Prelim dc.dock setup (06a6a5c9) · Commits · 钟慕尧 / deepchem

deepchem/init.py

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		@@ -14,3 +14,4 @@ import deepchem.nn
		import deepchem.splits
		import deepchem.trans
		import deepchem.utils
		import deepchem.dock

deepchem/dock/init.py

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		"""
		Imports all submodules
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		from deepchem.dock.pose_generation import VinaPoseGenerator

deepchem/dock/pose_generation.py

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		"""
		Generates protein-ligand docked poses using Autodock Vina.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "GPL"

		import os
		from subprocess import call

		class VinaPoseGenerator(object):

		def __init__(self):
		"""Initializes Vina Pose generation"""
		current_dir = os.path.dirname(os.path.realpath(__file__))
		self.vina_dir = os.path.join(current_dir, "autodock_vina_1_1_2_linux_x86")
		if not os.path.exists(self.vina_dir):
		print("Vina not available. Downloading")
		wget_cmd = "wget http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz"
		call(wget_cmd.split())
		print("Downloaded Vina. Extracting")
		download_cmd = "tar xzvf autodock_vina_1_1_2_linux_x86.tgz"
		call(download_cmd.split())
		print("Moving to final location")
		mv_cmd = "mv autodock_vina_1_1_2_linux_x86 %s" % current_dir
		call(mv_cmd.split())
		print("Cleanup: removing downloaded vina tar.gz")
		rm_cmd = "rm autodock_vina_1_1_2_linux_x86.tgz"
		call(rm_cmd.split())
		self.vina_cmd = os.path.join(self.vina_dir, "bin/vina")


		def generate_poses(self, pdb_file, ligand_file):
		"""Generates the docked complex and outputs the file."""
		pass

