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Qyfu's Conformator/RDkit based db2 generate pipeline scripts were added. #1

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136f20f
Qiuyu's Version First submit
ffallrain Mar 12, 2021
829fb9d
Add an example and expected output
ffallrain Mar 12, 2021
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1 change: 1 addition & 0 deletions README.md
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# make_dockable

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10,486 changes: 10,486 additions & 0 deletions example/expect_output/input/conformer.input.mol2
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1 change: 1 addition & 0 deletions example/expect_output/input/input.smi
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OC[C@H]1OC(N2C=NC3=C(NC4CCCCC4)N=CN=C32)[C@H](O)[C@@H]1O CHEMBL85549
1 change: 1 addition & 0 deletions example/expect_output/input/name.txt
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name.txt 1 CHEMBL85549 OC[C@H]1OC(N2C=NC3=C(NC4CCCCC4)N=CN=C32)[C@H](O)[C@@H]1O | NO_LONG_NAME
108 changes: 108 additions & 0 deletions example/expect_output/input/output.mol2
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@<TRIPOS>MOLECULE
CHEMBL85549
48 51 1 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 O1 1.9760 -1.8040 -0.8120 O.3 1 LIG -0.5600
2 C2 1.8140 -1.6330 0.5890 C.3 1 LIG 0.0900
3 C3 1.3090 -0.2270 0.8720 C.3 1 LIG 0.1000
4 O4 2.2600 0.6950 0.3790 O.3 1 LIG -0.3400
5 C5 1.5540 1.8560 -0.0340 C.3 1 LIG 0.2700
6 N6 1.8320 3.0250 0.8120 N.pl3 1 LIG -0.4900
7 C7 2.3680 4.1960 0.3650 C.2 1 LIG 0.2700
8 N8 2.4680 5.0050 1.3960 N.2 1 LIG -0.4600
9 C9 2.0030 4.3670 2.5110 C.ar 1 LIG -0.1200
10 C10 1.8870 4.7680 3.8380 C.ar 1 LIG 0.5000
11 N11 2.3040 6.0560 4.1960 N.3 1 LIG -0.7000
12 C12 2.1920 6.5040 5.5910 C.3 1 LIG 0.1600
13 C13 0.7310 6.6990 5.9660 C.3 1 LIG -0.1200
14 C14 0.6130 7.1570 7.4110 C.3 1 LIG -0.1100
15 C15 1.3780 8.4580 7.5970 C.3 1 LIG -0.1200
16 C16 2.8410 8.2650 7.2310 C.3 1 LIG -0.1000
17 C17 2.9600 7.8000 5.7880 C.3 1 LIG -0.1200
18 N18 1.3840 3.9300 4.7560 N.ar 1 LIG -0.5800
19 C19 0.9910 2.6990 4.3940 C.ar 1 LIG 0.3700
20 N20 1.0950 2.3070 3.1130 N.ar 1 LIG -0.5400
21 C21 1.5920 3.1060 2.1520 C.ar 1 LIG 0.3300
22 C22 0.0700 1.5520 0.0610 C.3 1 LIG 0.0200
23 O23 -0.4870 2.0150 1.2820 O.3 1 LIG -0.4900
