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ljmartin/hbonds-with-rdkit.ipynb

Created January 2, 2024 09:03
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hbonds-with-rdkit.ipynb
{
"cells": [
{
"cell_type": "markdown",
"id": "6fa12a1b-fe24-4443-a124-7e6acd14b3e6",
"metadata": {},
"source": [
"# hbonds with rdkit"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "9143520e-ff3a-409a-9de9-fb63cdebe926",
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from rdkit import Chem\n",
"from scipy.spatial.distance import cdist"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "c1f02f79-bf6a-4f2b-b26a-ed5b6533b973",
"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",
" thank you to biotite for the math\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",
"\n",
"\n",
"def hbonds(combin, distance_cutoff = 3.5): \n",
" 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 on the first line, originally was [!$(*=[O,N,P,S])]\n",
" ##AND: changed the last term from $([nH0,o;+0]) to $([nD2,o;+0]),\n",
" ##because the original would catch the middle N in C-N(C)=N\n",
" HAcceptorSmarts = Chem.MolFromSmarts('[$([O;H1;v2]-[!$(*=[N,P,S])]),' +\n",
" '$([O;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),' +\n",
" '$([nD2,o;+0])]')\n",
"\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)])\n",
" \n",
" #get associated hydrogens of donors:\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)\n",
" dist_hbd_to_hba = cdist(xyz[hbds], xyz[hbas])\n",
"\n",
" #apply the distance cutoff between HBA and HBD atoms (not hydrogens)\n",
" ltcutoff = dist_hbd_to_hba<distance_cutoff\n",
" \n",
" #record triplets of hbd, h, and hba:\n",
" 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",
"\n",
" #calculate angles of HBD -> H -> HBA :\n",
" angles = angle(xyz[source_hbd], xyz[source_h], xyz[source_hba])\n",
"\n",
" #apply angle cutoff\n",
" #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 binary 'yes' and 'no' hbonds.\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(120)\n",
" \n",
" m = angles>cutoff_angle_rad\n",
"\n",
" return source_h, source_hba, m"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "3f276349-3312-4e9a-962f-103416875bfd",
"metadata": {},
"outputs": [],
"source": [
"pocket = Chem.MolFromPDBFile(f'./pock.pdb',removeHs=False)\n",
"ligand = Chem.MolFromMolFile('ligand.sdf', removeHs=False)\n"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "0e309776-e790-4019-af16-310868ffa5bc",
"metadata": {},
"outputs": [],
"source": [
"combin = Chem.CombineMols(ligand, pocket)\n",
"Chem.SanitizeMol(combin)\n",
"combin.UpdatePropertyCache()"
]
},
{
"cell_type": "markdown",
"id": "ad67e7c9-767e-4759-a7ca-a22dd61e852a",
"metadata": {},
"source": [
"perform the hbond calculation"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "163a7db9-0be6-4ce8-bd2c-cee0d0505932",
"metadata": {},
"outputs": [],
"source": [
"source_h, source_hba, has_hbond = hbonds(combin)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "73f642c4-555a-4910-a684-05b14b23e308",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"573 µs ± 12 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)\n"
]
}
],
"source": [
"%%timeit\n",
"source_h, source_hba, has_hbond = hbonds(combin)"
]
},
{
"cell_type": "markdown",
"id": "ec1d5be2-f01c-428a-a084-4d2d2b932597",
"metadata": {},
"source": [
"draw hbonds between acceptor and donor hydrogens"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "c16e5533-5636-4e73-90d7-59d01a95c52f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"21\n",
"30\n"
]
},
{
"data": {
