Skip to content

Instantly share code, notes, and snippets.

@ljmartin

ljmartin/hbond_w_rdkit_example.ipynb

Created November 26, 2023 04:09
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save ljmartin/aac7014a46263eca6b25de57cce61eea to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save ljmartin/aac7014a46263eca6b25de57cce61eea to your computer and use it in GitHub Desktop.
Download ZIP
Display the source blob
Display the rendered blob
Raw
hbond_w_rdkit_example.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 8,
"id": "86fcd028-7904-4f3b-8096-03dbd699a7b8",
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from rdkit import Chem\n",
"from scipy.spatial.distance import cdist\n"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "791bf658-b1c8-4ce2-a4b3-bf9f17317961",
"metadata": {},
"outputs": [],
"source": [
"HDonorSmarts = Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]')\n",
"# change log for HAcceptorSmarts:\n",
"# v2, 1-Nov-2008, GL : fix amide-N exclusion; remove Fs from definition\n",
"\n",
"##note that Lewis removed sulfur \n",
"##and removed the O from the bit at the start, originally was [!$(*=[O,N,P,S])]\n",
"\n",
"HAcceptorSmarts = Chem.MolFromSmarts('[$([O;H1;v2]-[!$(*=[N,P,S])]),' +\n",
" '$([O;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),' +\n",
" '$([nH0,o;+0])]')"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "eb016c6b-f76d-401c-991f-5b5dd0e4804d",
"metadata": {},
"outputs": [],
"source": [
"pocket = Chem.MolFromPDBFile('./pock.pdb',removeHs=False)\n",
"ligand = Chem.MolFromMolFile('./targets/pde10a_8di4/scoring/1_pocket.fix.sdf', removeHs=False)\n",
"combin = Chem.CombineMols(ligand, pocket)\n",
"\n",
"#combin = Chem.MolFromPDBFile('./targets/pde10a_8di4/scoring/1_pocket_mol_1_1.pdb')\n",
"Chem.SanitizeMol(combin)\n",
"combin.UpdatePropertyCache()\n",
"\n",
"\n",
"#combin = Chem.MolFromPDBFile('/Users/ljmartin/Desktop/mol.pdb', removeHs=False)\n",
"xyz = combin.GetConformer(0).GetPositions()\n",
"hbas = np.array([i[0] for i in combin.GetSubstructMatches(HAcceptorSmarts)])\n",
"hbds = np.array([i[0] for i in combin.GetSubstructMatches(HDonorSmarts)])"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "8ff1b9b0-3b50-4be4-86a4-6fc9083ea815",
"metadata": {},
"outputs": [],
"source": [
"#get associated hydrogens:\n",
"hbdHs = []\n",
"for hbd in hbds:\n",
" atom = combin.GetAtomWithIdx(int(hbd))\n",
" neighbours = atom.GetNeighbors()\n",
" neighbs = []\n",
" for neighb in neighbours:\n",
" if neighb.GetAtomicNum()==1:\n",
" neighbs.append(neighb)\n",
" hbdHs.append(neighbs)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "22d540bf-9286-469b-af38-a09f6a4e6e8d",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([[14.327, 15.254, 48.572],\n",
" [ 7.055, 12.419, 49.847],\n",
" [ 5.353, 3.147, 42.895],\n",
" [ 3.453, 6.435, 52.039],\n",
" [ 6.347, 5.718, 48.294],\n",
" [ 2.7 , 8.617, 50.384],\n",
" [ 2.181, 13.216, 52.706],\n",
" [ 3.203, 14.96 , 50.461],\n",
" [ 0.258, 14.744, 51.397],\n",
" [ 9.692, 17.846, 46.868],\n",
" [ 9.479, 18.59 , 44.134],\n",
" [ 3.846, 18.272, 40.978],\n",
" [12.566, 16.211, 41.644],\n",
" [ 6.899, 17.311, 34.678],\n",
" [-0.777, 19.828, 37.498],\n",
" [-0.49 , 18.744, 40.105],\n",
" [ 2.084, 17.271, 43.312],\n",
" [-2.676, 14.557, 40.043]])"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dist_hbd_to_hba = cdist(xyz[hbds], xyz[hbas])\n",
"cutoff = 3.5\n",
"ltcutoff = dist_hbd_to_hba<cutoff\n",
"xyz[hbds]\n"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "0b578c29-9c4e-436f-84d4-4a70703aafaa",
"metadata": {},
"outputs": [],
"source": [
"source_hbd = []\n",
"source_h = []\n",
"source_hba = []\n",
"for hbd_idx,hba_idx in zip(*ltcutoff.nonzero()):\n",
" hbd = hbds[hbd_idx]\n",
" hba = hbas[hba_idx]\n",
" #hydroxyl is a donor and acceptor, so skip self comparisons:\n",
" if hbd==hba:\n",
" continue\n",
" hbdH = hbdHs[hbd_idx]\n",
" for h in hbdH:\n",
" idx = h.GetIdx()\n",
" source_hbd.append(hbd)\n",
" source_h.append(idx)\n",
" source_hba.append(hba)\n",
"source_hbd = np.array(source_hbd)\n",
"source_h = np.array(source_h)\n",
"source_hba = np.array(source_hba)\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "a676f5cd-8978-45be-9b19-401d97255973",
"metadata": {},
"outputs": [],
"source": [
"def angle(atoms1, atoms2, atoms3, box=None):\n",
" \"\"\"\n",
" atoms1 is coordinates of atoms1, a natoms by 3 vector.\n",
" props to biotite for the method.\n",
" \"\"\"\n",
" v1 = atoms2-atoms1\n",
" v2 = atoms2-atoms3\n",
" #normalize:\n",
" v1 = v1 / np.linalg.norm(v1, axis=-1)[:,None]\n",
" v2 = v2 / np.linalg.norm(v2, axis=-1)[:,None]\n",
"\n",
" return np.arccos((v1*v2).sum(axis=-1))\n"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "f8a3c8b8-de16-46d7-babf-c4e3ed64b80b",
"metadata": {},
"outputs": [],
"source": [
"angles = angle(xyz[source_hbd], xyz[source_h], xyz[source_hba])\n",
"distances = np.linalg.norm(xyz[source_h]-xyz[source_hba], axis=1)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "fcf053b5-e79a-45fa-8266-d6c91707fabc",
"metadata": {},
"outputs": [],
"source": [
"#lower this number to be more accepting of worse bonds. \n",
"#best angle is 180degrees.\n",
"#120 is a reasonable one if you want to have 'yes' and 'no' hbonding.\n",
"#but feel free to make it like 50 if you want to do smoooth \n",
"#scoring of hbonds based on the angle or distance value. \n",
"cutoff_angle_rad = np.deg2rad(110)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "e1d2c601-7b52-4a70-9ae3-261302312242",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"5"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"m = angles>cutoff_angle_rad\n",
"m = m & (distances<3.5)\n",
"m.sum()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "a335dbbc-adcf-4488-9975-a430834125be",
"metadata": {},
"outputs": [],
"source": [
"import py3Dmol\n",
"def viewProt(mol, view=None, color='orange',confid=0):\n",
" if view is None:\n",
" view = py3Dmol.view()\n",
" view.addModel(Chem.MolToMolBlock(mol,confId=confid), \"sdf\")\n",
"\n",
" model = view.getModel()\n",
" model.setStyle({}, {\"stick\": {\"colorscheme\": f\"{color}Carbon\"}})\n",
" view.zoomTo()\n",
" return view"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "a13170f6-db73-4569-a821-238b759d6636",
"metadata": {},
"outputs": [
{
"data": {