24 C24 0.0940 0.0410 0.0150 C.3 1 LIG 0.0900
25 O25 -1.0730 -0.5260 0.5950 O.3 1 LIG -0.5200
26 H 1.1210 -0.0870 1.8440 H 1 LIG 0.1100
27 H1 -0.4240 1.9270 -0.7230 H 1 LIG 0.0800
28 H2 0.2300 -0.2900 -0.9190 H 1 LIG 0.0900
29 H3 2.3080 -2.7280 -0.9990 H 1 LIG 0.3900
30 H4 2.6930 -1.7700 1.0450 H 1 LIG 0.0500
31 H5 1.1530 -2.3000 0.9310 H 1 LIG 0.0600
32 H6 1.7890 2.0680 -0.9820 H 1 LIG 0.1200
33 H7 2.6370 4.4020 -0.5760 H 1 LIG 0.2100
34 H8 2.6780 6.6720 3.5020 H 1 LIG 0.4200
35 H9 2.5850 5.8030 6.1860 H 1 LIG 0.0700
36 H10 0.2430 5.8340 5.8540 H 1 LIG 0.0700
37 H11 0.3270 7.3900 5.3670 H 1 LIG 0.0500
38 H12 0.9950 6.4570 8.0150 H 1 LIG 0.0600
39 H13 -0.3500 7.3020 7.6360 H 1 LIG 0.0600
40 H14 1.3110 8.7460 8.5520 H 1 LIG 0.0600
41 H15 0.9800 9.1620 7.0080 H 1 LIG 0.0600
42 H16 3.3260 9.1330 7.3400 H 1 LIG 0.0600
43 H17 3.2450 7.5790 7.8350 H 1 LIG 0.0600
44 H18 2.5860 8.5020 5.1830 H 1 LIG 0.0600
45 H19 3.9240 7.6500 5.5690 H 1 LIG 0.0600
46 H20 0.6200 2.0720 5.0790 H 1 LIG 0.1900
47 H21 -0.4920 3.0150 1.2880 H 1 LIG 0.3700
48 H22 -1.8620 -0.3360 0.0100 H 1 LIG 0.3800
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 1
4 4 5 1
5 5 6 1
6 6 7 1
7 7 8 2
8 8 9 1
9 9 10 ar
10 10 11 1
11 11 12 1
12 12 13 1
13 13 14 1
14 14 15 1
15 15 16 1
16 16 17 1
17 17 12 1
18 10 18 ar
19 18 19 ar
20 19 20 ar
21 20 21 ar
22 21 9 ar
23 21 6 1
24 5 22 1
25 22 23 1
26 22 24 1
27 24 3 1
28 24 25 1
29 3 26 1
30 22 27 1
31 24 28 1
32 1 29 1
33 2 30 1
34 2 31 1
35 5 32 1
36 7 33 1
37 11 34 1
38 12 35 1
39 13 36 1
40 13 37 1
41 14 38 1
42 14 39 1
43 15 40 1
44 15 41 1
45 16 42 1
46 16 43 1
47 17 44 1
48 17 45 1
49 19 46 1
50 23 47 1
51 25 48 1
@<TRIPOS>SUBSTRUCTURE
1 LIG 1 RESIDUE 1 A LIG 1
49 changes: 49 additions & 0 deletions example/expect_output/input/output.solv
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outputinput.mol2 48 0.0 -11.95 353.94 0.66 -11.29
-0.5600 0.30 12.47 -1.30 -1.00
0.0900 0.09 7.03 0.13 0.22
0.1000 0.21 3.55 0.16 0.37
-0.3400 -1.04 10.68 -1.10 -2.14
0.2700 -0.22 4.18 0.32 0.10
-0.4900 -0.34 2.51 -1.34 -1.68
0.2700 -0.32 12.77 3.23 2.91
-0.4600 -1.30 11.28 -2.25 -3.55
-0.1200 -0.66 6.84 0.75 0.09
0.5000 2.40 7.33 1.98 4.38
-0.7000 -2.01 5.45 -1.59 -3.60
0.1600 0.31 2.51 0.24 0.55
-0.1200 -0.24 5.54 0.24 -0.00
-0.1100 -0.07 6.22 0.27 0.20
-0.1200 0.08 6.14 0.26 0.34
-0.1000 0.10 6.18 0.27 0.37
-0.1200 0.04 5.62 0.24 0.28
-0.5800 -3.20 8.94 -1.78 -4.98