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2.5430 22.8260 34.0810 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.6630 23.6550 32.8070 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1640 22.8810 31.5990 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1350 21.6300 31.6370 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.5940 23.5270 30.6150 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7740 24.9140 34.8090 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2310 23.9960 35.1450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8520 22.1190 33.9310 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4280 22.3950 34.2590 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2980 24.4070 32.9820 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7600 24.0250 32.5890 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7920 23.0300 37.6440 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7450 22.2870 38.9120 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 1.3260 22.3040 39.5450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7920 21.2240 39.7730 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8550 22.7640 39.8810 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6300 22.2430 41.2930 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.2330 22.3460 39.3600 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4200 23.8050 37.5760 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9480 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0\\n 13.6380 17.7100 43.8860 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.2390 16.4410 43.4600 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 13.8490 16.0360 42.0200 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.7080 15.5890 41.2380 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.9150 15.3270 44.4760 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.8480 14.1360 44.3970 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.5510 13.0620 45.4250 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.8700 13.2770 46.6130 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.0040 12.0040 45.0420 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.1080 17.7530 44.7330 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 15.2310 16.5680 43.4700 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.9820 15.0080 44.3070 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.9740 15.7130 45.3970 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 15.7840 14.4580 44.5380 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 14.7680 13.7320 43.4860 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 16.5280 42.3120 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 7.1910 17.1900 31.7380 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.9810 18.4700 32.4460 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 7.1720 18.4410 33.9800 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.6330 19.4460 34.5180 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.5670 18.8800 32.0300 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.3730 18.2120 30.6840 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.0710 16.8820 30.8260 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 7.6200 19.1400 32.0680 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8920 18.5510 32.6910 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4950 19.8740 31.9470 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.4010 18.0830 30.4890 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7900 18.7550 29.9550 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4610 16.1970 31.2240 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.4060 16.5560 29.9420 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 6.5740 16.4930 34.2030 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 3.0370 24.7650 35.4690 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1450 23.6290 35.3170 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 2.0420 22.7280 36.5740 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2650 21.7890 36.5720 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.5430 22.8260 34.0810 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.6630 