"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_17009713681401632\" style=\"position: relative; width: 640px; height: 480px\">\n <p id=\"3dmolwarning_17009713681401632\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>\n <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n return new Promise((resolve, reject) => {\n //this is to ignore the existence of requirejs amd\n var savedexports, savedmodule;\n if (typeof exports !== 'undefined') savedexports = exports;\n else exports = {}\n if (typeof module !== 'undefined') savedmodule = module;\n else module = {}\n\n var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\n exports = savedexports;\n module = savedmodule;\n resolve();\n };\n var firstScriptTag = document.getElementsByTagName('script')[0];\n firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.min.js');\n}\n\nvar viewer_17009713681401632 = null;\nvar warn = document.getElementById(\"3dmolwarning_17009713681401632\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_17009713681401632 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17009713681401632\"),{backgroundColor:\"white\"});\nviewer_17009713681401632.zoomTo();\n\tviewer_17009713681401632.addModel(\"1\\n RDKit 3D\\n\\n239235 0 0 0 0 0 0 0 0999 V2000\\n 2.6469 14.9536 46.4845 Cl 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3906 14.1885 45.0596 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0188 12.9548 45.1950 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0777 12.2541 46.5429 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5923 12.3785 44.0659 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5231 13.0225 42.8910 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9132 14.2122 42.7797 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8620 14.9003 41.4262 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7333 14.0720 40.1817 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5654 14.8787 40.6685 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4042 10.8004 44.2070 Cl 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3547 14.7830 43.8576 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5648 11.3861 46.4463 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5587 12.8349 47.1997 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1486 12.0805 46.8692 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4041 15.7363 41.3404 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7129 13.0743 40.2453 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2156 14.3432 39.3487 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7669 14.4186 41.0568 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2696 15.6875 40.1602 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.3270 15.2540 48.5720 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.1090 14.6890 49.1540 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 13.2750 13.3280 49.8260 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.7950 13.1730 50.9520 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.9940 14.6260 48.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.6960 14.0320 48.5960 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.9180 14.6900 49.5340 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.2520 12.7990 48.1310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.7090 14.1540 49.9720 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.0420 12.2660 48.5450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.2610 12.9560 49.4490 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.0550 12.4190 49.8470 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.3390 15.5330 47.6120 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.8040 15.3260 49.8620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.3190 14.0720 47.3370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.8110 15.5570 47.7870 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.2300 15.5650 49.9030 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.8170 12.2870 47.4850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.1680 14.6340 50.6620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.7350 11.3830 48.1890 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.4930 12.8970 50.5220 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.3530 3.1470 42.8950 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0670 3.6820 42.4900 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 3.5540 3.0690 41.1780 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3500 3.0980 40.9310 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.1240 5.2310 42.4450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7960 5.9480 42.6760 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2690 5.6840 44.0580 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9220 7.4520 42.4200 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1110 3.7670 43.0960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4110 3.4350 43.2030 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4660 5.5000 41.5450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.7650 5.5360 43.1500 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1340 5.5820 42.0220 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4010 6.1650 44.1810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1260 4.7020 44.1780 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9290 6.0100 44.7340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0380 7.8920 42.5790 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6040 7.8400 43.0400 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2060 7.6060 41.4740 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4530 6.4350 52.0390 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4270 7.0270 51.1330 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 4.0080 8.4150 50.6520 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8500 9.2960 50.5400 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.6650 6.1210 49.9150 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1020 6.2300 49.3610 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.9220 6.8620 49.9970 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.3470 5.7180 48.2940 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.0410 5.5500 51.8210 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.2930 7.1180 51.6250 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0240 6.3810 49.1930 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4970 5.1730 50.1840 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7000 8.6170 50.3840 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1680 9.8830 49.8850 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 1.5360 10.7750 50.9600 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9240 11.7740 50.5750 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0500 9.6120 48.8540 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2730 8.5280 47.7950 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.0010 8.3410 46.9450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4790 8.8230 46.9510 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0630 