From 400fcc1104df2fbd6b13d96203f959b60bd6ff30 Mon Sep 17 00:00:00 2001 From: blancoapa Date: Wed, 8 May 2024 14:01:21 +0200 Subject: [PATCH] fix bug in peptide section of the tutorial --- tutorials/pyMBE_tutorial.ipynb | 936 ++++++++++++++++++++++++++++++++- 1 file changed, 907 insertions(+), 29 deletions(-) diff --git a/tutorials/pyMBE_tutorial.ipynb b/tutorials/pyMBE_tutorial.ipynb index 5731a0b..2e6be2b 100644 --- a/tutorials/pyMBE_tutorial.ipynb +++ b/tutorials/pyMBE_tutorial.ipynb @@ -904,7 +904,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 15, "metadata": {}, "outputs": [], "source": [ @@ -941,7 +941,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ @@ -961,7 +961,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -982,9 +982,650 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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namepmb_typeparticle_idresidue_idmolecule_idaciditysigmacutoffoffsetepsilonstate_one
labeles_typecharge
0BB-PDhaparticle000inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
1COOH-PDhaparticle100inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
2NH3-PDhaparticle200inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
9BB-PDhaparticle310inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
10COOH-PDhaparticle410inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
12NH3-PDhaparticle510inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
15BB-PDhaparticle620inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
16COOH-PDhaparticle720inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
18NH3-PDhaparticle820inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
21BB-PDhaparticle930inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
22COOH-PDhaparticle1030inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
24NH3-PDhaparticle1130inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
28BB-PDhaparticle1240inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
29COOH-PDhaparticle1340inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
31NH3-PDhaparticle1440inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
35BB-PDhaparticle1550inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
36COOH-PDhaparticle1650inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
38NH3-PDhaparticle1750inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
42BB-PDhaparticle1860inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
43COOH-PDhaparticle1960inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
45NH3-PDhaparticle2060inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
49BB-PDhaparticle2170inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
50COOH-PDhaparticle2270inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
52NH3-PDhaparticle2370inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
56BB-PDhaparticle2480inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
57COOH-PDhaparticle2580inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
59NH3-PDhaparticle2680inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
63BB-PDhaparticle2790inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
64COOH-PDhaparticle2890inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
66NH3-PDhaparticle2990inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
\n", + "
" + ], + "text/plain": [ + " name pmb_type particle_id residue_id molecule_id acidity \\\n", + " \n", + "0 BB-PDha particle 0 0 0 inert \n", + "1 COOH-PDha particle 1 0 0 inert \n", + "2 NH3-PDha particle 2 0 0 inert \n", + "9 BB-PDha particle 3 1 0 inert \n", + "10 COOH-PDha particle 4 1 0 inert \n", + "12 NH3-PDha particle 5 1 0 inert \n", + "15 BB-PDha particle 6 2 0 inert \n", + "16 COOH-PDha particle 7 2 0 inert \n", + "18 NH3-PDha particle 8 2 0 inert \n", + "21 BB-PDha particle 9 3 0 inert \n", + "22 COOH-PDha particle 10 3 0 inert \n", + "24 NH3-PDha particle 11 3 0 inert \n", + "28 BB-PDha particle 12 4 0 inert \n", + "29 COOH-PDha particle 13 4 0 inert \n", + "31 NH3-PDha particle 14 4 0 inert \n", + "35 BB-PDha particle 15 5 0 inert \n", + "36 COOH-PDha particle 16 5 0 inert \n", + "38 NH3-PDha particle 17 5 0 inert \n", + "42 BB-PDha particle 18 6 0 inert \n", + "43 COOH-PDha particle 19 6 0 inert \n", + "45 NH3-PDha particle 20 6 0 inert \n", + "49 BB-PDha particle 21 7 0 inert \n", + "50 COOH-PDha particle 22 7 0 inert \n", + "52 NH3-PDha particle 23 7 0 inert \n", + "56 BB-PDha particle 24 8 0 inert \n", + "57 COOH-PDha particle 25 8 0 inert \n", + "59 NH3-PDha particle 26 8 0 inert \n", + "63 BB-PDha particle 27 9 0 inert \n", + "64 COOH-PDha particle 28 9 0 inert \n", + "66 NH3-PDha particle 29 9 0 inert \n", + "\n", + " sigma cutoff offset \\\n", + " \n", + "0 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "1 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "2 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "9 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "10 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "12 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "15 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "16 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "18 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "21 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "22 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "24 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "28 