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ptosco/fixedCtd.ipynb

Last active February 8, 2023 06:50
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Add fixed point to force field, set distance constraints to it and finally set a position constraint on it
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fixedCtd.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"import sys\n",
"import rdkit\n",
"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": {
"collapsed": true
},
"outputs": [],
"source": [
"m = Chem.MolFromSmiles('c1ccccc1CCCCCCCN')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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W1pr1M2TAIvxBfX09KioqpCpCWb4rtW7GjBkoKirCqFGjYDAYkJWVhW+//RZLliyBnZ2d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\nCImISGr/By+LjOK+nHsOAAAAAElFTkSuQmCC\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x213fffccda0>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"m"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mH = Chem.AddHs(m)\n",
"AllChem.EmbedMolecule(mH, useExpTorsionAnglePrefs = False, useBasicKnowledge = False)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x213fffccda0>"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"m"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div id=\"3dmolviewer_14776388786397417\" style=\"position: relative; width: 400px; height: 400px\">\n",
"<script>\n",
"if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('http://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
"$3Dmolpromise.done(function() {\n",
"var viewer = $3Dmol.createViewer($(\"#3dmolviewer_14776388786397417\"),{backgroundColor:\"white\"});\n",
"\tviewer.addModel(\"\\n RDKit 3D\\n\\n 35 35 0 0 0 0 0 0 0 0999 V2000\\n -3.2890 0.1351 1.4702 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.5441 -0.4429 1.4984 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.3301 -0.4195 0.3562 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.9936 0.5062 -0.6238 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.7371 1.1020 -0.6371 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.8439 0.9128 0.4110 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3920 0.9108 0.0417 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.1182 -0.4062 -0.6163 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.3131 -0.6442 -0.9681 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2839 0.2991 -0.3304 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.6709 -0.0403 -0.8612 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6093 -0.4566 0.2478 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9757 0.1669 0.0105 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.3298 0.9366 1.1976 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.5463 -0.2131 2.1838 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.7345 -1.2837 2.1674 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -6.2458 -1.0043 0.2636 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.6425 0.5685 -1.4953 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3764 1.3524 -1.6371 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8288 1.0496 0.9744 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2451 1.7834 -0.6288 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7323 -0.4453 -1.5503 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5526 -1.1931 0.0532 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.4640 -0.6333 -2.0620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5567 -1.6817 -0.6341 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.3388 0.1931 0.7623 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0749 1.3469 -0.5982 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1265 0.8174 -1.4045 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.6369 -0.8924 -1.5826 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7584 -1.5652 0.2708 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2195 -0.1962 1.2583 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7450 -0.6062 -0.2049 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9420 0.9107 -0.8268 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.6853 0.3004 1.9550 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4215 1.3486 1.5394 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 2 0\\n 2 3 1 0\\n 3 4 2 0\\n 4 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 11 1 0\\n 11 12 1 0\\n 12 13 1 0\\n 13 14 1 0\\n 6 1 1 0\\n 1 15 1 0\\n 2 16 1 0\\n 3 17 1 0\\n 4 18 1 0\\n 5 19 1 0\\n 7 20 1 0\\n 7 21 1 0\\n 8 22 1 0\\n 8 23 1 0\\n 9 24 1 0\\n 9 25 1 0\\n 10 26 1 0\\n 10 27 1 0\\n 11 28 1 0\\n 11 29 1 0\\n 12 30 1 0\\n 12 31 1 0\\n 13 32 1 0\\n 13 33 1 0\\n 14 34 1 0\\n 14 35 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer.setStyle({\"stick\": {}});\n",
"\tviewer.zoomTo();\n",
"viewer.render();\n",
"});\n",
"</script>"
],
"text/plain": [
"<py3Dmol.view at 0x21380b60518>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"p = py3Dmol.view(width = 400, height = 400)\n",
"p.addModel(Chem.MolToMolBlock(mH), 'sdf')\n",
"p.setStyle({'stick':{}})\n",
"p.zoomTo()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Get indices for the benzene ring heavy atoms"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"c = mH.GetSubstructMatch(Chem.MolFromSmarts('c1ccccc1'))"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(0, 1, 2, 3, 4, 5)"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"c"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Get the nitrogen index just to make sure that it moves during the minimization"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"nIdx = mH.GetSubstructMatch(Chem.MolFromSmarts('N'))"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(13,)"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"nIdx"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ctd = Chem.rdGeometry.Point3D(0.0, 0.0, 0.0)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"cH = mH.GetConformer()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This is where the nitrogen initially lies"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[5.329771716296932, 0.9365511048445183, 1.19756387379814]"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list(cH.GetAtomPosition(nIdx[0]))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Get the initial position of the centroid"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"for i in c:\n",
" ctd += cH.GetAtomPosition(i)\n",
"ctd /= float(len(c))"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"mp = AllChem.MMFFGetMoleculeProperties(mH)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ff = AllChem.MMFFGetMoleculeForceField(mH, mp)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Add an extra point to the forcefield for the centroid and get its index"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ep = ff.AddExtraPoint(ctd.x, ctd.y, ctd.z) - 1"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"35"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ep"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Compute the current distance between each benzene heavy atom and the centroid, and constrain it to stay as it is"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"for i in c:\n",
" d = cH.GetAtomPosition(i).Distance(ctd)\n",
" ff.MMFFAddDistanceConstraint(ep, i, False, d, d, 5.0)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Finally, add a position contraint on the centroid, so that it does not move from its current position"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ff.MMFFAddPositionConstraint(ep, 0.0, 5.0)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Check where the centroid initially lies"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[-4.122963502416918, 0.29894914861169203, 0.41247045505622665]"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list(ctd)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Re-initialize the force field as we added an additional point and the positions array needs to be updated, then minimize"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ff.Initialize()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Check the initial energy"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"69.80100037688061"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ff.CalcEnergy()"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ff.Minimize()"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
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"<script>\n",
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"$3Dmolpromise.done(function() {\n",
"var viewer = $3Dmol.createViewer($(\"#3dmolviewer_14776388791463912\"),{backgroundColor:\"white\"});\n",
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"text/plain": [
"<py3Dmol.view at 0x213fe7fd198>"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"p = py3Dmol.view(width = 400, height = 400)\n",
"p.addModel(Chem.MolToMolBlock(mH), 'sdf')\n",
"p.setStyle({'stick':{}})\n",
"p.zoomTo()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Check that the centroid hasn't moved during the minimization"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[-4.122963502416918, 0.29894914861169203, 0.41247045505622665]"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list(ff.GetExtraPointPos(0))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Check that the rest of the molecule has actually been optimized"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[6.517997450444338, 0.6256671030204412, 1.1085129129686233]"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list(cH.GetAtomPosition(nIdx[0]))"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"16.75989066251583"
]
},
"execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ff.CalcEnergy()"
]
}
],
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