0.3700 1.70 12.72 3.21 4.91
-0.5400 -2.98 8.50 -1.72 -4.70
0.3300 1.30 5.64 1.54 2.84
0.0200 -0.04 4.04 0.17 0.13
-0.4900 -1.04 9.80 -0.94 -1.98
0.0900 -0.01 3.21 0.13 0.12
-0.5200 -0.47 13.20 -1.26 -1.73
0.1100 0.36 7.18 0.25 0.61
0.0800 -0.58 7.35 0.26 -0.32
0.0900 -0.14 6.35 0.22 0.08
0.3900 -2.16 9.18 -1.22 -3.38
0.0500 0.05 7.35 0.26 0.31
0.0600 0.02 7.35 0.26 0.28
0.1200 -0.74 7.28 0.25 -0.49
0.2100 -1.69 7.35 0.26 -1.43
0.4200 0.77 8.63 -0.57 0.20
0.0700 0.18 7.29 0.25 0.43
0.0700 0.19 6.31 0.22 0.41
0.0500 0.11 7.35 0.26 0.37
0.0600 0.07 7.35 0.26 0.33
0.0600 0.04 7.35 0.26 0.30
0.0600 -0.08 7.35 0.26 0.18
0.0600 -0.05 7.36 0.26 0.21
0.0600 -0.14 7.35 0.26 0.12
0.0600 -0.04 7.34 0.26 0.22
0.0600 -0.07 7.35 0.26 0.19
0.0600 -0.04 7.35 0.26 0.22
0.1900 0.48 7.35 0.26 0.74
0.3700 0.56 7.28 -0.96 -0.40
0.3800 -1.64 9.19 -1.22 -2.86
110 changes: 110 additions & 0 deletions example/expect_output/input/outputinput.mol2
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@<TRIPOS>MOLECULE
CHEMBL85549
48 51 1 0 0
SMALL
No Charge or Current Charge


@<TRIPOS>ATOM
1 O1 1.9760 -1.8040 -0.8120 O.3 1 LIG 0.000000
2 C2 1.8140 -1.6330 0.5890 C.3 1 LIG 0.000000
3 C3 1.3090 -0.2270 0.8720 C.3 1 LIG 0.000000
4 O4 2.2600 0.6950 0.3790 O.3 1 LIG 0.000000
5 C5 1.5540 1.8560 -0.0340 C.3 1 LIG 0.000000
6 N6 1.8320 3.0250 0.8120 N.pl3 1 LIG 0.000000
7 C7 2.3680 4.1960 0.3650 C.2 1 LIG 0.000000
8 N8 2.4680 5.0050 1.3960 N.2 1 LIG 0.000000
9 C9 2.0030 4.3670 2.5110 C.ar 1 LIG 0.000000
10 C10 1.8870 4.7680 3.8380 C.ar 1 LIG 0.000000
11 N11 2.3040 6.0560 4.1960 N.3 1 LIG 0.000000
12 C12 2.1920 6.5040 5.5910 C.3 1 LIG 0.000000
13 C13 0.7310 6.6990 5.9660 C.3 1 LIG 0.000000
14 C14 0.6130 7.1570 7.4110 C.3 1 LIG 0.000000
15 C15 1.3780 8.4580 7.5970 C.3 1 LIG 0.000000
16 C16 2.8410 8.2650 7.2310 C.3 1 LIG 0.000000
17 C17 2.9600 7.8000 5.7880 C.3 1 LIG 0.000000
18 N18 1.3840 3.9300 4.7560 N.ar 1 LIG 0.000000
19 C19 0.9910 2.6990 4.3940 C.ar 1 LIG 0.000000
20 N20 1.0950 2.3070 3.1130 N.ar 1 LIG 0.000000
21 C21 1.5920 3.1060 2.1520 C.ar 1 LIG 0.000000
22 C22 0.0700 1.5520 0.0610 C.3 1 LIG 0.000000
23 O23 -0.4870 2.0150 1.2820 O.3 1 LIG 0.000000
24 C24 0.0940 0.0410 0.0150 C.3 1 LIG 0.000000
25 O25 -1.0730 -0.5260 0.5950 O.3 1 LIG 0.000000
26 H 1.1210 -0.0870 1.8440 H 1 LIG 0.000000
27 H1 -0.4240 1.9270 -0.7230 H 1 LIG 0.000000
28 H2 0.2300 -0.2900 -0.9190 H 1 LIG 0.000000
