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ptosco/o3a_restraints.ipynb

Created June 18, 2019 13:39
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O3A alignment with restraints
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o3a_restraints.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"import py3Dmol"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"def drawit(mols, p=None, width=400, height=300):\n",
" if p is None:\n",
" p = py3Dmol.view(width=width, height=height)\n",
" p.removeAllModels()\n",
" if (not isinstance(mols, list)):\n",
" mols = [mols]\n",
" for m, conf_id in mols:\n",
" if (conf_id == -1):\n",
" conf_ids = [c.GetId() for c in m.GetConformers()]\n",
" else:\n",
" conf_ids = [conf_id]\n",
" for cid in conf_ids:\n",
" mb = Chem.MolToMolBlock(m, confId=cid)\n",
" p.addModel(mb,'sdf')\n",
" p.setStyle({'stick':{}})\n",
" p.setBackgroundColor('0xeeeeee')\n",
" p.zoomTo()\n",
" return p.show()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"ref_smi = \"C1CCCCC1CCCC1CNCCC1\""
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"query_smi = \"N1CC(CC)CCC1\""
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"ref_mol = Chem.MolFromSmiles(ref_smi)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x252e962a850>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ref_mol"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"query_mol = Chem.MolFromSmiles(query_smi)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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RI0bI4/EoMTFRI0eOVMeOHU1HBhyBIgSakfnz5ysvL0/l5eXy+Xzyer3y+XyKj49XixZcLQVcD0UINDNVVVVq3bq16RhA2KAIAQBW41gJAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAahQhAMBqFCEAwGoUIQDAav8LrrtGaKhCg2MAAAAASUVORK5CYII=\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x252e962e4e0>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"query_mol"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ref_3d = Chem.AddHs(ref_mol)\n",
"AllChem.EmbedMolecule(ref_3d)\n",
"AllChem.MMFFOptimizeMolecule(ref_3d, nonBondedThresh=100.0)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This is the 3D structure of the reference:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
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" <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"drawit((ref_3d, -1))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now I generate 25 conformations for the query:"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[(0, 6.434917277700814),\n",
" (0, -1.052469370349446),\n",
" (0, -0.23505038677481543),\n",
" (0, 1.1997422952838075),\n",
" (0, -0.23505038677203857),\n",
" (0, 7.280227050051471),\n",
" (0, -0.23505038567558495),\n",
" (0, 9.676841241598177),\n",
" (0, 0.16608597479334555),\n",
" (0, 1.1282121470743727),\n",
" (0, 1.1282121449498401),\n",
" (0, 7.922127247651736),\n",
" (0, 7.106166583898964),\n",
" (0, 6.970282015419307),\n",
" (0, 7.156480120590095),\n",
" (0, 7.831207419132442),\n",
" (0, -1.1106049376542138),\n",
" (0, -1.0524693700742567),\n",
" (0, -0.17299876606123532),\n",
" (0, 5.965608402042746),\n",
" (0, 0.16608596761051636),\n",
" (0, 7.931544056142387),\n",
" (0, 5.573348938476216),\n",
" (0, -1.1106049382376288),\n",
" (0, -0.23505038608454107)]"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"query_3d = Chem.AddHs(query_mol)\n",
"AllChem.EmbedMultipleConfs(query_3d, numConfs=25)\n",
"AllChem.MMFFOptimizeMoleculeConfs(query_3d, nonBondedThresh=100.0)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"And I generate an `O3A` object for each conformation. I push the `O3A` objects to a list, each as a tuple with the respective `ConfId`:"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"o3a_list = [(cid, AllChem.GetO3A(query_3d, ref_3d, prbCid=cid\n",
" )) for cid in range(query_3d.GetNumConformers())]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"I sort the list by decreasing `O3A` score such that the first element will be the `(ConfId, O3A)` tuple corresponding the conformation with the best O3A score:"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"o3a_list.sort(key=lambda o: o[1].Score(), reverse=True)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[(13, <rdkit.Chem.rdMolAlign.O3A at 0x252e975fb20>),\n",
" (14, <rdkit.Chem.rdMolAlign.O3A at 0x252e975f030>),\n",
" (1, <rdkit.Chem.rdMolAlign.O3A at 0x252f1365d00>),\n",
" (15, <rdkit.Chem.rdMolAlign.O3A at 0x252e975f990>),\n",
" (18, <rdkit.Chem.rdMolAlign.O3A at 0x252f13537b0>),\n",