deepchem/dock/tests/1jld_ligand.sdf

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		1jld_ligand

		Created by X-TOOL on Fri Sep 26 17:34:13 2014
		99101 0 0 0 0 0 0 0 0999 V2000
		51.4700 25.4350 9.3670 O 0 0 0 1 0 1
		50.5590 24.7130 8.9000 C 0 0 0 1 0 3
		48.1710 24.2520 8.6240 N 0 0 0 1 0 2
		49.1780 25.0630 9.0140 C 0 0 0 1 0 3
		48.7950 26.2640 9.6010 C 0 0 0 2 0 3
		47.4710 26.5910 9.7860 C 0 0 0 2 0 3
		46.4930 25.6790 9.4010 C 0 0 0 1 0 3
		45.1340 25.9660 9.6050 C 0 0 0 2 0 3
		44.1780 25.0330 9.2070 C 0 0 0 2 0 3
		44.5670 23.8590 8.5830 C 0 0 0 2 0 3
		45.9120 23.5790 8.4230 C 0 0 0 2 0 3
		46.8650 24.4980 8.8280 C 0 0 0 1 0 3
		50.8130 23.5560 8.2440 N 0 0 0 2 0 3
		52.0030 22.8000 7.8570 C 0 0 0 2 0 4
		51.9010 22.5860 6.3820 C 0 0 0 1 0 3
		51.5660 21.5230 5.8780 O 0 0 0 1 0 1
		52.2940 21.5030 8.6990 C 0 0 0 2 0 4
		52.2630 21.7830 10.0830 O 0 0 0 2 0 2
		53.6660 20.9320 8.4200 C 0 0 0 4 0 4
		53.0020 23.2400 1.9740 C 0 0 0 3 0 4
		52.1260 23.6900 5.6800 N 0 0 0 2 0 3
		51.9530 23.7360 4.2490 C 0 0 0 2 0 4
		51.4800 25.1470 3.9090 C 0 0 0 3 0 4
		50.2000 25.4940 4.6090 C 0 0 0 1 0 3
		49.0140 24.8240 4.3060 C 0 0 0 2 0 3
		50.1550 26.4840 5.5930 C 0 0 0 2 0 3
		47.8180 25.1670 4.9520 C 0 0 0 2 0 3
		48.9750 26.8020 6.2710 C 0 0 0 2 0 3
		47.7900 26.1530 5.9400 C 0 0 0 2 0 3
		53.1780 23.2420 3.4810 C 0 0 0 2 0 4
		54.2820 24.0700 3.7580 O 0 0 0 2 0 2
		53.8160 22.1940 1.3720 N 0 0 0 2 0 3
		53.3310 21.0160 1.0390 C 0 0 0 1 0 3
		52.1730 20.6780 1.2170 O 0 0 0 1 0 1
		54.3530 20.0750 0.4120 C 0 0 0 2 0 4
		55.0150 19.0140 1.3740 C 0 0 0 1 0 4
		54.1180 17.8190 1.6870 C 0 0 0 4 0 4
		56.2290 18.4800 0.6270 C 0 0 0 4 0 4
		55.3950 19.6960 2.6770 C 0 0 0 4 0 4
		53.7680 19.5300 -0.9070 C 0 0 0 3 0 4
		53.5070 20.6100 -1.9390 C 0 0 0 1 0 3
		54.4620 21.3520 -2.5570 O 0 0 0 1 0 1
		52.2540 20.8780 -2.3260 N 0 0 0 2 0 3
		51.9150 21.8640 -3.3120 C 0 0 0 2 0 4
		51.3430 21.1730 -4.5400 C 0 0 0 3 0 4
		52.0920 19.8800 -4.9720 C 0 0 0 4 0 4
		50.8200 22.7680 -2.7800 C 0 0 0 3 0 4
		51.1740 23.6170 -1.5270 C 0 0 0 4 0 4
		49.5601 26.9617 9.9216 H 0 0 0 1 0 1
		47.1946 27.5431 10.2243 H 0 0 0 1 0 1
		44.8324 26.8999 10.0655 H 0 0 0 1 0 1
		43.1266 25.2267 9.3864 H 0 0 0 1 0 1
		43.8197 23.1620 8.2213 H 0 0 0 1 0 1
		46.2203 22.6389 7.9800 H 0 0 0 1 0 1
		49.9718 23.1029 7.9489 H 0 0 0 1 0 1
		52.8688 23.4564 8.0289 H 0 0 0 1 0 1
		51.5289 20.7511 8.4556 H 0 0 0 1 0 1
		52.4410 20.9870 10.5700 H 0 0 0 1 0 1
		53.8190 20.0303 9.0311 H 0 0 0 1 0 1
		54.4325 21.6798 8.6715 H 0 0 0 1 0 1
		53.7446 20.6704 7.3545 H 0 0 0 1 0 1
		53.3098 24.2163 1.5713 H 0 0 0 1 0 1
		51.9440 23.0607 1.7324 H 0 0 0 1 0 1
		52.4248 24.5157 6.1585 H 0 0 0 1 0 1
		51.1353 23.0479 3.9885 H 0 0 0 1 0 1
		51.3208 25.2162 2.8228 H 0 0 0 1 0 1
		52.2565 25.8647 4.2123 H 0 0 0 1 0 1
		49.0175 24.0323 3.5655 H 0 0 0 1 0 1
		51.0633 27.0224 5.8385 H 0 0 0 1 0 1
		46.9002 24.6584 4.6800 H 0 0 0 1 0 1
		48.9832 27.5527 7.0530 H 0 0 0 1 0 1
		46.8624 26.4080 6.4397 H 0 0 0 1 0 1
		53.3964 22.2158 3.8114 H 0 0 0 1 0 1