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "29 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "31 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "35 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "36 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "38 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "42 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "43 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "45 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "49 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "50 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "52 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "56 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "57 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "59 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "63 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "64 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "66 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", + "\n", + " epsilon state_one \n", + " label es_type charge \n", + "0 1 reduced_energy BB-PDha 0 0 \n", + "1 1 reduced_energy COOH-PDha 1 0 \n", + "2 1 reduced_energy NH3-PDha 2 0 \n", + "9 1 reduced_energy BB-PDha 0 0 \n", + "10 1 reduced_energy COOH-PDha 1 0 \n", + "12 1 reduced_energy NH3-PDha 2 0 \n", + "15 1 reduced_energy BB-PDha 0 0 \n", + "16 1 reduced_energy COOH-PDha 1 0 \n", + "18 1 reduced_energy NH3-PDha 2 0 \n", + "21 1 reduced_energy BB-PDha 0 0 \n", + "22 1 reduced_energy COOH-PDha 1 0 \n", + "24 1 reduced_energy NH3-PDha 2 0 \n", + "28 1 reduced_energy BB-PDha 0 0 \n", + "29 1 reduced_energy COOH-PDha 1 0 \n", + "31 1 reduced_energy NH3-PDha 2 0 \n", + "35 1 reduced_energy BB-PDha 0 0 \n", + "36 1 reduced_energy COOH-PDha 1 0 \n", + "38 1 reduced_energy NH3-PDha 2 0 \n", + "42 1 reduced_energy BB-PDha 0 0 \n", + "43 1 reduced_energy COOH-PDha 1 0 \n", + "45 1 reduced_energy NH3-PDha 2 0 \n", + "49 1 reduced_energy BB-PDha 0 0 \n", + "50 1 reduced_energy COOH-PDha 1 0 \n", + "52 1 reduced_energy NH3-PDha 2 0 \n", + "56 1 reduced_energy BB-PDha 0 0 \n", + "57 1 reduced_energy COOH-PDha 1 0 \n", + "59 1 reduced_energy NH3-PDha 2 0 \n", + "63 1 reduced_energy BB-PDha 0 0 \n", + "64 1 reduced_energy COOH-PDha 1 0 \n", + "66 1 reduced_energy NH3-PDha 2 0 " + ] + }, + "execution_count": 18, + "metadata": {}, + 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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: []\n", + "Index: []" + ] + }, + "execution_count": 34, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "pmb.destroy_pmb_object_in_system(name = diblock_polymer, \n", " espresso_system = espresso_system)\n", @@ -1607,7 +2356,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 35, "metadata": {}, "outputs": [], "source": [ @@ -1625,14 +2374,122 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 36, "metadata": {}, "outputs": [], "source": [ + "pmb.load_interaction_parameters (filename = pmb.get_resource('parameters/peptides/Lunkad2021.json'))\n", "pmb.load_interaction_parameters (filename = pmb.get_resource('parameters/peptides/Lunkad2021.json'))\n", "pmb.add_bonds_to_espresso (espresso_system = espresso_system)" ] }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " name pmb_type particle_id particle_id2 residue_id molecule_id \\\n", + " \n", + "0 CA particle 0 NaN 0 NaN \n", + "1 D particle NaN NaN NaN NaN \n", + "2 E particle NaN NaN NaN NaN \n", + "3 H particle NaN NaN NaN NaN \n", + "4 Y particle NaN NaN NaN NaN \n", + "5 K particle NaN NaN NaN NaN \n", + "6 CA-CA bond NaN NaN NaN NaN \n", + "7 CA-D bond NaN NaN NaN NaN \n", + "8 CA-E bond NaN NaN NaN NaN \n", + "9 CA-H bond NaN NaN NaN NaN \n", + "10 CA-Y bond NaN NaN NaN NaN \n", + "11 CA-K bond NaN NaN NaN NaN \n", + "12 AA-K residue NaN NaN 0 NaN \n", + "13 AA-E residue NaN NaN NaN NaN \n", + "14 KKKKKEEEEE molecule NaN NaN NaN 0 \n", + "\n", + " acidity pka central_bead side_chains ... state_one \\\n", + " ... label es_type charge \n", + "0 inert NaN NaN NaN ... CA 0 0 \n", + "1 inert NaN NaN NaN ... D 1 None \n", + "2 inert NaN NaN NaN ... E 2 None \n", + "3 inert NaN NaN NaN ... H 3 None \n", + "4 inert NaN NaN NaN ... Y 4 None \n", + "5 inert NaN NaN NaN ... K 5 None \n", + "6 NaN NaN NaN NaN ... NaN NaN NaN \n", + "7 NaN NaN NaN NaN ... NaN NaN NaN \n", + "8 NaN NaN NaN NaN ... NaN NaN NaN \n", + "9 NaN NaN NaN NaN ... NaN NaN NaN \n", + "10 NaN NaN NaN NaN ... NaN NaN NaN \n", + "11 NaN NaN NaN NaN ... NaN NaN NaN \n", + "12 NaN NaN CA [K] ... NaN NaN NaN \n", + "13 NaN NaN CA [E] ... NaN NaN NaN \n", + "14 NaN NaN NaN NaN ... NaN NaN NaN \n", + "\n", + " state_two sequence \\\n", + " label es_type charge \n", + "0 NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN \n", + "2 NaN NaN NaN NaN \n", + "3 NaN NaN NaN NaN \n", + "4 NaN NaN NaN NaN \n", + "5 NaN NaN NaN NaN \n", + "6 NaN NaN NaN NaN \n", + "7 NaN NaN NaN NaN \n", + "8 NaN NaN NaN NaN \n", + "9 NaN NaN NaN NaN \n", + "10 NaN NaN NaN NaN \n", + "11 NaN NaN NaN NaN \n", + "12 NaN NaN NaN NaN \n", + "13 NaN NaN NaN NaN \n", + "14 NaN NaN NaN [K, K, K, K, K, E, E, E, E, E] \n", + "\n", + " bond_object \\\n", + " \n", + "0 NaN \n", + "1 NaN \n", + "2 NaN \n", + "3 NaN \n", + "4 NaN \n", + "5 NaN \n", + "6 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", + "7 