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Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

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Olamide Isreal
2026-03-17 17:57:24 +01:00
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155
examples/small_molecule/7s69_glycan.sdf Normal file
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53 54 1 0 0 0 0
53 55 1 0 0 0 0
53127 1 0 0 0 0
54128 1 0 0 0 0
54129 1 0 0 0 0
54130 1 0 0 0 0
55 56 1 0 0 0 0
55131 1 0 0 0 0
55132 1 0 0 0 0
56 57 1 0 0 0 0
56 64 1 0 0 0 0
56133 1 0 0 0 0
57 58 1 0 0 0 0
57134 1 0 0 0 0
57135 1 0 0 0 0
58 59 1 0 0 0 0
58 61 1 0 0 0 0
58136 1 0 0 0 0
59 60 1 0 0 0 0
60137 1 0 0 0 0
60138 1 0 0 0 0
60139 1 0 0 0 0
61 62 1 0 0 0 0
61 63 1 0 0 0 0
61140 1 0 0 0 0
62141 1 0 0 0 0
63 64 1 0 0 0 0
63142 1 0 0 0 0
63143 1 0 0 0 0
64144 1 0 0 0 0
64145 1 0 0 0 0
65 66 2 0 0 0 0
65 68 1 0 0 0 0
65 69 1 0 0 0 0
66 67 1 0 0 0 0
66146 1 0 0 0 0
67147 1 0 0 0 0
68148 1 0 0 0 0
68149 1 0 0 0 0
68150 1 0 0 0 0
M END
> <OPENEYE_ISO_SMILES>
Cc1ccc(s1)[C@@H]\2C[C@@H]3CC[C@H]([C@@](O3)(C(=O)C(=O)N4CCCC[C@H]4C(=O)O[C@@H](CC(=O)[C@@H](/C=C(/[C@H]([C@H](C(=O)[C@@H](C[C@@H](/C=C/C=C/C=C2\C)C)C)OC)O)\C)C)[C@H](C)C[C@@H]5CC[C@H]([C@@H](C5)OC)O)O)C
> <OPENEYE_INCHI>
InChI=1S/C55H81NO12S/c1-32-16-12-11-13-17-33(2)42(48-24-20-39(8)69-48)30-41-22-19-38(7)55(64,68-41)52(61)53(62)56-25-15-14-18-43(56)54(63)67-46(35(4)28-40-21-23-44(57)47(29-40)65-9)31-45(58)34(3)27-37(6)50(60)51(66-10)49(59)36(5)26-32/h11-13,16-17,20,24,27,32,34-36,38,40-44,46-47,50-51,57,60,64H,14-15,18-19,21-23,25-26,28-31H2,1-10H3/b13-11+,16-12+,33-17+,37-27+/t32-,34-,35-,36-,38-,40+,41+,42-,43+,44-,46+,47-,50-,51+,55-/m1/s1
> <OPENEYE_INCHIKEY>
SDSGJAIFUCCAOV-MSLSVLDMSA-N
> <FORMULA>
C55H81NO12S
$$$$

129
examples/small_molecule/NSW_ideal.sdf Normal file
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@@ -0,0 +1,129 @@
NSW
-OEChem-02232415193D
53 57 0 0 0 0 0 0 0999 V2000
5.9220 -0.3020 1.2970 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4470 1.1670 -0.1420 N 0 0 0 0 0 0 0 0 0 0 0 0
0.2000 0.5990 0.0490 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8390 2.2820 1.6000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4190 4.1380 -0.0250 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0970 4.8230 -0.0410 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6580 3.7710 0.7410 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2910 -1.6780 0.1420 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.5360 -2.0330 0.9170 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3400 -0.7150 -1.3020 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5200 0.5160 -1.4970 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4840 -0.2350 -0.6170 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8140 -1.5440 -0.9150 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6890 -2.2400 -0.1020 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2500 -1.6170 1.0030 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0380 0.3850 0.4880 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9010 1.0040 0.8040 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3180 3.4280 0.7480 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8580 5.1930 -0.8030 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1970 5.5360 -0.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0560 -0.8580 0.1180 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3880 -1.2680 0.8980 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.5990 -3.2100 0.1850 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.5100 -3.6190 -0.5740 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3600 -2.8590 -0.5970 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9650 -1.2700 -0.6360 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1540 0.3180 -1.0070 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.9960 0.2710 0.8210 N 0 0 0 0 0 0 0 0 0 0 0 0