7.8610 50.5350 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9050 10.3890 49.4370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8850 10.4700 48.3670 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2310 9.3570 49.3680 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4440 7.6680 48.2750 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.1580 7.6320 46.2580 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7600 8.0680 47.5370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2270 9.2020 46.4890 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5960 8.0980 46.2720 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3540 9.6990 46.4850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2910 8.8680 47.5330 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1810 13.2160 52.7060 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3430 14.6910 52.7140 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 1.0560 15.4090 52.2430 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7880 16.5290 52.6700 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4950 15.1260 51.8350 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2030 14.9600 50.4610 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7980 12.6480 52.1610 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5380 14.9800 53.6510 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3000 14.5780 52.0630 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6880 16.0910 52.0100 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6960 15.6490 49.9300 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2580 14.7440 51.3970 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0320 15.2770 50.9360 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -2.1080 15.2340 52.0270 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2230 15.7050 51.7920 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5250 14.5260 49.6730 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.4510 14.4710 48.5690 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0030 13.1340 50.0280 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5520 13.8480 51.0650 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8920 16.2350 50.6850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3080 15.0300 49.3080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8120 13.9790 47.7770 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2030 15.4010 48.2990 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.3590 13.9970 48.9150 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3160 12.6680 49.2000 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2510 12.6180 50.4370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.7580 13.1970 50.6810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.6920 17.8460 46.8680 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.4310 16.8380 45.8470 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 9.8800 17.3520 44.4700 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.6000 16.6570 43.7430 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.9120 16.4980 45.8560 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 7.5560 15.6760 47.0980 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5100 15.7690 44.5880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1590 15.5140 47.3280 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.9420 18.1950 47.4290 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.9490 16.0120 46.0680 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.4020 17.3570 45.8950 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.9520 16.1310 47.8960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.9620 14.7680 46.9970 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.5320 15.5620 44.6180 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.7040 16.3470 43.7950 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.0290 14.9170 44.5150 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0180 14.9680 48.1540 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7340 16.4120 47.4450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7440 15.0490 46.5460 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.4790 18.5900 44.1340 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.8320 19.1880 42.8600 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 11.2900 19.5740 42.7980 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.8830 19.4590 41.7490 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.8940 20.3500 42.5290 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5350 19.8400 42.1000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.4580 19.8590 42.9740 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.3640 19.2150 40.8710 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.2190 19.3600 42.6000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1340 18.6970 40.4910 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.0560 18.7980 41.3470 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8460 18.2720 40.9780 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.9220 19.1130 44.7790 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.6860 18.4890 42.1600 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.2910 20.8900 41.7870 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.7870 20.9260 43.3400 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.5770 20.2400 43.8910 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.1420 19.1370 40.2480 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4470 19.4060 43.2340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0290 18.2530 39.6010 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7330 17.8670 40.0710 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.5660 16.2110 41.6440 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.1490 15.9410 40.2670 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 12.8880 16.8530 39.2730 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.3930 16.3680 38.2660 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.6440 16.1790 40.