		54.4273 24.0988 4.6964 H 0 0 0 1 0 1
		54.7845 22.3779 1.2043 H 0 0 0 1 0 1
		55.1940 20.7180 0.1131 H 0 0 0 1 0 1
		54.6483 17.1287 2.3596 H 0 0 0 1 0 1
		53.8631 17.2972 0.7528 H 0 0 0 1 0 1
		53.1964 18.1700 2.1742 H 0 0 0 1 0 1
		56.9041 19.3131 0.3815 H 0 0 0 1 0 1
		55.9015 17.9879 -0.3007 H 0 0 0 1 0 1
		56.7588 17.7532 1.2603 H 0 0 0 1 0 1
		56.0421 20.5596 2.4637 H 0 0 0 1 0 1
		55.9336 18.9843 3.3199 H 0 0 0 1 0 1
		54.4846 20.0381 3.1909 H 0 0 0 1 0 1
		52.8176 19.0230 -0.6843 H 0 0 0 1 0 1
		54.4791 18.8061 -1.3315 H 0 0 0 1 0 1
		51.5101 20.3605 -1.9030 H 0 0 0 1 0 1
		52.8061 22.4517 -3.5774 H 0 0 0 1 0 1
		51.3766 21.8838 -5.3788 H 0 0 0 1 0 1
		50.2973 20.9069 -4.3264 H 0 0 0 1 0 1
		51.6068 19.4557 -5.8634 H 0 0 0 1 0 1
		52.0597 19.1465 -4.1529 H 0 0 0 1 0 1
		53.1391 20.1233 -5.2053 H 0 0 0 1 0 1
		49.9583 22.1345 -2.5227 H 0 0 0 1 0 1
		50.5376 23.4617 -3.5856 H 0 0 0 1 0 1
		50.3046 24.2266 -1.2396 H 0 0 0 1 0 1
		52.0235 24.2762 -1.7588 H 0 0 0 1 0 1
		51.4443 22.9491 -0.6959 H 0 0 0 1 0 1
		2 1 2 0 0 2
		2 4 1 0 0 2
		4 3 4 0 0 1
		4 5 4 0 0 1
		5 6 4 0 0 1
		6 7 4 0 0 1
		12 7 4 0 0 1
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		8 9 4 0 0 1
		10 9 4 0 0 1
		11 10 4 0 0 1
		12 11 4 0 0 1
		3 12 4 0 0 1
		15 14 1 0 0 2
		14 17 1 0 0 2
		14 13 1 0 0 2
		17 18 1 0 0 2
		17 19 1 0 0 2
		15 16 2 0 0 2
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		22 30 1 0 0 2
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		24 26 4 0 0 1
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		28 29 4 0 0 1
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		33 34 2 0 0 2
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		36 38 1 0 0 2
		36 37 1 0 0 2
		40 41 1 0 0 2
		41 43 1 0 0 2
		41 42 2 0 0 2
		43 44 1 0 0 2
		44 47 1 0 0 2
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		45 46 1 0 0 2
		47 48 1 0 0 2
		13 2 1 0 0 2
		20 32 1 0 0 2
		21 15 1 0 0 2
		5 49 1 0 0 2
		6 50 1 0 0 2
		8 51 1 0 0 2
		9 52 1 0 0 2
		10 53 1 0 0 2
		11 54 1 0 0 2
		13 55 1 0 0 2
		14 56 1 0 0 2
		17 57 1 0 0 2
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		19 61 1 0 0 2
		20 62 1 0 0 2
		20 63 1 0 0 2
		21 64 1 0 0 2
		22 65 1 0 0 2
		23 66 1 0 0 2
		23 67 1 0 0 2
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		26 69 1 0 0 2
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		28 71 1 0 0 2
		29 72 1 0 0 2
		30 73 1 0 0 2
		31 74 1 0 0 2
		32 75 1 0 0 2
		35 76 1 0 0 2
		37 77 1 0 0 2
		37 78 1 0 0 2
		37 79 1 0 0 2
		38 80 1 0 0 2
		38 81 1 0 0 2
		38 82 1 0 0 2
		39 83 1 0 0 2
		39 84 1 0 0 2
		39 85 1 0 0 2
		40 86 1 0 0 2
		40 87 1 0 0 2
		43 88 1 0 0 2
		44 89 1 0 0 2
		45 90 1 0 0 2
		45 91 1 0 0 2
		46 92 1 0 0 2
		46 93 1 0 0 2
		46 94 1 0 0 2
		47 95 1 0 0 2
		47 96 1 0 0 2
		48 97 1 0 0 2
		48 98 1 0 0 2
		48 99 1 0 0 2
		M END
		> <MOLECULAR_FORMULA>
		C37H51N5O6

		> <MOLECULAR_WEIGHT>
		661.4

		> <NUM_HB_ATOMS>
		11

		> <NUM_ROTOR>
		15

		> <XLOGP2>
		4.08

		$$$$

deepchem/dock/tests/1jld_protein.pdb

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