" (17, <rdkit.Chem.rdMolAlign.O3A at 0x252f1353710>),\n",
" (11, <rdkit.Chem.rdMolAlign.O3A at 0x252e975fda0>),\n",
" (9, <rdkit.Chem.rdMolAlign.O3A at 0x252e975f850>),\n",
" (10, <rdkit.Chem.rdMolAlign.O3A at 0x252e975fa80>),\n",
" (22, <rdkit.Chem.rdMolAlign.O3A at 0x252f1353e90>),\n",
" (23, <rdkit.Chem.rdMolAlign.O3A at 0x252f1353620>),\n",
" (2, <rdkit.Chem.rdMolAlign.O3A at 0x252e8365a30>),\n",
" (4, <rdkit.Chem.rdMolAlign.O3A at 0x252e8365990>),\n",
" (6, <rdkit.Chem.rdMolAlign.O3A at 0x252e8365120>),\n",
" (21, <rdkit.Chem.rdMolAlign.O3A at 0x252f13535d0>),\n",
" (24, <rdkit.Chem.rdMolAlign.O3A at 0x252f1353800>),\n",
" (16, <rdkit.Chem.rdMolAlign.O3A at 0x252d17efc10>),\n",
" (7, <rdkit.Chem.rdMolAlign.O3A at 0x252e8365490>),\n",
" (12, <rdkit.Chem.rdMolAlign.O3A at 0x252e975fdf0>),\n",
" (19, <rdkit.Chem.rdMolAlign.O3A at 0x252f1353b70>),\n",
" (5, <rdkit.Chem.rdMolAlign.O3A at 0x252e8365300>),\n",
" (0, <rdkit.Chem.rdMolAlign.O3A at 0x252f1365b70>),\n",
" (8, <rdkit.Chem.rdMolAlign.O3A at 0x252e975fb70>),\n",
" (20, <rdkit.Chem.rdMolAlign.O3A at 0x252f1353d00>),\n",
" (3, <rdkit.Chem.rdMolAlign.O3A at 0x252e83655d0>)]"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o3a_list"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"best_o3a = o3a_list[0]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This is the reciprocal arrangement of query and reference before I apply any alignment. As expected, they are not aligned yet:"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
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]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"drawit([(ref_3d, -1), (query_3d, best_o3a[0])])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now I make a copy of `query_3d` such that I have a clean copy not affected by any transformation:"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
"query_3d_copy = Chem.Mol(query_3d)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now I do the alignment:"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.24382599379689626"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"best_o3a[1].Align()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"I can now verify that that conformation of `query_3d` is now indeed aligned against `ref3d`. AS expected, the piperidine ring in `query_3d` matches the piperidine ring in `ref_3d`:"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
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"\tviewer_15608646584233444.removeAllModels();\n",
"\tviewer_15608646584233444.addModel(\"\\n RDKit 3D\\n\\n 42 43 0 0 0 0 0 0 0 0999 V2000\\n -3.3691 -1.3739 0.8807 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.6934 -0.6196 0.7251 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.4936 0.8859 0.6378 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.6024 1.2685 -0.5440 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.5513 0.2079 -0.8865 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1396 -0.6033 0.3496 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.9820 -1.5817 0.0621 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.4191 -1.0345 0.3760 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8399 0.1613 -0.4816 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3185 0.5796 -0.3504 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7573 0.8196 1.1003 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.1079 1.3766 1.2143 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.0002 1.0240 0.1086 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.6911 -0.3453 -0.4853 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2712 -0.4058 -1.0515 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4671 -2.3436 0.3760 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2033 -1.5997 1.9419 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.1990 -0.9652 -0.1857 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.3582 -0.8672 1.5604 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.4603 1.3943 0.5500 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0376 1.2433 1.5697 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2199 1.4500 -1.4320 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1075 2.2204 -0.3159 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.6972 0.6998 -1.3595 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9643 -0.4725 -1.6434 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8205 0.0947 1.1355 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.1060 -2.4786 