Merge pull request #444 from rbharath/vina_tf (53718b6d) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -23,3 +23,4 @@ from deepchem.feat.nnscore_utils import hydrogenate_and_compute_partial_charges
		from deepchem.feat.binding_pocket_features import BindingPocketFeaturizer
		from deepchem.feat.one_hot import OneHotFeaturizer
		from deepchem.feat.raw_featurizer import RawFeaturizer
		from deepchem.feat.atomic_coordinates import AtomicCoordinates

deepchem/feat/atomic_coordinates.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -177,7 +177,7 @@ class NeighborListComplexAtomicCoordinates(ComplexFeaturizer):
		complex_pdb: list
		Should be a list of lines of the PDB file.
		"""
		mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file)
		mol_coords, _ = rdkit_util.load_molecule(mol_pdb_file)
		protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file)
		system_coords = rdkit_util.merge_molecules_xyz(mol_coords, protein_coords)

deepchem/models/tf_new_models/multitask_classifier.py

+1 −1

Original line number	Diff line number	Diff line
		"""
		Implements a multitask classifier.
		Implements a multitask graph convolutional classifier.
		"""
		from __future__ import print_function
		from __future__ import division

deepchem/models/tf_new_models/multitask_regressor.py

+11 −0

Original line number	Diff line number	Diff line
		"""
		Implements a multitask graph-convolutional regression.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Han Altae-Tran and Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "GPL"