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", + "8 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", + "9 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", + "10 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", + "11 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", + "12 NaN \n", + "13 NaN \n", + "14 NaN \n", + "\n", + " parameters_of_the_potential l0 \n", + " \n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "2 NaN NaN \n", + "3 NaN NaN \n", + "4 NaN NaN \n", + "5 NaN NaN \n", + "6 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.776371 \n", + "7 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.744156 \n", + "8 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.870000 \n", + "9 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.904000 \n", + "10 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 1.296000 \n", + "11 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 1.116000 \n", + "12 NaN NaN \n", + "13 NaN NaN \n", + "14 NaN NaN \n", + "\n", + "[15 rows x 26 columns]\n" + ] + } + ], + "source": [ + "print(pmb.df)" + ] + }, { "cell_type": "markdown", "metadata": {}, @@ -1642,9 +2499,30 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 37, "metadata": {}, - "outputs": [], + "outputs": [ + { + "ename": "ValueError", + "evalue": "Charge has to be a float. -- Got an NoneType", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[37], line 5\u001b[0m\n\u001b[1;32m 1\u001b[0m pmb\u001b[38;5;241m.\u001b[39mdefine_peptide(name \u001b[38;5;241m=\u001b[39m sequence, \n\u001b[1;32m 2\u001b[0m sequence \u001b[38;5;241m=\u001b[39m sequence, \n\u001b[1;32m 3\u001b[0m model \u001b[38;5;241m=\u001b[39m model)\n\u001b[0;32m----> 5\u001b[0m \u001b[43mpmb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_pmb_object\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43msequence\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[43m \u001b[49m\u001b[43mnumber_of_objects\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mN_peptide\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 8\u001b[0m \u001b[43m \u001b[49m\u001b[43mposition\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43m[\u001b[49m\u001b[43mBox_L\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mreduced_length\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmagnitude\u001b[49m\u001b[38;5;241;43m/\u001b[39;49m\u001b[38;5;241;43m2\u001b[39;49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:1009\u001b[0m, in \u001b[0;36mpymbe_library.create_pmb_object\u001b[0;34m(self, name, number_of_objects, espresso_system, position, use_default_bond)\u001b[0m\n\u001b[1;32m 1007\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcreate_residue(name\u001b[38;5;241m=\u001b[39mname, number_of_residues\u001b[38;5;241m=\u001b[39mnumber_of_objects, espresso_system\u001b[38;5;241m=\u001b[39mespresso_system, central_bead_position\u001b[38;5;241m=\u001b[39mposition,use_default_bond\u001b[38;5;241m=\u001b[39muse_default_bond)\n\u001b[1;32m 1008\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m pmb_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolecule\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m-> 1009\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_molecule\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnumber_of_molecules\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnumber_of_objects\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43muse_default_bond\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muse_default_bond\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlist_of_first_residue_positions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mposition\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n", + "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:884\u001b[0m, in \u001b[0;36mpymbe_library.create_molecule\u001b[0;34m(self, name, number_of_molecules, espresso_system, list_of_first_residue_positions, use_default_bond)\u001b[0m\n\u001b[1;32m 879\u001b[0m \u001b[38;5;66;03m# Generate an arbitrary random unit vector\u001b[39;00m\n\u001b[1;32m 880\u001b[0m backbone_vector \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_random_points_in_a_sphere(center\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m0\u001b[39m,\u001b[38;5;241m0\u001b[39m,\u001b[38;5;241m0\u001b[39m], \n\u001b[1;32m 881\u001b[0m radius\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m, \n\u001b[1;32m 882\u001b[0m n_samples\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 883\u001b[0m on_surface\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 884\u001b[0m residues_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_residue\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mresidue\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 885\u001b[0m \u001b[43m \u001b[49m\u001b[43mnumber_of_residues\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 886\u001b[0m \u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 887\u001b[0m \u001b[43m \u001b[49m\u001b[43mcentral_bead_position\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mresidue_position\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 888\u001b[0m \u001b[43m \u001b[49m\u001b[43muse_default_bond\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43muse_default_bond\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 889\u001b[0m \u001b[43m \u001b[49m\u001b[43mbackbone_vector\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbackbone_vector\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 890\u001b[0m residue_id \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mnext\u001b[39m(\u001b[38;5;28miter\u001b[39m(residues_info))\n\u001b[1;32m 891\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m index \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mresidue_id\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m==\u001b[39mresidue_id]\u001b[38;5;241m.