0.6834 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0211 -1.9242 -0.9793 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1302 -1.8570 0.2427 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.4579 -0.7599 1.4369 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2260 1.0253 -0.1998 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.6278 -0.0498 -1.5371 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4053 1.5399 -0.8808 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7367 -0.1223 1.6614 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0554 1.4952 1.6028 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0616 2.3921 1.2925 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9258 1.7859 -0.6773 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0328 1.0451 0.4731 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 -1.1127 0.2912 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4130 -0.5903 -1.2726 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9153 -1.4394 -0.9875 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2947 -0.1630 -2.1216 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 5 6 1 0\\n 6 7 1 0\\n 7 8 1 0\\n 8 9 1 0\\n 9 10 1 0\\n 10 11 1 0\\n 11 12 1 0\\n 12 13 1 0\\n 13 14 1 0\\n 14 15 1 0\\n 6 1 1 0\\n 15 10 1 0\\n 1 16 1 0\\n 1 17 1 0\\n 2 18 1 0\\n 2 19 1 0\\n 3 20 1 0\\n 3 21 1 0\\n 4 22 1 0\\n 4 23 1 0\\n 5 24 1 0\\n 5 25 1 0\\n 6 26 1 0\\n 7 27 1 0\\n 7 28 1 0\\n 8 29 1 0\\n 8 30 1 0\\n 9 31 1 0\\n 9 32 1 0\\n 10 33 1 0\\n 11 34 1 0\\n 11 35 1 0\\n 12 36 1 0\\n 13 37 1 0\\n 13 38 1 0\\n 14 39 1 0\\n 14 40 1 0\\n 15 41 1 0\\n 15 42 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_15608646584233444.addModel(\"\\n RDKit 3D\\n\\n 23 23 0 0 0 0 0 0 0 0999 V2000\\n 4.1308 1.2350 1.2569 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.6932 1.1367 0.9803 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3469 0.4838 -0.3743 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8668 0.0732 -0.4766 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.4368 -1.0864 0.4114 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3191 -0.6615 -0.6700 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.7704 -0.1669 -0.6620 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9482 1.1741 0.0536 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3237 2.0894 1.7776 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2441 0.5849 1.8114 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2548 2.1422 1.0016 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4978 1.2467 -1.1525 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2392 0.9434 -0.2476 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.6502 -0.1971 -1.5178 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.6002 -0.8721 1.4707 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6327 -1.2792 0.2756 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9694 -2.0069 0.1559 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2170 -1.4455 0.0905 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.0927 -1.1286 -1.6355 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4008 -0.9313 -0.1907 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1286 -0.0640 -1.6934 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0033 1.2965 0.3226 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.7008 2.0066 -0.6166 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 3 6 1 0\\n 6 7 1 0\\n 7 8 1 0\\n 8 1 1 0\\n 1 9 1 0\\n 2 10 1 0\\n 2 11 1 0\\n 3 12 1 0\\n 4 13 1 0\\n 4 14 1 0\\n 5 15 1 0\\n 5 16 1 0\\n 5 17 1 0\\n 6 18 1 0\\n 6 19 1 0\\n 7 20 1 0\\n 7 21 1 0\\n 8 22 1 0\\n 8 23 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_15608646584233444.setStyle({\"stick\": {}});\n",
"\tviewer_15608646584233444.setBackgroundColor(\"0xeeeeee\");\n",
"\tviewer_15608646584233444.zoomTo();\n",
"viewer_15608646584233444.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"drawit([(ref_3d, -1), (query_3d, best_o3a[0])])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
" Instead, I will now attempt to align `query_3d_copy` forcing the match of its piperidine ring to the reference cyclohexane ring:"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"piperidine_query = Chem.MolFromSmarts(\"CC1CNCCC1\")"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
"cyclohexane_query = Chem.MolFromSmarts(\"CC1CCCCC1\")"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x252e8365260>"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"piperidine_query"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"data": {