29 H3 2.3080 -2.7280 -0.9990 H 1 LIG 0.000000
30 H4 2.6930 -1.7700 1.0450 H 1 LIG 0.000000
31 H5 1.1530 -2.3000 0.9310 H 1 LIG 0.000000
32 H6 1.7890 2.0680 -0.9820 H 1 LIG 0.000000
33 H7 2.6370 4.4020 -0.5760 H 1 LIG 0.000000
34 H8 2.6780 6.6720 3.5020 H 1 LIG 0.000000
35 H9 2.5850 5.8030 6.1860 H 1 LIG 0.000000
36 H10 0.2430 5.8340 5.8540 H 1 LIG 0.000000
37 H11 0.3270 7.3900 5.3670 H 1 LIG 0.000000
38 H12 0.9950 6.4570 8.0150 H 1 LIG 0.000000
39 H13 -0.3500 7.3020 7.6360 H 1 LIG 0.000000
40 H14 1.3110 8.7460 8.5520 H 1 LIG 0.000000
41 H15 0.9800 9.1620 7.0080 H 1 LIG 0.000000
42 H16 3.3260 9.1330 7.3400 H 1 LIG 0.000000
43 H17 3.2450 7.5790 7.8350 H 1 LIG 0.000000
44 H18 2.5860 8.5020 5.1830 H 1 LIG 0.000000
45 H19 3.9240 7.6500 5.5690 H 1 LIG 0.000000
46 H20 0.6200 2.0720 5.0790 H 1 LIG 0.000000
47 H21 -0.4920 3.0150 1.2880 H 1 LIG 0.000000
48 H22 -1.8620 -0.3360 0.0100 H 1 LIG 0.000000
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 1
4 4 5 1
5 5 6 1
6 6 7 1
7 7 8 2
8 8 9 1
9 9 10 ar
10 10 11 1
11 11 12 1
12 12 13 1
13 13 14 1
14 14 15 1
15 15 16 1
16 16 17 1
17 17 12 1
18 10 18 ar
19 18 19 ar
20 19 20 ar
21 20 21 ar
22 21 9 ar
23 21 6 1
24 5 22 1
25 22 23 1
26 22 24 1
27 24 3 1
28 24 25 1
29 3 26 1
30 22 27 1
31 24 28 1
32 1 29 1
33 2 30 1
34 2 31 1
35 5 32 1
36 7 33 1
37 11 34 1
38 12 35 1
39 13 36 1
40 13 37 1
41 14 38 1
42 14 39 1
43 15 40 1
44 15 41 1
45 16 42 1
46 16 43 1
47 17 44 1
48 17 45 1
49 19 46 1
50 23 47 1
51 25 48 1
@<TRIPOS>SUBSTRUCTURE
1 LIG 1 TEMP 0 **** **** 0 ROOT
1 change: 1 addition & 0 deletions example/input/input.smi
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OC[C@H]1OC(N2C=NC3=C(NC4CCCCC4)N=CN=C32)[C@H](O)[C@@H]1O CHEMBL85549
1 change: 1 addition & 0 deletions example/run_script/run.sh
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~/Software/db2_converter/ligand/generate/build_ligand.sh input 100
1 change: 1 addition & 0 deletions ligand/amsol/.gitignore
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amsol-mod4
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8 changes: 8 additions & 0 deletions ligand/amsol/README
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1. Install notes

You need to download, compile & install AMSOL7.1 here. The executable should be named
amsol7.1

2. Location

http://comp.chem.umn.edu/amsol/
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