0.1460 -0.5340 -0.6580 N 0 3 0 0 0 0 0 0 0 0 0 0
1.6180 -1.6500 -2.0280 O 0 0 0 0 0 0 0 0 0 0 0 0
7.1200 -2.2960 1.7980 O 0 0 0 0 0 0 0 0 0 0 0 0
-6.7310 -3.9620 0.2060 O 0 0 0 0 0 0 0 0 0 0 0 0
6.3530 0.1830 2.1600 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7700 1.9970 0.2440 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.4750 2.1920 2.4810 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1890 2.4660 1.9120 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6270 3.8710 -0.0190 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.1440 5.0900 -0.0470 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3610 3.2140 1.3420 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.3860 -1.7150 1.5030 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7620 1.5790 -1.4770 H 0 0 0 0 0 0 0 0 0 0 0 0
3.5960 0.1460 -2.5200 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3810 -2.0270 -1.7780 H 0 0 0 0 0 0 0 0 0 0 0 0
5.9460 -3.2620 -0.3350 H 0 0 0 0 0 0 0 0 0 0 0 0
4.7780 1.4080 0.7180 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.1550 5.7500 -1.4040 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5410 6.3580 -1.4210 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.3390 -0.3520 1.4680 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.5640 -4.5340 -1.1460 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5130 -3.1770 -1.1870 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0160 -2.1870 -1.2050 H 0 0 0 0 0 0 0 0 0 0 0 0
6.6980 -2.7710 2.5270 H 0 0 0 0 0 0 0 0 0 0 0 0
-7.3690 -3.7310 -0.4820 H 0 0 0 0 0 0 0 0 0 0 0 0
6 7 2 0 0 0 0
6 20 1 0 0 0 0
7 18 1 0 0 0 0
19 20 2 0 0 0 0
24 25 2 0 0 0 0
23 24 1 0 0 0 0
8 25 1 0 0 0 0
23 32 1 0 0 0 0
4 18 1 0 0 0 0
5 18 2 0 0 0 0
9 23 2 0 0 0 0
15 31 1 0 0 0 0
4 17 1 0 0 0 0
5 19 1 0 0 0 0
17 28 2 0 0 0 0
21 28 1 0 0 0 0
8 21 1 0 0 0 0
8 22 2 0 0 0 0
3 17 1 0 0 0 0
1 15 2 0 0 0 0
14 15 1 0 0 0 0
21 26 2 0 0 0 0
9 22 1 0 0 0 0
1 16 1 0 0 0 0
13 14 2 0 0 0 0
2 3 1 0 0 0 0
3 29 2 0 0 0 0
26 29 1 0 0 0 0
2 27 1 0 0 0 0
12 16 2 0 0 0 0
10 29 1 0 0 0 0
12 13 1 0 0 0 0
11 12 1 0 0 0 0
10 27 1 0 0 0 0
11 27 1 0 0 0 0
10 30 2 0 0 0 0
1 33 1 0 0 0 0
2 34 1 0 0 0 0
4 35 1 0 0 0 0
4 36 1 0 0 0 0
5 37 1 0 0 0 0
6 38 1 0 0 0 0
7 39 1 0 0 0 0
9 40 1 0 0 0 0
11 41 1 0 0 0 0
11 42 1 0 0 0 0
13 43 1 0 0 0 0
14 44 1 0 0 0 0
16 45 1 0 0 0 0
19 46 1 0 0 0 0
20 47 1 0 0 0 0
22 48 1 0 0 0 0
24 49 1 0 0 0 0
25 50 1 0 0 0 0
26 51 1 0 0 0 0
31 52 1 0 0 0 0
32 53 1 0 0 0 0
M CHG 1 29 1
M END
> <OPENEYE_ISO_SMILES>
c1ccc(cc1)Cc2c3[nH]n(c(=O)[n+]3cc(n2)c4ccc(cc4)O)Cc5ccc(cc5)O
> <OPENEYE_INCHI>
InChI=1S/C25H20N4O3/c30-20-10-6-18(7-11-20)15-29-25(32)28-16-23(19-8-12-21(31)13-9-19)26-22(24(28)27-29)14-17-4-2-1-3-5-17/h1-13,16,30-31H,14-15H2/p+1
> <OPENEYE_INCHIKEY>
FAFQJYQLYIUGAT-UHFFFAOYSA-O
> <FORMULA>
C25H21N4O3+
$$$$

116
examples/small_molecule/XG4.sdf Normal file
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@@ -0,0 +1,116 @@
XG4
-OEChem-02232415213D
48 50 0 1 0 0 0 0 0999 V2000
7.5710 2.0160 -0.3960 N 0 0 0 0 0 0 0 0 0 0 0 0
7.4820 0.6990 -0.7370 C 0 0 0 0 0 0 0 0 0 0 0 0
8.5980 0.0580 -1.2130 N 0 0 0 0 0 0 0 0 0 0 0 0
6.3590 0.0260 -0.6220 N 0 0 0 0 0 0 0 0 0 0 0 0
5.2470 0.6100 -0.1630 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2730 1.9610 0.2040 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4880 2.6730 0.0750 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5580 3.8500 0.3880 O 0 0 0 0 0 0 0 0 0 0 0 0