\u001b[39mindex:\n", + "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:1149\u001b[0m, in \u001b[0;36mpymbe_library.create_residue\u001b[0;34m(self, name, espresso_system, number_of_residues, central_bead_position, use_default_bond, backbone_vector)\u001b[0m\n\u001b[1;32m 1145\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1146\u001b[0m bead_position\u001b[38;5;241m=\u001b[39mcentral_bead_position\u001b[38;5;241m+\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_trial_perpendicular_vector(vector\u001b[38;5;241m=\u001b[39mbackbone_vector,\n\u001b[1;32m 1147\u001b[0m magnitude\u001b[38;5;241m=\u001b[39ml0)\n\u001b[0;32m-> 1149\u001b[0m side_bead_id \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_particle\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mside_chain_element\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 1150\u001b[0m \u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1151\u001b[0m \u001b[43m \u001b[49m\u001b[43mposition\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[43mbead_position\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 1152\u001b[0m \u001b[43m \u001b[49m\u001b[43mnumber_of_particles\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m 1153\u001b[0m index \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mparticle_id\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m==\u001b[39mside_bead_id]\u001b[38;5;241m.\u001b[39mindex\u001b[38;5;241m.\u001b[39mvalues[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m 1154\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_value_to_df(key\u001b[38;5;241m=\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mresidue_id\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 1155\u001b[0m index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mint\u001b[39m (index),\n\u001b[1;32m 1156\u001b[0m new_value\u001b[38;5;241m=\u001b[39mresidue_id, \n\u001b[1;32m 1157\u001b[0m verbose\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m)\n", + "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:982\u001b[0m, in \u001b[0;36mpymbe_library.create_particle\u001b[0;34m(self, name, espresso_system, number_of_particles, position, fix)\u001b[0m\n\u001b[1;32m 980\u001b[0m espresso_system\u001b[38;5;241m.\u001b[39mpart\u001b[38;5;241m.\u001b[39madd (\u001b[38;5;28mid\u001b[39m\u001b[38;5;241m=\u001b[39mbead_id, pos \u001b[38;5;241m=\u001b[39m particle_position, \u001b[38;5;28mtype\u001b[39m \u001b[38;5;241m=\u001b[39m es_type, q \u001b[38;5;241m=\u001b[39m q,fix \u001b[38;5;241m=\u001b[39m[fix,fix,fix]) \n\u001b[1;32m 981\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 982\u001b[0m \u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpart\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43madd\u001b[49m\u001b[43m \u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mid\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbead_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpos\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mparticle_position\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mtype\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mes_type\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mq\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mq\u001b[49m\u001b[43m)\u001b[49m \n\u001b[1;32m 983\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_value_to_df(key\u001b[38;5;241m=\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mparticle_id\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m),index\u001b[38;5;241m=\u001b[39mdf_index,new_value\u001b[38;5;241m=\u001b[39mbead_id, verbose\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m) \n\u001b[1;32m 984\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m created_pid_list\n", + "File \u001b[0;32mparticle_data.pyx:1792\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleList.add\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32mparticle_data.pyx:1834\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleList._place_new_particle\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32mparticle_data.pyx:1446\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleHandle.update\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32mparticle_data.pyx:578\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleHandle.q.__set__\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32mutils.pyx:69\u001b[0m, in \u001b[0;36mespressomd.utils.check_type_or_throw_except\u001b[0;34m()\u001b[0m\n", + "\u001b[0;31mValueError\u001b[0m: Charge has to be a float. -- Got an NoneType" + ] + } + ], "source": [ "pmb.define_peptide(name = sequence, \n", " sequence = sequence, \n", @@ -1748,7 +2626,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.10" + "version": "3.10.12" }, "vscode": { "interpreter": {