Mercurial > repos > bgruening > openbabel_addh
changeset 8:883fe4f7f1b2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
| author | bgruening |
|---|---|
| date | Fri, 10 May 2019 08:53:02 -0400 |
| parents | d2e6d682bcd0 |
| children | 0691e5e97cd5 |
| files | test-data/ob_prepare_ligands.sdf test-data/ob_prepare_ligands1.mol2 test-data/ob_prepare_ligands1.pdbqt test-data/ob_prepare_ligands2.mol2 test-data/ob_prepare_ligands2.pdbqt |
| diffstat | 5 files changed, 1122 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands1.mol2 Fri May 10 08:53:02 2019 -0400 @@ -0,0 +1,96 @@ +@<TRIPOS>MOLECULE +***** + 42 46 0 0 0 +SMALL +GASTEIGER + +@<TRIPOS>ATOM + 1 O -8.6396 0.9568 0.0000 O.3 1 UNL1 -0.5067 + 2 C -7.6023 1.5602 0.0000 C.ar 1 UNL1 0.1175 + 3 C -7.6071 3.0602 0.0000 C.ar 1 UNL1 -0.0201 + 4 C -6.3104 3.8143 0.0000 C.ar 1 UNL1 -0.0576 + 5 C -5.0090 3.0685 0.0000 C.ar 1 UNL1 -0.0508 + 6 C -5.0040 1.5682 0.0000 C.ar 1 UNL1 0.0226 + 7 C -6.3008 0.8143 0.0000 C.ar 1 UNL1 -0.0095 + 8 C -3.7006 0.8244 0.0000 C.ar 1 UNL1 0.1627 + 9 N -3.7006 -0.6045 0.0000 N.ar 1 UNL1 -0.2088 + 10 C -2.4915 -1.3190 0.0000 C.ar 1 UNL1 0.1687 + 11 N -2.5059 -2.8197 0.0000 N.pl3 1 UNL1 -0.3078 + 12 C -1.2156 -3.5847 0.0000 C.3 1 UNL1 0.0371 + 13 C -1.2329 -5.0846 0.0000 C.3 1 UNL1 0.0634 + 14 O -2.5404 -5.8196 0.0000 O.3 1 UNL1 -0.3767 + 15 C -3.8308 -5.0547 0.0000 C.3 1 UNL1 0.0634 + 16 C -3.8135 -3.5548 0.0000 C.3 1 UNL1 0.0371 + 17 C -1.2274 -0.6045 0.0000 C.ar 1 UNL1 0.1961 + 18 O 0.0000 -1.3190 0.0000 O.2 1 UNL1 -0.4317 + 19 C 1.2274 -0.6045 0.0000 C.ar 1 UNL1 0.2301 + 20 N 2.4732 -1.3190 0.0000 N.ar 1 UNL1 -0.2204 + 21 C 3.7372 -0.6045 0.0000 C.ar 1 UNL1 0.0314 + 22 C 3.7372 0.8244 0.0000 C.ar 1 UNL1 -0.0427 + 23 C 2.4732 1.5389 0.0000 C.ar 1 UNL1 -0.0459 + 24 C 1.2274 0.8244 0.0000 C.ar 1 UNL1 0.0660 + 25 C -1.2274 0.8244 0.0000 C.ar 1 UNL1 0.1241 + 26 N -2.4915 1.5389 0.0000 N.ar 1 UNL1 -0.2233 + 27 H -9.4526 1.4227 0.0000 H 1 UNL1 0.2921 + 28 H -8.5025 3.5734 0.0000 H 1 UNL1 0.0654 + 29 H -6.3137 4.8463 0.0000 H 1 UNL1 0.0619 + 30 H -4.1170 3.5874 0.0000 H 1 UNL1 0.0625 + 31 H -6.2976 -0.2177 