		import os
		import sys
		import numpy as np

deepchem/models/tf_new_models/tests/1jld_ligand.pdb

0 → 100644

+220 −0

Original line number	Diff line number	Diff line
		COMPND 1jld_ligand
		AUTHOR GENERATED BY OPEN BABEL 2.3.2
		HETATM 1 O LIG 1 51.470 25.435 9.367 1.00 0.00 O
		HETATM 2 C LIG 1 50.559 24.713 8.900 1.00 0.00 C
		HETATM 3 N LIG 1 48.171 24.252 8.624 1.00 0.00 N
		HETATM 4 C LIG 1 49.178 25.063 9.014 1.00 0.00 C
		HETATM 5 C LIG 1 48.795 26.264 9.601 1.00 0.00 C
		HETATM 6 C LIG 1 47.471 26.591 9.786 1.00 0.00 C
		HETATM 7 C LIG 1 46.493 25.679 9.401 1.00 0.00 C
		HETATM 8 C LIG 1 45.134 25.966 9.605 1.00 0.00 C
		HETATM 9 C LIG 1 44.178 25.033 9.207 1.00 0.00 C
		HETATM 10 C LIG 1 44.567 23.859 8.583 1.00 0.00 C
		HETATM 11 C LIG 1 45.912 23.579 8.423 1.00 0.00 C
		HETATM 12 C LIG 1 46.865 24.498 8.828 1.00 0.00 C
		HETATM 13 N LIG 1 50.813 23.556 8.244 1.00 0.00 N
		HETATM 14 C LIG 1 52.003 22.800 7.857 1.00 0.00 C
		HETATM 15 C LIG 1 51.901 22.586 6.382 1.00 0.00 C
		HETATM 16 O LIG 1 51.566 21.523 5.878 1.00 0.00 O
		HETATM 17 C LIG 1 52.294 21.503 8.699 1.00 0.00 C
		HETATM 18 O LIG 1 52.263 21.783 10.083 1.00 0.00 O
		HETATM 19 C LIG 1 53.666 20.932 8.420 1.00 0.00 C
		HETATM 20 C LIG 1 53.002 23.240 1.974 1.00 0.00 C
		HETATM 21 N LIG 1 52.126 23.690 5.680 1.00 0.00 N
		HETATM 22 C LIG 1 51.953 23.736 4.249 1.00 0.00 C
		HETATM 23 C LIG 1 51.480 25.147 3.909 1.00 0.00 C
		HETATM 24 C LIG 1 50.200 25.494 4.609 1.00 0.00 C
		HETATM 25 C LIG 1 49.014 24.824 4.306 1.00 0.00 C
		HETATM 26 C LIG 1 50.155 26.484 5.593 1.00 0.00 C
		HETATM 27 C LIG 1 47.818 25.167 4.952 1.00 0.00 C
		HETATM 28 C LIG 1 48.975 26.802 6.271 1.00 0.00 C
		HETATM 29 C LIG 1 47.790 26.153 5.940 1.00 0.00 C
		HETATM 30 C LIG 1 53.178 23.242 3.481 1.00 0.00 C
		HETATM 31 O LIG 1 54.282 24.070 3.758 1.00 0.00 O
		HETATM 32 N LIG 1 53.816 22.194 1.372 1.00 0.00 N
		HETATM 33 C LIG 1 53.331 21.016 1.039 1.00 0.00 C
		HETATM 34 O LIG 1 52.173 20.678 1.217 1.00 0.00 O
		HETATM 35 C LIG 1 54.353 20.075 0.412 1.00 0.00 C
		HETATM 36 C LIG 1 55.015 19.014 1.374 1.00 0.00 C
		HETATM 37 C LIG 1 54.118 17.819 1.687 1.00 0.00 C
		HETATM 38 C LIG 1 56.229 18.480 0.627 1.00 0.00 C
		HETATM 39 C LIG 1 55.395 19.696 2.677 1.00 0.00 C
		HETATM 40 C LIG 1 53.768 19.530 -0.907 1.00 0.00 C
		HETATM 41 C LIG 1 53.507 20.610 -1.939 1.00 0.00 C
		HETATM 42 O LIG 1 54.462 21.352 -2.557 1.00 0.00 O
		HETATM 43 N LIG 1 52.254 20.878 -2.326 1.00 0.00 N
		HETATM 44 C LIG 1 51.915 21.864 -3.312 1.00 0.00 C
		HETATM 45 C LIG 1 51.343 21.173 -4.540 1.00 0.00 C
		HETATM 46 C LIG 1 52.092 19.880 -4.972 1.00 0.00 C
		HETATM 47 C LIG 1 50.820 22.768 -2.780 1.00 0.00 C
		HETATM 48 C LIG 1 51.174 23.617 -1.527 1.00 0.00 C
		HETATM 49 H LIG 1 49.560 26.962 9.922 1.00 0.00 H
		HETATM 50 H LIG 1 47.195 27.543 10.224 1.00 0.00 H
		HETATM 51 H LIG 1 44.832 26.900 10.066 1.00 0.00 H
		HETATM 52 H LIG 1 43.127 25.227 9.386 1.00 0.00 H
		HETATM 53 H LIG 1 43.820 23.162 8.221 1.00 0.00 H
		HETATM 54 H LIG 1 46.220 22.639 7.980 1.00 0.00 H
		HETATM 55 H LIG 1 49.972 23.103 7.949 1.00 0.00 H
		HETATM 56 H LIG 1 52.869 23.456 8.029 1.00 0.00 H
		HETATM 57 H LIG 1 51.529 20.751 8.456 1.00 0.00 H
		HETATM 58 H LIG 1 52.441 20.987 10.570 1.00 0.00 H
		HETATM 59 H LIG 1 53.819 20.030 9.031 1.00 0.00 H
		HETATM 60 H LIG 1 54.432 21.680 8.671 1.00 0.00 H
		HETATM 61 H LIG 1 53.745 20.670 7.354 1.00 0.00 H
		HETATM 62 H LIG 1 53.310 24.216 1.571 1.00 0.00 H
		HETATM 63 H LIG 1 51.944 23.061 1.732 1.00 0.00 H
		HETATM 64 H LIG 1 52.425 24.516 6.159 1.00 0.00 H
		HETATM 65 H LIG 1 51.135 23.048 3.989 1.00 0.00 H
		HETATM 66 H LIG 1 51.321 25.216 2.823 1.00 0.00 H
		HETATM 67 H LIG 1 52.257 25.865 4.212 1.00 0.00 H