23.6550 32.8070 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1640 22.8810 31.5990 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1350 21.6300 31.6370 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.5940 23.5270 30.6150 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7740 24.9140 34.8090 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2310 23.9960 35.1450 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8520 22.1190 33.9310 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4280 22.3950 34.2590 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2980 24.4070 32.9820 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7600 24.0250 32.5890 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7920 23.0300 37.6440 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7450 22.2870 38.9120 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 1.3260 22.3040 39.5450 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7920 21.2240 39.7730 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8550 22.7640 39.8810 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6300 22.2430 41.2930 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.2330 22.3460 39.3600 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4200 23.8050 37.5760 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9480 21.3330 38.6920 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8280 23.7630 39.9130 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3630 22.5700 41.8900 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7500 22.5740 41.6340 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6290 21.2430 41.2830 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.9390 22.6600 39.9950 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.2730 21.3500 39.2840 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.3880 22.7550 38.4610 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 1 3 2 0\\n 3 4 1 0\\n 3 5 1 0\\n 5 6 1 0\\n 6 7 1 0\\n 7 8 1 0\\n 8 9 2 0\\n 9 10 1 0\\n 9 11 1 0\\n 11 12 2 0\\n 12 13 1 0\\n 12 14 1 0\\n 5 15 2 0\\n 15 16 1 0\\n 16 17 1 0\\n 17 18 1 0\\n 18 19 1 0\\n 19 20 1 0\\n 20 21 1 0\\n 21 22 2 0\\n 22 23 1 0\\n 23 24 2 0\\n 24 25 1 0\\n 25 26 2 0\\n 26 27 1 0\\n 23 28 1 0\\n 28 29 1 0\\n 29 30 2 0\\n 16 31 2 0\\n 31 1 1 0\\n 14 8 1 0\\n 30 21 1 0\\n 28 27 2 0\\n 4 32 1 0\\n 4 33 1 0\\n 4 34 1 0\\n 6 35 1 0\\n 7 36 1 0\\n 7 37 1 0\\n 10 38 1 0\\n 10 39 1 0\\n 10 40 1 0\\n 13 41 1 0\\n 13 42 1 0\\n 13 43 1 0\\n 18 44 1 0\\n 18 45 1 0\\n 19 46 1 0\\n 19 47 1 0\\n 20 48 1 0\\n 20 49 1 0\\n 24 50 1 0\\n 25 51 1 0\\n 26 52 1 0\\n 27 53 1 0\\n 29 54 1 0\\n 30 55 1 0\\n 57 56 1 0\\n 58 57 1 0\\n 59 58 2 0\\n 60 57 1 0\\n 61 60 1 0\\n 62 61 2 0\\n 63 61 1 0\\n 64 62 1 0\\n 65 63 2 0\\n 66 65 1 0\\n 66 64 2 0\\n 67 66 1 0\\n 68 56 1 0\\n 57 69 1 1\\n 70 60 1 0\\n 71 60 1 0\\n 72 62 1 0\\n 73 63 1 0\\n 74 64 1 0\\n 75 65 1 0\\n 76 67 1 0\\n 77 58 1 0\\n 78 77 1 0\\n 79 78 1 0\\n 80 79 2 0\\n 81 78 1 0\\n 82 81 1 0\\n 83 82 1 0\\n 84 82 2 0\\n 85 83 2 0\\n 86 85 1 0\\n 86 84 1 0\\n 87 77 1 0\\n 78 88 1 1\\n 89 81 1 0\\n 90 81 1 0\\n 91 84 1 0\\n 92 85 1 0\\n 93 86 1 0\\n 95 94 1 0\\n 96 95 1 0\\n 97 96 2 0\\n 98 95 1 0\\n 99 98 1 0\\n100 99 1 0\\n101 99 1 0\\n102 94 1 0\\n 95103 1 1\\n104 98 1 0\\n105 98 1 0\\n106 99 1 0\\n107100 1 0\\n108100 1 0\\n109100 1 0\\n110101 1 0\\n111101 1 0\\n112101 1 0\\n114113 1 0\\n115114 1 0\\n116115 2 0\\n117114 1 0\\n118117 1 0\\n119118 2 0\\n120118 1 0\\n121113 1 0\\n114122 1 1\\n123117 1 0\\n124117 1 0\\n125115 1 0\\n126125 1 0\\n127126 1 0\\n128127 2 0\\n129126 1 0\\n130129 1 0\\n131130 1 0\\n132130 1 0\\n133125 1 0\\n126134 1 6\\n135129 1 0\\n136129 1 0\\n137130 1 0\\n138131 1 0\\n139131 1 0\\n140131 1 0\\n141132 1 0\\n142132 1 0\\n143132 1 0\\n145144 1 0\\n146145 1 0\\n147146 2 0\\n148145 1 0\\n149148 1 0\\n150144 1 0\\n145151 1 1\\n152148 1 0\\n153148 1 0\\n154149 1 0\\n155146 