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.7390 15.1010 40.6070 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.1690 13.7930 40.6740 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.4180 15.3770 40.9190 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.3030 12.7880 41.0780 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5640 14.3740 41.3470 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.0150 13.0940 41.4410 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.8930 16.5070 42.3210 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.3530 14.9870 40.0470 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.4600 16.2990 39.1270 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.4150 17.0210 40.5910 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.1120 13.5670 40.4300 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.0760 16.3130 40.8340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.6170 11.8390 41.1050 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6180 14.5900 41.5860 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.4070 12.3740 41.7750 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.8990 17.3110 34.6780 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.0830 17.2930 36.1430 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 8.5410 17.3490 36.5600 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.8270 17.7890 37.6590 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.3600 16.1370 36.8420 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6130 14.8170 36.2230 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1730 13.4650 37.3150 S 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.7350 13.0750 37.8840 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.3430 16.6080 34.2350 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6630 18.1330 36.4870 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.3770 16.3160 36.8130 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6650 16.1030 37.7940 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5850 14.7470 35.9990 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0710 14.7440 35.3850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.6740 12.3120 38.5280 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.3150 12.8140 37.1120 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.1300 13.8700 38.3450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7770 19.8280 37.4980 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2960 18.4620 37.6640 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5530 17.9010 39.0550 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8580 16.7160 39.1940 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2240 20.2970 38.2600 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.6890 18.4490 37.4930 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7580 17.8790 36.9960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.4900 18.7440 40.1050 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8260 18.3310 41.4550 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -2.3150 17.9870 41.4940 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.6700 16.9190 41.9890 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5130 19.4270 42.4790 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9200 19.3690 43.0350 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1650 18.0780 43.7820 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5190 17.7790 44.7730 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0840 17.2710 43.3120 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2010 19.6880 39.9480 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2980 17.5130 41.6840 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.1510 19.3350 43.2430 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6450 20.3160 42.0390 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0590 20.1380 43.6590 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5670 19.4340 42.2760 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2760 16.4070 43.7770 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5930 17.5190 42.4880 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.6760 14.5570 40.0430 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1560 13.5460 40.9630 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -3.1760 13.2950 42.0680 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3390 12.1590 42.4780 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8410 14.0260 41.5770 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.1830 13.0140 42.4740 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.6330 12.0270 41.9490 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.3180 13.0930 43.8520 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2680 11.1120 42.7870 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.3090 12.1730 44.6830 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0960 11.1900 44.1470 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1730 15.4090 39.9010 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.9960 12.6950 40.4620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0260 14.8490 42.1130 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2090 14.2470 40.8340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7680 11.9700 40.9600 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8740 13.8210 44.2530 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8500 10.3980 42.3970 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.1850 12.2290 45.6740 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5460 10.5280 44.7460 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 2 0\\n 3 4 1 0\\n 3 5 1 0\\n 5 6 2 0\\n 6 7 1 0\\n 7 8 1 0\\n 8 9 1 0\\n 9 10 1 0\\n 10 8 1 0\\n 5 11 1 0\\n 2 12 1 0\\n 12 7 2 0\\n 4 13 1 0\\n 4 14 1 0\\n 4 15 1 0\\n 8 16 1 0\\n 9 17 1 0\\n 9 18 1 0\\n 10 19 1 0\\n 10 20 1 0\\n 22 21 1 0\\n 23 22 1 0\\n 24 23 2 0\\n 25 22 1 0\\n 26 25 1 0\\n 27 26 2 0\\n 28 26 1 0\\n 29 27 1 0\\n 30 28 2 0\\n 31 30 1 0\\n 31 29 2 0\\n 32 31 1 0\\n 33 21 1 0\\n 22 34 1 1\\n 35 25 1 0\\n 36 25 1 0\\n 37 27 1 0\\n 38 28 1 0\\n 39 29 1 0\\n 40 30 1 0\\n 41 32 1 0\\n 43 42 1 0\\n 44 43 1 0\\n 45 44 2 0\\n 46 43 1 0\\n 47 46 1 0\\n 48 47 1 0\\n 49 47 1 0\\n 50 42 1 0\\n 43 51 1 1\\n 52 46 1 0\\n 53 46 1 0\\n 54 47 1 0\\n 55 48 1 0\\n 56 48 1 0\\n 57 48 1 0\\n 58 49 1 0\\n 59 49 1 0\\n 60 49 1 0\\n 62 61 1 0\\n 63 62 1 0\\n 64 63 2 0\\n 65 62 1 0\\n 66 65 1 0\\n 67 66 2 0\\n 68 66 1 0\\n 69 61 1 0\\n 62 70 1 1\\n 71 65 1 0\\n 72 65 1 0\\n 73 63 1 0\\n 74 73 1 0\\n 75 74 1 0\\n 76 75 2 0\\n 77 74 1 0\\n 78 77 1 0\\n 79 78 1 0\\n 80 78 1 0\\n 81 73 1 0\\n 74 82 1 6\\n 83 77 1 0\\n 84 77 1 0\\n 85 78 1 0\\n 86 79 1 0\\n 87 79 1 0\\n 88 79 1 0\\n 89 80 1 0\\n 90 80 1 0\\n 91 80 1 0\\n 93 92 1 0\\n 94 93 1 0\\n 95 94 2 0\\n 96 93 1 0\\n 97 96 1 0\\n 98 92 1 0\\n 93 99 1 1\\n100 96 1 0\\n101 96 1 0\\n102 97 1 0\\n103 94 1 0\\n104103 1 0\\n105104 1 0\\n106105 2 0\\n107104 1 0\\n108107 1 0\\n109107 1 0\\n110103 1 0\\n104111 1 6\\n112107 1 0\\n113108 1 0\\n114108 1 0\\n115108 1 0\\n116109 1 0\\n117109 1 0\\n118109 1 0\\n120119 1 0\\n121120 1 0\\n122121 2 0\\n123120 1 0\\n124123 1 0\\n125123 1 0\\n126124 1 0\\n127119 1 0\\n120128 1 1\\n123129 1 1\\n130124 1 0\\n131124 1 0\\n132125 1 