0.0000 H 1 UNL1 0.0661 + 32 H -0.2828 -3.0604 0.0000 H 1 UNL1 0.0487 + 33 H -0.2952 -4.1304 0.0000 H 1 UNL1 0.0487 + 34 H -0.3125 -5.6302 0.0000 H 1 UNL1 0.0575 + 35 H -1.2452 -6.1545 0.0000 H 1 UNL1 0.0575 + 36 H -4.7635 -5.5790 0.0000 H 1 UNL1 0.0575 + 37 H -4.7512 -4.5091 0.0000 H 1 UNL1 0.0575 + 38 H -4.7339 -3.0092 0.0000 H 1 UNL1 0.0487 + 39 H -3.8012 -2.4849 0.0000 H 1 UNL1 0.0487 + 40 H 4.6286 -1.1246 0.0000 H 1 UNL1 0.0831 + 41 H 4.6286 1.3445 0.0000 H 1 UNL1 0.0633 + 42 H 2.4700 2.5709 0.0000 H 1 UNL1 0.0626 +@<TRIPOS>BOND + 1 1 2 1 + 2 2 3 ar + 3 3 4 ar + 4 4 5 ar + 5 5 6 ar + 6 6 7 ar + 7 2 7 ar + 8 6 8 1 + 9 8 9 ar + 10 9 10 ar + 11 10 11 1 + 12 11 12 1 + 13 12 13 1 + 14 13 14 1 + 15 14 15 1 + 16 15 16 1 + 17 11 16 1 + 18 10 17 ar + 19 17 18 ar + 20 18 19 ar + 21 19 20 ar + 22 20 21 ar + 23 21 22 ar + 24 22 23 ar + 25 23 24 ar + 26 19 24 ar + 27 24 25 ar + 28 17 25 ar + 29 25 26 ar + 30 8 26 ar + 31 1 27 1 + 32 3 28 1 + 33 4 29 1 + 34 5 30 1 + 35 7 31 1 + 36 12 32 1 + 37 12 33 1 + 38 13 34 1 + 39 13 35 1 + 40 15 36 1 + 41 15 37 1 + 42 16 38 1 + 43 16 39 1 + 44 21 40 1 + 45 22 41 1 + 46 23 42 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands1.pdbqt Fri May 10 08:53:02 2019 -0400 @@ -0,0 +1,41 @@ +REMARK Name = +REMARK 2 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: O_1 and C_2 +REMARK 2 A between atoms: C_6 and C_8 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 -3.701 0.824 0.000 0.00 0.00 +0.163 A +ATOM 2 N UNL 1 -2.491 1.539 0.000 0.00 0.00 -0.223 NA +ATOM 3 C UNL 1 -1.227 0.824 0.000 0.00 0.00 +0.124 A +ATOM 4 C UNL 1 -1.227 -0.605 0.000 0.00 0.00 +0.196 A +ATOM 5 O UNL 1 0.000 -1.319 0.000 0.00 0.00 -0.432 OA +ATOM 6 C UNL 1 1.227 -0.605 0.000 0.00 0.00 +0.230 A +ATOM 7 N UNL 1 2.473 -1.319 0.000 0.00 0.00 -0.220 NA +ATOM 8 C UNL 1 3.737 -0.605 0.000 0.00 0.00 +0.114 A +ATOM 9 C UNL 1 3.737 0.824 0.000 0.00 0.00 +0.021 A +ATOM 10 C UNL 1 2.473 1.539 0.000 0.00 0.00 +0.017 A +ATOM 11 C UNL 1 -2.491 -1.319 0.000 0.00 0.00 +0.169 A +ATOM 12 N UNL 1 -2.506 -2.820 0.000 0.00 0.00 -0.308 N +ATOM 13 C UNL 1 -3.813 -3.555 0.000 0.00 0.00 +0.134 C +ATOM 14 C UNL 1 -3.831 -5.055 0.000 0.00 0.00 +0.178 C +ATOM 15 O UNL 1 -2.540 -5.820 0.000 0.00 0.00 -0.377 OA +ATOM 16 C UNL 1 -1.233 -5.085 0.000 0.00 0.00 +0.178 C +ATOM 17 C UNL 1 -1.216 -3.585 0.000 0.00 0.00 +0.134 C +ATOM 18 C UNL 1 1.227 0.824 0.000 0.00 0.00 +0.066 A +ATOM 19 N UNL 1 -3.701 -0.605 0.000 0.00 0.00 -0.209 NA +ENDROOT +BRANCH 1 22 +ATOM 20 C UNL 1 -7.602 1.560 0.000 0.00 0.00 +0.118 A +ATOM 21 C UNL 1 -6.301 0.814 0.000 0.00 0.00 +0.057 A +ATOM 22 C UNL 1 -5.004 1.568 0.000 0.00 0.00 +0.023 A +ATOM 23 C UNL 1 -5.009 3.068 0.000 0.00 0.00 +0.012 A +ATOM 24 C UNL 1 -6.310 3.814 0.000 0.00 0.00 +0.004 A +ATOM 25 C UNL 1 -7.607 3.060 0.000 0.00 0.00 +0.045 A +BRANCH 20 26 +ATOM 26 O UNL 1 -8.640 0.957 0.000 0.00 0.00 -0.507 OA +ATOM 27 H UNL 1 -9.453 1.423 0.000 0.00 0.00 +0.292 HD +ENDBRANCH 20 26 +ENDBRANCH 1 22 +TORSDOF 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands2.mol2 Fri May 10 08:53:02 2019 -0400 @@ -0,0 +1,162 @@ +@<TRIPOS>MOLECULE +***** + 73 81 0 0 0 +SMALL +GASTEIGER + +@<TRIPOS>ATOM + 1 C -4.7204 3.3431 0.0000 C.3 1 UNL1 0.0371 + 2 O -4.1471 2.2890 0.0000 O.3 1 UNL1 -0.3732 + 3 C -2.6500 2.2500 0.0000 C.3 1 UNL1 0.1246 + 4 C -1.8100 3.5000 0.0000 C.3 1 UNL1 0.0607 + 5 C -0.2400 3.5200 0.0000 C.3 1 UNL1 0.0140 + 6 C 0.5000 2.1800 0.0000 C.3 1 UNL1 0.1404 + 7 O -1.0600 2.1800 0.0000 O.3 1 UNL1 -0.3282 + 8 C -1.8300 0.9300 0.0000 C.3 1 UNL1 0.1744 + 9 C -3.0300 0.9300 0.0000 C.3 1 UNL1 -0.0136 + 10 N -0.9800 -0.7800 0.0000 N.ar 1 UNL1 -0.3070 + 11 C -2.1300 -1.4600 0.0000 C.ar 1 UNL1 0.0527 + 12 C -3.3200 -0.7600 0.0000 C.ar 1 UNL1 -0.0375 + 13 C -4.5500 -1.4800 0.0000 C.ar 1 UNL1 -0.0598 + 14 C -4.5800 -2.7700 0.0000 C.ar 1 UNL1 -0.0611 + 15 C -3.3400 -3.4700 0.0000 C.ar 1 UNL1 -0.0520 + 16 C -2.1300 -2.7900 0.0000 C.ar 1 UNL1 0.0081 + 17 C 0.2400 -2.7700 0.0000 C.ar 1 UNL1 0.0151 + 18 C 1.4300 -3.4700 0.0000 C.ar 1 UNL1 -0.0078 + 19 C 1.7600 -4.9700 0.0000 C.3 1 UNL1 0.0385 + 20 N 3.2600 -5.0800 0.0000 N.am 1 UNL1 -0.3072 + 21 C 3.8500 -3.6300 0.0000 C.2 1 UNL1 0.2453 + 22 O 4.9971 -3.2777 0.0000 O.2 1 UNL1 -0.2702 + 23 C 2.6600 -2.7500 