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"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x252e975ebc0>"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cyclohexane_query"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
"query_3d_piperidine_indices = query_3d.GetSubstructMatch(piperidine_query)"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(3, 2, 1, 0, 7, 6, 5)"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"query_3d_piperidine_indices"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [],
"source": [
"ref_3d_cyclohexane_indices = ref_3d.GetSubstructMatch(cyclohexane_query)"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(6, 5, 0, 1, 2, 3, 4)"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ref_3d_cyclohexane_indices"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"I request a 1-1 match of piperdine atoms against cyclohexane atoms:"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"constraint_map = list(zip(query_3d_piperidine_indices,\n",
" ref_3d_cyclohexane_indices))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This is going to be my constraints map:"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[(3, 6), (2, 5), (1, 0), (0, 1), (7, 2), (6, 3), (5, 4)]"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"constraint_map"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [],
"source": [
"o3a_list2 = [(cid, AllChem.GetO3A(query_3d_copy, ref_3d, prbCid=cid,\n",
" constraintMap=constraint_map)) for cid in range(\n",
" query_3d_copy.GetNumConformers())]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"I sort the list by decreasing `O3A` score such that the first element will be the `(ConfId, O3A)` tuple corresponding the conformation with the best O3A score:"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [],
"source": [
"o3a_list2.sort(key=lambda o: o[1].Score(), reverse=True)"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[(22, <rdkit.Chem.rdMolAlign.O3A at 0x252f254da80>),\n",
" (23, <rdkit.Chem.rdMolAlign.O3A at 0x252f254dd50>),\n",
" (4, <rdkit.Chem.rdMolAlign.O3A at 0x252f254dee0>),\n",
" (2, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d800>),\n",
" (6, <rdkit.Chem.rdMolAlign.O3A at 0x252f254ddf0>),\n",
" (24, <rdkit.Chem.rdMolAlign.O3A at 0x252f254dc10>),\n",
" (16, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d530>),\n",
" (15, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d1c0>),\n",
" (18, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d300>),\n",
" (17, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d990>),\n",
" (14, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d170>),\n",
" (19, <rdkit.Chem.rdMolAlign.O3A at 0x252f254df30>),\n",
" (13, <rdkit.Chem.rdMolAlign.O3A at 0x252f254dda0>),\n",
" (7, <rdkit.Chem.rdMolAlign.O3A at 0x252f254df80>),\n",
" (12, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d940>),\n",
" (0, <rdkit.Chem.rdMolAlign.O3A at 0x252e9626da0>),\n",
" (1, <rdkit.Chem.rdMolAlign.O3A at 0x252e9626490>),\n",
" (20, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d120>),\n",
" (3, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d670>),\n",
" (5, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d8a0>),\n",
" (21, <rdkit.Chem.rdMolAlign.O3A at 0x252f254dd00>),\n",
" (8, <rdkit.Chem.rdMolAlign.O3A at 0x252f254db20>),\n",
" (9, <rdkit.Chem.rdMolAlign.O3A at 0x252f254dad0>),\n",
" (10, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d620>),\n",
" (11, <rdkit.Chem.rdMolAlign.O3A at 0x252f254d4e0>)]"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o3a_list2"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [],
"source": [
"best_o3a2 = o3a_list2[0]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now I do the alignment:"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.31097391168230054"
]
},
"execution_count": 34,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"best_o3a2[1].Align()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"I can now verify that this tame the piperidine ring in `query_3d` indeed aligned against the cyclohexane ring in `ring_3d`:"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [
{
"data": {
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" <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"drawit([(ref_3d, -1), (query_3d_copy, best_o3a2[0])])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
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