0\\n133125 1 0\\n134125 1 0\\n135126 1 0\\n136126 1 0\\n137126 1 0\\n138121 1 0\\n139138 1 0\\n140139 1 0\\n141140 2 0\\n142139 1 0\\n143142 1 0\\n144143 2 0\\n145143 1 0\\n146144 1 0\\n147145 2 0\\n148146 2 0\\n148147 1 0\\n149148 1 0\\n150138 1 0\\n139151 1 6\\n152142 1 0\\n153142 1 0\\n154144 1 0\\n155145 1 0\\n156146 1 0\\n157147 1 0\\n158149 1 0\\n160159 1 0\\n161160 1 0\\n162161 2 0\\n163160 1 0\\n164163 1 0\\n165164 2 0\\n166164 1 0\\n167165 1 0\\n168166 2 0\\n169168 1 0\\n169167 2 0\\n170159 1 0\\n160171 1 6\\n172163 1 0\\n173163 1 0\\n174165 1 0\\n175166 1 0\\n176167 1 0\\n177168 1 0\\n178169 1 0\\n180179 1 0\\n181180 1 0\\n182181 2 0\\n183180 1 0\\n184183 1 0\\n185184 1 0\\n186185 1 0\\n187179 1 0\\n180188 1 1\\n189183 1 0\\n190183 1 0\\n191184 1 0\\n192184 1 0\\n193186 1 0\\n194186 1 0\\n195186 1 0\\n197196 1 0\\n198197 1 0\\n199198 2 0\\n200196 1 0\\n201197 1 0\\n202197 1 0\\n203198 1 0\\n204203 1 0\\n205204 1 0\\n206205 2 0\\n207204 1 0\\n208207 1 0\\n209208 1 0\\n210209 2 0\\n211209 1 0\\n212203 1 0\\n204213 1 1\\n214207 1 0\\n215207 1 0\\n216208 1 0\\n217208 1 0\\n218211 1 0\\n219211 1 0\\n221220 1 0\\n222221 1 0\\n223222 2 0\\n224221 1 0\\n225224 1 0\\n226225 2 0\\n227225 1 0\\n228226 1 0\\n229227 2 0\\n230228 2 0\\n230229 1 0\\n231220 1 0\\n221232 1 6\\n233224 1 0\\n234224 1 0\\n235226 1 0\\n236227 1 0\\n237228 1 0\\n238229 1 0\\n239230 1 0\\nM END\\n\",\"sdf\");\n\t\tviewer_17009713681401632.getModel().setStyle({},{\"stick\": {\"colorscheme\": \"orangeCarbon\"}});\n\tviewer_17009713681401632.zoomTo();\n\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 0.552, \"y\": 13.848, \"z\": 51.065}, \"end\": {\"x\": 0.924, \"y\": 11.774, \"z\": 50.575}, \"radius\": 0.1, \"dashed\": true});\n\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 11.893, \"y\": 16.507, \"z\": 42.321}, \"end\": {\"x\": 10.6, \"y\": 16.657, \"z\": 43.743}, \"radius\": 0.1, \"dashed\": true});\n\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 2.276, \"y\": 16.407, \"z\": 43.777}, \"end\": {\"x\": 3.3547, \"y\": 14.783, \"z\": 43.8576}, \"radius\": 0.1, \"dashed\": true});\n\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 2.593, \"y\": 17.519, \"z\": 42.488}, \"end\": {\"x\": 3.846, \"y\": 18.272, \"z\": 40.978}, \"radius\": 0.1, \"dashed\": true});\n\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": -2.173, \"y\": 15.409, \"z\": 39.901}, \"end\": {\"x\": -0.858, \"y\": 16.716, \"z\": 39.194}, \"radius\": 0.1, \"dashed\": true});\nviewer_17009713681401632.render();\n});\n</script>",
"text/html": [
"<div id=\"3dmolviewer_17009713681401632\" style=\"position: relative; width: 640px; height: 480px\">\n",
" <p id=\"3dmolwarning_17009713681401632\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>\n",
" <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
" </div>\n",
"<script>\n",
"\n",
"var loadScriptAsync = function(uri){\n",
" return new Promise((resolve, reject) => {\n",
" //this is to ignore the existence of requirejs amd\n",
" var savedexports, savedmodule;\n",
" if (typeof exports !== 'undefined') savedexports = exports;\n",
" else exports = {}\n",
" if (typeof module !== 'undefined') savedmodule = module;\n",
" else module = {}\n",
"\n",
" var tag = document.createElement('script');\n",
" tag.src = uri;\n",
" tag.async = true;\n",
" tag.onload = () => {\n",
" exports = savedexports;\n",
" module = savedmodule;\n",
" resolve();\n",
" };\n",
" var firstScriptTag = document.getElementsByTagName('script')[0];\n",
" firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
"});\n",
"};\n",
"\n",
"if(typeof $3Dmolpromise === 'undefined') {\n",
"$3Dmolpromise = null;\n",
" $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.min.js');\n",
"}\n",
"\n",
"var viewer_17009713681401632 = null;\n",
"var warn = document.getElementById(\"3dmolwarning_17009713681401632\");\n",
"if(warn) {\n",
" warn.parentNode.removeChild(warn);\n",
"}\n",
"$3Dmolpromise.then(function() {\n",
"viewer_17009713681401632 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17009713681401632\"),{backgroundColor:\"white\"});\n",
"viewer_17009713681401632.zoomTo();\n",
"\tviewer_17009713681401632.addModel(\"1\\n RDKit 3D\\n\\n239235 0 0 0 0 0 0 0 0999 V2000\\n 2.6469 14.9536 46.4845 Cl 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3906 14.1885 45.0596 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0188 12.9548 45.1950 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0777 12.2541 46.5429 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5923 12.3785 44.0659 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5231 13.0225 42.8910 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9132 14.2122 42.7797 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8620 14.9003 41.4262 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7333 14.0720 40.1817 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5654 14.8787 40.6685 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4042 10.8004 44.2070 Cl 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3547 14.7830 43.8576 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5648 11.3861 46.4463 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5587 12.8349 47.1997 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1486 12.0805 46.8692 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4041 15.7363 41.3404 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7129 13.0743 40.2453 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2156 14.3432 39.3487 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7669 14.4186 41.0568 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2696 15.6875 40.1602 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.3270 15.2540 48.5720 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.1090 14.6890 49.1540 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 13.2750 13.3280 49.8260 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.7950 13.1730 50.9520 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.9940 14.6260 48.