0.0000 C.ar 1 UNL1 0.0518 + 24 C 2.6800 -1.4600 0.0000 C.ar 1 UNL1 0.0221 + 25 C 3.7900 0.5600 0.0000 C.ar 1 UNL1 0.0085 + 26 C 4.9600 1.2800 0.0000 C.ar 1 UNL1 -0.0520 + 27 C 4.9600 2.6300 0.0000 C.ar 1 UNL1 -0.0611 + 28 C 3.8100 3.2900 0.0000 C.ar 1 UNL1 -0.0598 + 29 C 2.6400 2.5900 0.0000 C.ar 1 UNL1 -0.0375 + 30 C 2.6400 1.2400 0.0000 C.ar 1 UNL1 0.0524 + 31 N 1.4900 0.5400 0.0000 N.ar 1 UNL1 -0.3115 + 32 C 1.4500 -0.7600 0.0000 C.ar 1 UNL1 0.0774 + 33 C 0.2400 -1.4400 0.0000 C.ar 1 UNL1 0.0772 + 34 N -2.5511 4.8030 0.0000 N.am 1 UNL1 -0.2947 + 35 C -1.9442 5.8382 0.0000 C.3 1 UNL1 0.0039 + 36 C -4.0519 4.8135 0.0000 C.2 1 UNL1 0.2467 + 37 O -4.6588 3.7783 0.0000 O.2 1 UNL1 -0.2700 + 38 C -4.7941 6.1180 0.0000 C.ar 1 UNL1 0.0369 + 39 C -6.2940 6.1306 0.0000 C.ar 1 UNL1 -0.0496 + 40 C -7.0331 7.4359 0.0000 C.ar 1 UNL1 -0.0610 + 41 C -6.2722 8.7286 0.0000 C.ar 1 UNL1 -0.0617 + 42 C -4.7723 8.7160 0.0000 C.ar 1 UNL1 -0.0610 + 43 C -4.0332 7.4108 0.0000 C.ar 1 UNL1 -0.0496 + 44 H -4.1620 4.2558 0.0000 H 1 UNL1 0.0524 + 45 H -5.7901 3.3703 0.0000 H 1 UNL1 0.0524 + 46 H -5.2316 4.2831 0.0000 H 1 UNL1 0.0524 + 47 H -3.1408 3.2008 0.0000 H 1 UNL1 0.0663 + 48 H -2.8793 3.5399 0.0000 H 1 UNL1 0.0529 + 49 H 0.2979 4.4450 0.0000 H 1 UNL1 0.0328 + 50 H 0.8299 3.5081 0.0000 H 1 UNL1 0.0328 + 51 H -0.4215 2.7238 0.0000 H 1 UNL1 0.0839 + 52 H -3.5650 1.8566 0.0000 H 1 UNL1 0.0277 + 53 H -3.5650 0.0034 0.0000 H 1 UNL1 0.0277 + 54 H -4.1000 0.9300 0.0000 H 1 UNL1 0.0277 + 55 H -3.3189 0.2720 0.0000 H 1 UNL1 0.0638 + 56 H -5.4393 -0.9563 0.0000 H 1 UNL1 0.0618 + 57 H -5.4772 -3.2799 0.0000 H 1 UNL1 0.0618 + 58 H -3.3410 -4.5020 0.0000 H 1 UNL1 0.0624 + 59 H 1.0595 -5.7788 0.0000 H 1 UNL1 0.0512 + 60 H 2.1687 -5.9589 0.0000 H 1 UNL1 0.0512 + 61 H 3.7793 -5.9164 0.0000 H 1 UNL1 0.1493 + 62 H 5.8609 0.7766 0.0000 H 1 UNL1 0.0624 + 63 H 5.8531 3.1472 0.0000 H 1 UNL1 0.0618 + 64 H 3.8006 4.3220 0.0000 H 1 UNL1 0.0618 + 65 H 1.7423 3.0990 0.0000 H 1 UNL1 0.0638 + 66 H -0.8742 5.8311 0.0000 H 1 UNL1 0.0429 + 67 H -2.4730 6.7684 0.0000 H 1 UNL1 0.0429 + 68 H -1.4030 6.7613 0.0000 H 1 UNL1 0.0429 + 69 H -6.8175 5.2412 0.0000 H 1 UNL1 0.0625 + 70 H -8.0651 7.4446 0.0000 H 1 UNL1 0.0618 + 71 H -6.7807 9.6266 0.0000 H 1 UNL1 0.0618 + 72 H -4.2488 9.6054 0.0000 H 1 UNL1 0.0618 + 73 H -3.0012 7.4022 0.0000 H 1 UNL1 0.0625 +@<TRIPOS>BOND + 1 1 2 1 + 2 3 2 1 + 3 3 4 1 + 4 4 5 1 + 5 6 5 1 + 6 6 7 1 + 7 7 8 1 + 8 3 8 1 + 9 8 9 1 + 10 8 10 1 + 11 10 11 ar + 12 11 12 ar + 13 12 13 ar + 14 13 14 ar + 15 14 15 ar + 16 15 16 ar + 17 11 16 ar + 18 16 17 ar + 19 17 18 ar + 20 18 19 1 + 21 19 20 1 + 22 20 21 am + 23 21 22 2 + 24 21 23 1 + 25 18 23 ar + 26 23 24 ar + 27 24 25 ar + 28 25 26 ar + 29 26 27 ar + 30 27 28 ar + 31 28 29 ar + 32 29 30 ar + 33 25 30 ar + 34 30 31 ar + 35 6 31 1 + 36 31 32 ar + 37 24 32 ar + 38 32 33 ar + 39 10 33 ar + 40 17 33 ar + 41 4 34 1 + 42 34 35 1 + 43 34 36 am + 44 36 37 2 + 45 36 38 1 + 46 38 39 ar + 47 39 40 ar + 48 40 41 ar + 49 41 42 ar + 50 42 43 ar + 51 38 43 ar + 52 1 44 1 + 53 1 45 1 + 54 1 46 1 + 55 3 47 1 + 56 4 48 1 + 57 5 49 1 + 58 5 50 1 + 59 6 51 1 + 60 9 52 1 + 61 9 53 1 + 62 9 54 1 + 63 12 55 1 + 64 13 56 1 + 65 14 57 1 + 66 15 58 1 + 67 19 59 1 + 68 19 60 1 + 69 20 61 1 + 70 26 62 1 + 71 27 63 1 + 72 28 64 1 + 73 29 65 1 + 74 35 66 1 + 75 35 67 1 + 76 35 68 1 + 77 39 69 1 + 78 40 70 1 + 79 41 71 1 + 80 42 72 1 + 81 43 73 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands2.pdbqt Fri May 10 08:53:02 2019 -0400 @@ -0,0 +1,64 @@ +REMARK Name = +REMARK 6 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and O_2 +REMARK 2 A between atoms: O_2 and C_3 +REMARK 3 A between atoms: C_4 and N_34 +REMARK 4 A between atoms: C_8 and C_9 +REMARK 5 A between atoms: N_34 and C_35 +REMARK 6 A between atoms: C_36 and C_38 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 -2.650 2.250 0.000 0.00 0.00 +0.191 C +ATOM 2 C UNL 1 -1.830 0.930 0.000 0.00 0.00 +0.174 C +ATOM 3 N UNL 1 -0.980 -0.780 0.000 0.00 0.00 -0.307 N +ATOM 4 C UNL 1 0.240 -1.440 0.000 0.00 0.00 +0.077 A +ATOM 5 C UNL 1 0.240 -2.770 0.000 0.00 0.00 +0.015 A +ATOM 6 C UNL 1 1.430 -3.470 0.000 0.00 0.00 -0.008 A +ATOM 7 C UNL 1 2.660 -2.750 0.000 0.00 0.00 +0.052 A +ATOM 8 C UNL 1 2.680 -1.460 