		HETATM 68 H LIG 1 49.017 24.032 3.566 1.00 0.00 H
		HETATM 69 H LIG 1 51.063 27.022 5.838 1.00 0.00 H
		HETATM 70 H LIG 1 46.900 24.658 4.680 1.00 0.00 H
		HETATM 71 H LIG 1 48.983 27.553 7.053 1.00 0.00 H
		HETATM 72 H LIG 1 46.862 26.408 6.440 1.00 0.00 H
		HETATM 73 H LIG 1 53.396 22.216 3.811 1.00 0.00 H
		HETATM 74 H LIG 1 54.427 24.099 4.696 1.00 0.00 H
		HETATM 75 H LIG 1 54.785 22.378 1.204 1.00 0.00 H
		HETATM 76 H LIG 1 55.194 20.718 0.113 1.00 0.00 H
		HETATM 77 H LIG 1 54.648 17.129 2.360 1.00 0.00 H
		HETATM 78 H LIG 1 53.863 17.297 0.753 1.00 0.00 H
		HETATM 79 H LIG 1 53.196 18.170 2.174 1.00 0.00 H
		HETATM 80 H LIG 1 56.904 19.313 0.382 1.00 0.00 H
		HETATM 81 H LIG 1 55.901 17.988 -0.301 1.00 0.00 H
		HETATM 82 H LIG 1 56.759 17.753 1.260 1.00 0.00 H
		HETATM 83 H LIG 1 56.042 20.560 2.464 1.00 0.00 H
		HETATM 84 H LIG 1 55.934 18.984 3.320 1.00 0.00 H
		HETATM 85 H LIG 1 54.485 20.038 3.191 1.00 0.00 H
		HETATM 86 H LIG 1 52.818 19.023 -0.684 1.00 0.00 H
		HETATM 87 H LIG 1 54.479 18.806 -1.331 1.00 0.00 H
		HETATM 88 H LIG 1 51.510 20.360 -1.903 1.00 0.00 H
		HETATM 89 H LIG 1 52.806 22.452 -3.577 1.00 0.00 H
		HETATM 90 H LIG 1 51.377 21.884 -5.379 1.00 0.00 H
		HETATM 91 H LIG 1 50.297 20.907 -4.326 1.00 0.00 H
		HETATM 92 H LIG 1 51.607 19.456 -5.863 1.00 0.00 H
		HETATM 93 H LIG 1 52.060 19.146 -4.153 1.00 0.00 H
		HETATM 94 H LIG 1 53.139 20.123 -5.205 1.00 0.00 H
		HETATM 95 H LIG 1 49.958 22.134 -2.523 1.00 0.00 H
		HETATM 96 H LIG 1 50.538 23.462 -3.586 1.00 0.00 H
		HETATM 97 H LIG 1 50.305 24.227 -1.240 1.00 0.00 H
		HETATM 98 H LIG 1 52.023 24.276 -1.759 1.00 0.00 H
		HETATM 99 H LIG 1 51.444 22.949 -0.696 1.00 0.00 H
		CONECT 1 2
		CONECT 2 1 4 13
		CONECT 3 4 12
		CONECT 4 2 3 5
		CONECT 5 4 6 49
		CONECT 6 5 7 50
		CONECT 7 6 12 8
		CONECT 8 7 9 51
		CONECT 9 8 10 52
		CONECT 10 9 11 53
		CONECT 11 10 12 54
		CONECT 12 7 11 3
		CONECT 13 14 2 55
		CONECT 14 15 17 13 56
		CONECT 14
		CONECT 15 14 16 21
		CONECT 16 15
		CONECT 17 14 18 19 57
		CONECT 17
		CONECT 18 17 58
		CONECT 19 17 59 60 61
		CONECT 19
		CONECT 20 30 32 62 63
		CONECT 20
		CONECT 21 22 15 64
		CONECT 22 30 23 21 65
		CONECT 22
		CONECT 23 22 24 66 67
		CONECT 23
		CONECT 24 23 26 25
		CONECT 25 24 27 68
		CONECT 26 24 28 69
		CONECT 27 25 29 70
		CONECT 28 29 26 71
		CONECT 29 27 28 72
		CONECT 30 20 31 22 73
		CONECT 30
		CONECT 31 30 74
		CONECT 32 33 20 75
		CONECT 33 32 35 34
		CONECT 34 33
		CONECT 35 33 40 36 76
		CONECT 35
		CONECT 36 35 39 38 37
		CONECT 36
		CONECT 37 36 77 78 79
		CONECT 37
		CONECT 38 36 80 81 82
		CONECT 38
		CONECT 39 36 83 84 85
		CONECT 39
		CONECT 40 35 41 86 87
		CONECT 40
		CONECT 41 40 43 42
		CONECT 42 41
		CONECT 43 41 44 88
		CONECT 44 43 47 45 89
		CONECT 44
		CONECT 45 44 46 90 91
		CONECT 45
		CONECT 46 45 92 93 94
		CONECT 46
		CONECT 47 44 48 95 96
		CONECT 47
		CONECT 48 47 97 98 99
		CONECT 48
		CONECT 49 5
		CONECT 50 6
		CONECT 51 8
		CONECT 52 9
		CONECT 53 10
		CONECT 54 11
		CONECT 55 13
		CONECT 56 14
		CONECT 57 17
		CONECT 58 18
		CONECT 59 19
		CONECT 60 19
		CONECT 61 19
		CONECT 62 20
		CONECT 63 20
		CONECT 64 21
		CONECT 65 22
		CONECT 66 23
		CONECT 67 23
		CONECT 68 25
		CONECT 69 26
		CONECT 70 27
		CONECT 71 28
		CONECT 72 29
		CONECT 73 30
		CONECT 74 31
		CONECT 75 32
		CONECT 76 35
		CONECT 77 37
		CONECT 78 37
		CONECT 79 37
		CONECT 80 38
		CONECT 81 38
		CONECT 82 38
		CONECT 83 39
		CONECT 84 39
		CONECT 85 39
		CONECT 86 40
		CONECT 87 40
		CONECT 88 43
		CONECT 89 44
		CONECT 90 45
		CONECT 91 45
		CONECT 92 46
		CONECT 93 46
		CONECT 94 46
		CONECT 95 47
		CONECT 96 47
		CONECT 97 48
		CONECT 98 48
		CONECT 99 48
		MASTER 0 0 0 0 0 0 0 0 99 0 99 0
		END

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