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.6960 14.0320 48.5960 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.9180 14.6900 49.5340 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.2520 12.7990 48.1310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.7090 14.1540 49.9720 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.0420 12.2660 48.5450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.2610 12.9560 49.4490 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.0550 12.4190 49.8470 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.3390 15.5330 47.6120 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.8040 15.3260 49.8620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.3190 14.0720 47.3370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.8110 15.5570 47.7870 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.2300 15.5650 49.9030 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.8170 12.2870 47.4850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.1680 14.6340 50.6620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.7350 11.3830 48.1890 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.4930 12.8970 50.5220 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.3530 3.1470 42.8950 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0670 3.6820 42.4900 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 3.5540 3.0690 41.1780 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3500 3.0980 40.9310 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.1240 5.2310 42.4450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7960 5.9480 42.6760 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2690 5.6840 44.0580 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9220 7.4520 42.4200 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1110 3.7670 43.0960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4110 3.4350 43.2030 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4660 5.5000 41.5450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.7650 5.5360 43.1500 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1340 5.5820 42.0220 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4010 6.1650 44.1810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1260 4.7020 44.1780 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9290 6.0100 44.7340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0380 7.8920 42.5790 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6040 7.8400 43.0400 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2060 7.6060 41.4740 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4530 6.4350 52.0390 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4270 7.0270 51.1330 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 4.0080 8.4150 50.6520 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8500 9.2960 50.5400 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.6650 6.1210 49.9150 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1020 6.2300 49.3610 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.9220 6.8620 49.9970 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.3470 5.7180 48.2940 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.0410 5.5500 51.8210 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.2930 7.1180 51.6250 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0240 6.3810 49.1930 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4970 5.1730 50.1840 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7000 8.6170 50.3840 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1680 9.8830 49.8850 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 1.5360 10.7750 50.9600 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9240 11.7740 50.5750 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0500 9.6120 48.8540 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2730 8.5280 47.7950 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.0010 8.3410 46.9450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4790 8.8230 46.9510 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0630 7.8610 50.5350 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9050 10.3890 49.4370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8850 10.4700 48.3670 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2310 9.3570 49.3680 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4440 7.6680 48.2750 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.1580 7.6320 46.2580 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7600 8.0680 47.5370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2270 9.2020 46.4890 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5960 8.0980 46.2720 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3540 9.6990 46.4850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2910 8.8680 47.5330 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1810 13.2160 52.7060 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3430 14.6910 52.7140 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 1.0560 15.4090 52.2430 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7880 16.5290 52.6700 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4950 15.1260 51.8350 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2030 14.9600 50.4610 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7980 12.6480 52.1610 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5380 14.9800 53.6510 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3000 14.5780 52.0630 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6880 16.0910 52.0100 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6960 15.6490 49.9300 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2580 14.7440 51.3970 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0320 15.2770 50.9360 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -2.1080 15.2340 52.0270 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2230 15.7050 51.7920 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5250 14.5260 49.6730 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.4510 14.4710 48.5690 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0030 13.1340 50.0280 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5520 13.8480 51.0650 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8920 16.2350 50.6850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3080 15.0300 49.3080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8120 13.9790 47.7770 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2030 15.4010 48.2990 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.3590 13.9970 48.9150 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3160 12.6680 49.2000 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2510 12.6180 50.4370 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.7580 13.1970 50.6810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.6920 17.8460 46.8680 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.4310 16.8380 45.8470 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 9.8800 17.3520 44.4700 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.6000 16.6570 43.7430 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.9120 16.4980 45.8560 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 7.5560 15.6760 47.0980 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5100 15.7690 44.5880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1590 