0.000 0.00 0.00 +0.022 A +ATOM 9 C UNL 1 3.790 0.560 0.000 0.00 0.00 +0.008 A +ATOM 10 C UNL 1 2.640 1.240 0.000 0.00 0.00 +0.052 A +ATOM 11 N UNL 1 1.490 0.540 0.000 0.00 0.00 -0.311 N +ATOM 12 C UNL 1 0.500 2.180 0.000 0.00 0.00 +0.224 C +ATOM 13 C UNL 1 -0.240 3.520 0.000 0.00 0.00 +0.080 C +ATOM 14 C UNL 1 2.640 2.590 0.000 0.00 0.00 +0.026 A +ATOM 15 C UNL 1 3.810 3.290 0.000 0.00 0.00 +0.002 A +ATOM 16 C UNL 1 4.960 2.630 0.000 0.00 0.00 +0.001 A +ATOM 17 C UNL 1 4.960 1.280 0.000 0.00 0.00 +0.010 A +ATOM 18 C UNL 1 3.850 -3.630 0.000 0.00 0.00 +0.245 C +ATOM 19 O UNL 1 4.997 -3.278 0.000 0.00 0.00 -0.270 OA +ATOM 20 N UNL 1 3.260 -5.080 0.000 0.00 0.00 -0.307 N +ATOM 21 H UNL 1 3.779 -5.916 0.000 0.00 0.00 +0.149 HD +ATOM 22 C UNL 1 1.760 -4.970 0.000 0.00 0.00 +0.141 C +ATOM 23 C UNL 1 -2.130 -2.790 0.000 0.00 0.00 +0.008 A +ATOM 24 C UNL 1 -3.340 -3.470 0.000 0.00 0.00 +0.010 A +ATOM 25 C UNL 1 -4.580 -2.770 0.000 0.00 0.00 +0.001 A +ATOM 26 C UNL 1 -4.550 -1.480 0.000 0.00 0.00 +0.002 A +ATOM 27 C UNL 1 -3.320 -0.760 0.000 0.00 0.00 +0.026 A +ATOM 28 C UNL 1 1.450 -0.760 0.000 0.00 0.00 +0.077 A +ATOM 29 C UNL 1 -2.130 -1.460 0.000 0.00 0.00 +0.053 A +ATOM 30 C UNL 1 -3.030 0.930 0.000 0.00 0.00 +0.069 C +ATOM 31 O UNL 1 -1.060 2.180 0.000 0.00 0.00 -0.328 OA +ATOM 32 C UNL 1 -1.810 3.500 0.000 0.00 0.00 +0.114 C +ENDROOT +BRANCH 32 33 +ATOM 33 N UNL 1 -2.551 4.803 0.000 0.00 0.00 -0.295 N +ATOM 34 C UNL 1 -4.052 4.814 0.000 0.00 0.00 +0.247 C +ATOM 35 O UNL 1 -4.659 3.778 0.000 0.00 0.00 -0.270 OA +ATOM 36 C UNL 1 -1.944 5.838 0.000 0.00 0.00 +0.132 C +BRANCH 34 37 +ATOM 37 C UNL 1 -4.794 6.118 0.000 0.00 0.00 +0.037 A +ATOM 38 C UNL 1 -4.033 7.411 0.000 0.00 0.00 +0.013 A +ATOM 39 C UNL 1 -4.772 8.716 0.000 0.00 0.00 +0.001 A +ATOM 40 C UNL 1 -6.272 8.729 0.000 0.00 0.00 +0.000 A +ATOM 41 C UNL 1 -7.033 7.436 0.000 0.00 0.00 +0.001 A +ATOM 42 C UNL 1 -6.294 6.131 0.000 0.00 0.00 +0.013 A +ENDBRANCH 34 37 +ENDBRANCH 32 33 +BRANCH 1 44 +ATOM 43 C UNL 1 -4.720 3.343 0.000 0.00 0.00 +0.194 C +ATOM 44 O UNL 1 -4.147 2.289 0.000 0.00 0.00 -0.373 OA +ENDBRANCH 1 44 +TORSDOF 3