1 0\\n156155 1 0\\n157156 1 0\\n158157 2 0\\n159156 1 0\\n160159 1 0\\n161159 1 0\\n162155 1 0\\n156163 1 6\\n164159 1 0\\n165160 1 0\\n166160 1 0\\n167160 1 0\\n168161 1 0\\n169161 1 0\\n170161 1 0\\n172171 1 0\\n173172 1 0\\n174173 2 0\\n175172 1 0\\n176175 1 0\\n177175 1 0\\n178176 1 0\\n179171 1 0\\n172180 1 1\\n175181 1 1\\n182176 1 0\\n183176 1 0\\n184177 1 0\\n185177 1 0\\n186177 1 0\\n187178 1 0\\n188178 1 0\\n189178 1 0\\n190173 1 0\\n191190 1 0\\n192191 1 0\\n193192 2 0\\n194191 1 0\\n195194 1 0\\n196195 2 0\\n197195 1 0\\n198196 1 0\\n199197 2 0\\n200198 2 0\\n200199 1 0\\n201200 1 0\\n202190 1 0\\n191203 1 6\\n204194 1 0\\n205194 1 0\\n206196 1 0\\n207197 1 0\\n208198 1 0\\n209199 1 0\\n210201 1 0\\n212211 1 0\\n213212 1 0\\n214213 2 0\\n215212 1 0\\n216215 1 0\\n217216 1 0\\n218217 2 0\\n219217 1 0\\n220211 1 0\\n212221 1 6\\n222215 1 0\\n223215 1 0\\n224216 1 0\\n225216 1 0\\n226213 1 0\\n227226 1 0\\n228227 1 0\\n229228 2 0\\n230227 1 0\\n231230 1 0\\n232231 2 0\\n233231 1 0\\n234232 1 0\\n235233 2 0\\n236235 1 0\\n236234 2 0\\n237226 1 0\\n227238 1 6\\n239230 1 0\\n240230 1 0\\n241232 1 0\\n242233 1 0\\n243234 1 0\\n244235 1 0\\n245236 1 0\\n247246 1 0\\n248247 1 0\\n249248 2 0\\n250247 1 0\\n251250 1 0\\n252251 1 0\\n252246 1 0\\n247253 1 6\\n254250 1 0\\n255250 1 0\\n256251 1 0\\n257251 1 0\\n258252 1 0\\n259252 1 0\\n260248 1 0\\n261260 1 0\\n262261 1 0\\n263262 2 0\\n264261 1 0\\n265264 1 0\\n266265 1 0\\n267266 1 0\\n268260 1 0\\n261269 1 1\\n270264 1 0\\n271264 1 0\\n272265 1 0\\n273265 1 0\\n274267 1 0\\n275267 1 0\\n276267 1 0\\n278277 1 0\\n279278 1 0\\n280279 2 0\\n281278 1 0\\n282281 1 0\\n283282 1 0\\n284283 2 0\\n285283 1 0\\n286277 1 0\\n278287 1 6\\n288281 1 0\\n289281 1 0\\n290282 1 0\\n291282 1 0\\n292279 1 0\\n293292 1 0\\n294293 1 0\\n295294 2 0\\n296293 1 0\\n297296 1 0\\n298296 1 0\\n299292 1 0\\n293300 1 6\\n301296 1 0\\n302297 1 0\\n303297 1 0\\n304297 1 0\\n305298 1 0\\n306298 1 0\\n307298 1 0\\n309308 1 0\\n310309 1 0\\n311310 2 0\\n312308 1 0\\n313309 1 0\\n314309 1 0\\n315310 1 0\\n316315 1 0\\n317316 1 0\\n318317 2 0\\n319316 1 0\\n320319 1 0\\n321320 1 0\\n322321 2 0\\n323321 1 0\\n324315 1 0\\n316325 1 1\\n326319 1 0\\n327319 1 0\\n328320 1 0\\n329320 1 0\\n330323 1 0\\n331323 1 0\\n333332 1 0\\n334333 1 0\\n335334 2 0\\n336333 1 0\\n337336 1 0\\n338337 2 0\\n339337 1 0\\n340338 1 0\\n341339 2 0\\n342340 2 0\\n342341 1 0\\n343332 1 0\\n333344 1 6\\n345336 1 0\\n346336 1 0\\n347338 1 0\\n348339 1 0\\n349340 1 0\\n350341 1 0\\n351342 1 0\\nM END\\n\",\"sdf\");\n",
"\t\tviewer_1704186055730783.getModel().setStyle({},{\"stick\": {\"colorscheme\": \"orangeCarbon\"}});\n",
"\tviewer_1704186055730783.zoomTo();\n",
"\tviewer_1704186055730783.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 3.733, \"y\": 17.867, \"z\": 40.071}, \"end\": {\"x\": 3.2504, \"y\": 17.3439, \"z\": 38.2343}, \"radius\": 0.1, \"dashed\": true});\n",
"\tviewer_1704186055730783.addCylinder({\"color\": \"darkblue\", \"start\": {\"x\": 2.276, \"y\": 16.407, \"z\": 43.777}, \"end\": {\"x\": 3.0731, \"y\": 14.6124, \"z\": 44.2631}, \"radius\": 0.1, \"dashed\": true});\n",
"viewer_1704186055730783.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/plain": [
"<py3Dmol.view at 0x7fc0f8520580>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import py3Dmol\n",
"\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\n",
"\n",
"# draw hbonds between acceptor and donor hydrogens\n",
"nligand = ligand.GetNumAtoms()\n",
"is_ligand = (source_h<nligand) | (source_hba<nligand)\n",
"\n",
"xyz = combin.GetConformer(0).GetPositions()\n",
"view = viewProt(combin)\n",
"\n",
"for hbd, hba in zip(source_h[has_hbond & is_ligand], source_hba[has_hbond &is_ligand]):\n",
"\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"
]
}
],
"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
}
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