", + "from molsysmt import systems" ] }, { "cell_type": "code", "execution_count": null, - "id": "6b3ace66-6693-479d-a2a1-6df688c4769f", + "id": "a673846b-5259-4acc-a751-9a9df5ba7a46", "metadata": {}, "outputs": [], "source": []