4.0270 2.2870 0.6270 N 0 0 0 0 0 0 0 0 0 0 0 0
3.2570 1.2420 0.5440 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9670 0.1810 0.0620 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.3540 -1.9400 -0.6300 P 0 0 1 0 0 0 0 0 0 0 0 0
-4.4150 -0.1240 -0.2370 P 0 0 1 0 0 0 0 0 0 0 0 0
-6.1130 2.2430 0.3070 P 0 0 0 0 0 0 0 0 0 0 0 0
3.4520 -1.1710 -0.1750 C 0 0 1 0 0 0 0 0 0 0 0 0
-2.9530 -2.8530 0.3690 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.9590 -0.4340 -1.5780 O 0 0 0 0 0 0 0 0 0 0 0 0
-7.0830 1.4520 1.0960 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7430 -2.0630 1.0480 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9280 -2.2930 -2.0920 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.0840 -1.1020 0.8530 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.8010 3.6270 1.0690 O 0 0 0 0 0 0 0 0 0 0 0 0
2.3450 -2.5490 1.5040 C 0 0 2 0 0 0 0 0 0 0 0 0
2.3820 -3.9270 1.8790 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.7470 -0.3500 -0.2430 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.7480 1.4050 0.1380 O 0 0 0 0 0 0 0 0 0 0 0 0
-6.7320 2.5590 -1.1450 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4970 -2.3470 0.2220 C 0 0 2 0 0 0 0 0 0 0 0 0
2.0250 -1.1280 -0.3430 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0180 -2.1810 0.5750 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7540 -2.1140 -0.6250 O 0 0 0 0 0 0 0 0 0 0 0 0
8.4160 2.4830 -0.4890 H 0 0 0 0 0 0 0 0 0 0 0 0
9.4340 0.5410 -1.3030 H 0 0 0 0 0 0 0 0 0 0 0 0
8.5510 -0.8790 -1.4600 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2120 1.2170 0.8170 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9200 -1.5950 -1.0630 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3670 -2.9100 0.7620 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2220 -1.4840 1.8370 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5780 -1.7320 -2.7980 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.7730 -0.9550 1.7570 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.5800 4.1840 1.2060 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9680 -1.9350 2.3210 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9720 -4.1170 2.6220 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.3430 -0.0830 0.6430 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.1490 3.0750 -1.7180 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6350 -3.1820 -0.4650 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3110 -3.0320 1.1710 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.1180 -1.2630 1.1470 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 7 1 0 0 0 0
1 32 1 0 0 0 0
2 4 2 0 0 0 0
2 3 1 0 0 0 0
3 33 1 0 0 0 0
3 34 1 0 0 0 0
4 5 1 0 0 0 0
5 11 1 0 0 0 0
5 6 2 0 0 0 0
6 9 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
9 10 2 0 0 0 0
10 11 1 0 0 0 0
10 35 1 0 0 0 0
11 15 1 0 0 0 0
12 31 1 0 0 0 0
12 16 2 0 0 0 0
12 20 1 0 0 0 0
12 25 1 0 0 0 0
13 17 2 0 0 0 0
13 25 1 0 0 0 0
13 21 1 0 0 0 0
13 26 1 0 0 0 0
14 18 2 0 0 0 0
14 26 1 0 0 0 0
14 22 1 0 0 0 0
14 27 1 0 0 0 0
15 29 1 0 0 0 0
15 19 1 0 0 0 0
15 36 1 0 0 0 0
19 23 1 0 0 0 0
19 37 1 0 0 0 0
19 38 1 0 0 0 0
20 39 1 0 0 0 0
21 40 1 0 0 0 0
22 41 1 0 0 0 0
23 28 1 0 0 0 0
23 24 1 0 0 0 0
23 42 1 0 0 0 0
24 43 1 0 0 0 0
25 44 1 0 0 0 0
27 45 1 0 0 0 0
28 29 1 0 0 0 0
28 30 1 0 0 0 0
28 46 1 0 0 0 0
30 31 1 0 0 0 0
30 47 1 0 0 0 0
30 48 1 0 0 0 0
M END
> <OPENEYE_ISO_SMILES>
c1nc2c(=O)[nH]c(nc2n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N
> <OPENEYE_INCHI>
InChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
> <OPENEYE_INCHIKEY>
DWGAAFQEGIMTIA-KVQBGUIXSA-N
> <FORMULA>
C10H17N6O12P3
$$$$