15.5140 47.3280 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.9420 18.1950 47.4290 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.9490 16.0120 46.0680 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.4020 17.3570 45.8950 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.9520 16.1310 47.8960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.9620 14.7680 46.9970 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.5320 15.5620 44.6180 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.7040 16.3470 43.7950 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.0290 14.9170 44.5150 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0180 14.9680 48.1540 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7340 16.4120 47.4450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7440 15.0490 46.5460 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.4790 18.5900 44.1340 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.8320 19.1880 42.8600 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 11.2900 19.5740 42.7980 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.8830 19.4590 41.7490 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.8940 20.3500 42.5290 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5350 19.8400 42.1000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.4580 19.8590 42.9740 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.3640 19.2150 40.8710 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.2190 19.3600 42.6000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1340 18.6970 40.4910 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.0560 18.7980 41.3470 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8460 18.2720 40.9780 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.9220 19.1130 44.7790 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.6860 18.4890 42.1600 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.2910 20.8900 41.7870 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.7870 20.9260 43.3400 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.5770 20.2400 43.8910 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.1420 19.1370 40.2480 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4470 19.4060 43.2340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0290 18.2530 39.6010 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7330 17.8670 40.0710 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.5660 16.2110 41.6440 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.1490 15.9410 40.2670 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 12.8880 16.8530 39.2730 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.3930 16.3680 38.2660 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.6440 16.1790 40.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.7390 15.1010 40.6070 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.1690 13.7930 40.6740 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.4180 15.3770 40.9190 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.3030 12.7880 41.0780 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5640 14.3740 41.3470 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.0150 13.0940 41.4410 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.8930 16.5070 42.3210 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.3530 14.9870 40.0470 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.4600 16.2990 39.1270 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 10.4150 17.0210 40.5910 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.1120 13.5670 40.4300 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.0760 16.3130 40.8340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 9.6170 11.8390 41.1050 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6180 14.5900 41.5860 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.4070 12.3740 41.7750 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.8990 17.3110 34.6780 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.0830 17.2930 36.1430 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 8.5410 17.3490 36.5600 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.8270 17.7890 37.6590 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.3600 16.1370 36.8420 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6130 14.8170 36.2230 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.1730 13.4650 37.3150 S 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.7350 13.0750 37.8840 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.3430 16.6080 34.2350 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6630 18.1330 36.4870 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.3770 16.3160 36.8130 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.6650 16.1030 37.7940 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.5850 14.7470 35.9990 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0710 14.7440 35.3850 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.6740 12.3120 38.5280 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.3150 12.8140 37.1120 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 8.1300 13.8700 38.3450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7770 19.8280 37.4980 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2960 18.4620 37.6640 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5530 17.9010 39.0550 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8580 16.7160 39.1940 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2240 20.2970 38.2600 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.6890 18.4490 37.4930 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7580 17.8790 36.9960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.4900 18.7440 40.1050 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8260 18.3310 41.4550 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -2.3150 17.9870 41.4940 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.6700 16.9190 41.9890 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5130 19.4270 42.4790 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9200 19.3690 43.0350 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1650 18.0780 43.7820 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5190 17.7790 44.7730 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0840 17.2710 43.3120 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2010 19.6880 39.9480 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2980 17.5130 41.6840 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.1510 19.3350 43.2430 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6450 20.3160 42.0390 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0590 20.1380 43.6590 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5670 19.4340 42.2760 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2760 16.4070 43.7770 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5930 17.5190 42.4880 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.6760 14.5570 40.0430 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1560 13.5460 40.9630 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -3.1760 13.2950 42.0680 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3390 12.1590 42.4780 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8410 14.0260 41.5770 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.1830 13.0140 42.4740 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.6330 12.0270 41.9490 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.3180 13.0930 43.8520 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2680 11.1120 42.7870 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.3090 12.1730 44.6830 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0960 11.1900 44.1470 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1730 15.4090 39.9010 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.9960 12.6950 40.4620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0260 14.8490 42.1130 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2090 14.2470 40.8340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7680 11.9700 40.9600 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8740 13.8210 44.2530 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8500 10.3980 42.3970 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.1850 12.2290 45.6740 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5460 10.5280 44.7460 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 2 0\\n 3 4 1 0\\n 3 5 1 0\\n 5 6 2 0\\n 6 7 1 0\\n 7 8 1 0\\n 8 9 1 0\\n 9 10 1 0\\n 10 8 1 0\\n 5 11 1 0\\n 2 12 1 0\\n 12 7 2 0\\n 4 13 1 0\\n 4 14 1 0\\n 4 15 1 0\\n 8 16 1 0\\n 9 17 1 0\\n 9 18 1 0\\n 10 19 1 0\\n 10 20 1 0\\n 22 21 1 0\\n 23 22 1 0\\n 24 23 2 0\\n 25 22 1 0\\n 26 25 1 0\\n 27 26 2 0\\n 28 26 1 0\\n 29 27 1 0\\n 30 28 2 0\\n 31 30 1 0\\n 31 29 2 0\\n 32 31 1 0\\n 33 21 1 0\\n 22 34 1 1\\n 35 25 1 0\\n 36 25 1 0\\n 37 27 1 0\\n 38 28 1 0\\n 39 29 1 0\\n 40 30 1 0\\n 41 32 1 0\\n 43 42 1 0\\n 44 43 1 0\\n 45 44 2 0\\n 46 43 1 0\\n 47 46 1 0\\n 48 47 1 0\\n 49 47 1 0\\n 50 42 1 0\\n 43 51 1 1\\n 52 46 1 0\\n 53 46 1 0\\n 54 47 1 0\\n 55 48 1 0\\n 56 48 1 0\\n 57 48 1 0\\n 58 49 1 0\\n 59 49 1 0\\n 60 49 1 0\\n 62 61 1 0\\n 63 62 1 0\\n 64 63 2 0\\n 65 62 1 0\\n 66 65 1 0\\n 67 66 2 0\\n 68 66 1 0\\n 69 61 1 0\\n 62 70 1 1\\n 71 65 1 0\\n 72 65 1 0\\n 73 63 1 0\\n 74 73 1 0\\n 75 74 1 0\\n 76 75 2 0\\n 77 74 1 0\\n 78 77 1 0\\n 79 78 1 0\\n 80 78 1 0\\n 81 73 1 0\\n 74 82 1 6\\n 83 77 1 0\\n 84 77 1 0\\n 85 78 1 0\\n 86 79 1 0\\n 87 79 1 0\\n 88 79 1 0\\n 89 80 1 0\\n 90 80 1 0\\n 91 80 1 0\\n 93 92 1 0\\n 94 93 1 0\\n 95 94 2 0\\n 96 93 1 0\\n 97 96 1 0\\n 98 92 1 0\\n 93 99 1 1\\n100 96 1 0\\n101 96 1 0\\n102 97 1 0\\n103 94 1 0\\n104103 1 0\\n105104 1 0\\n106105 2 0\\n107104 1 0\\n108107 1 0\\n109107 1 0\\n110103 1 0\\n104111 1 6\\n112107 1 0\\n113108 1 0\\n114108 1 0\\n115108 1 0\\n116109 1 0\\n117109 1 0\\n118109 1 0\\n120119 1 0\\n121120 1 0\\n122121 2 0\\n123120 1 0\\n124123 1 0\\n125123 1 0\\n126124 1 0\\n127119 1 0\\n120128 1 1\\n123129 1 1\\n130124 1 0\\n131124 1 0\\n132125 1 0\\n133125 1 0\\n134125 1 0\\n135126 1 0\\n136126 1 0\\n137126 1 0\\n138121 1 0\\n139138 1 0\\n140139 1 0\\n141140 2 0\\n142139 1 0\\n143142 1 0\\n144143 2 0\\n145143 1 0\\n146144 1 0\\n147145 2 0\\n148146 2 0\\n148147 1 0\\n149148 1 0\\n150138 1 0\\n139151 1 6\\n152142 1 0\\n153142 1 0\\n154144 1 0\\n155145 1 0\\n156146 1 0\\n157147 1 0\\n158149 1 0\\n160159 1 0\\n161160 1 0\\n162161 2 0\\n163160 1 0\\n164163 1 0\\n165164 2 0\\n166164 1 0\\n167165 1 0\\n168166 2 0\\n169168 1 0\\n169167 2 0\\n170159 1 0\\n160171 1 6\\n172163 1 0\\n173163 1 0\\n174165 1 0\\n175166 1 0\\n176167 1 0\\n177168 1 0\\n178169 1 0\\n180179 1 0\\n181180 1 0\\n182181 2 0\\n183180 1 0\\n184183 1 0\\n185184 1 0\\n186185 1 0\\n187179 1 0\\n180188 1 1\\n189183 1 0\\n190183 1 0\\n191184 1 0\\n192184 1 0\\n193186 1 0\\n194186 1 0\\n195186 1 0\\n197196 1 0\\n198197 1 0\\n199198 2 0\\n200196 1 0\\n201197 1 0\\n202197 1 0\\n203198 1 0\\n204203 1 0\\n205204 1 0\\n206205 2 0\\n207204 1 0\\n208207 1 0\\n209208 1 0\\n210209 2 0\\n211209 1 0\\n212203 1 0\\n204213 1 1\\n214207 1 0\\n215207 1 0\\n216208 1 0\\n217208 1 0\\n218211 1 0\\n219211 1 0\\n221220 1 0\\n222221 1 0\\n223222 2 0\\n224221 1 0\\n225224 1 0\\n226225 2 0\\n227225 1 0\\n228226 1 0\\n229227 2 0\\n230228 2 0\\n230229 1 0\\n231220 1 0\\n221232 1 6\\n233224 1 0\\n234224 1 0\\n235226 1 0\\n236227 1 0\\n237228 1 0\\n238229 1 0\\n239230 1 0\\nM END\\n\",\"sdf\");\n",
"\t\tviewer_17009713681401632.getModel().setStyle({},{\"stick\": {\"colorscheme\": \"orangeCarbon\"}});\n",
"\tviewer_17009713681401632.zoomTo();\n",
"\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 0.552, \"y\": 13.848, \"z\": 51.065}, \"end\": {\"x\": 0.924, \"y\": 11.774, \"z\": 50.575}, \"radius\": 0.1, \"dashed\": true});\n",
"\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 11.893, \"y\": 16.507, \"z\": 42.321}, \"end\": {\"x\": 10.6, \"y\": 16.657, \"z\": 43.743}, \"radius\": 0.1, \"dashed\": true});\n",
"\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 2.276, \"y\": 16.407, \"z\": 43.777}, \"end\": {\"x\": 3.3547, \"y\": 14.783, \"z\": 43.8576}, \"radius\": 0.1, \"dashed\": true});\n",
"\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 2.593, \"y\": 17.519, \"z\": 42.488}, \"end\": {\"x\": 3.846, \"y\": 18.272, \"z\": 40.978}, \"radius\": 0.1, \"dashed\": true});\n",
"\tviewer_17009713681401632.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": -2.173, \"y\": 15.409, \"z\": 39.901}, \"end\": {\"x\": -0.858, \"y\": 16.716, \"z\": 39.194}, \"radius\": 0.1, \"dashed\": true});\n",
"viewer_17009713681401632.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/plain": [
"<py3Dmol.view at 0x7f99104e8e50>"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"view = viewProt(combin)\n",
"\n",
"for hbd, hba in zip(source_h[m], source_hba[m]):\n",
"#for hbd in hyd_hbonds:\n",
" view.addCylinder({'color':'darkblue',\n",
" 'start':{'x':xyz[hbd][0],'y':xyz[hbd][1],'z':xyz[hbd][2]},\n",
" 'end':{'x':xyz[hba][0],'y':xyz[hba][1],'z':xyz[hba][2]},\n",
" 'radius':0.1, 'dashed':True});\n",
" \n",
"view\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "646f0097-ab40-4a21-bf64-411cb6c4290f",
"metadata": {},
"outputs": [],
"source": []
}
],
"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": "3.10.13"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment