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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ commit d3da4ff3bfb86ce0686a87c4987e94486854d839 |
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added:
rdock.xml test-data/1sj0_ligand.sd test-data/1sj0_rdock.mol2 test-data/1sj0_rdock.prm |
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| diff -r 000000000000 -r 63f3f7b17aa4 rdock.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdock.xml Fri May 12 09:56:42 2017 -0400 |
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| @@ -0,0 +1,46 @@ +<tool id="rdock" name="rDock" version="1.0"> + <description>Binding Mode Prediction in Proteins/RNA</description> + <requirements> + <requirement type="package" version="2013.1">rDock</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +ln -s '$inputmol2' inputmol2.mol2 && +ln -s '$inputsd' ligand.sd && +sed 's|RECEPTOR_FILE.*|RECEPTOR_FILE inputmol2.mol2|g' < '$inputprm' | sed 's|REF_MOL.*|REF_MOL ./ligand.sd|g' > new.prm && +rbcavity -r new.prm -was && +rbdock -r new.prm -p dock.prm -n 100 -i '$inputsd' -o output_docking_out && +sdsort -n -f'SCORE' output_docking_out.sd > sorted.sd && +sdrmsd '$inputsd' sorted.sd > '$output_rdock' + ]]></command> + <inputs> + <param name="inputprm" argument="-r" type="data" format="prm" label="Receptor param file (contains active site params)" /> + <param name="inputmol2" type="data" format="mol2" label="MOL2 file" /> + <param name="inputsd" argument="-i" type="data" format="sdf" label="Ligand SD file" /> + </inputs> + <outputs> + <data name="output_rdock" format="tabular" /> + </outputs> + <tests> + <test> + <param name="inputprm" value="1sj0_rdock.prm" /> + <param name="inputmol2" value="1sj0_rdock.mol2" /> + <param name="inputsd" value="1sj0_ligand.sd" /> + <output name="output_rdock"> + <assert_contents> + <has_n_columns n="2" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`rDock`_ is a fast and versatile open source docking program that can be used to dock small molecules against proteins and nucleic acids. +It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. + +.. _rDock: http://rdock.sourceforge.net/ + ]]></help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003571</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 63f3f7b17aa4 test-data/1sj0_ligand.sd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1sj0_ligand.sd Fri May 12 09:56:42 2017 -0400 |
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| @@ -0,0 +1,136 @@ +LIGAND + OpenBabel03061313403D + + 63 67 0 0 1 0 0 0 0 0999 V2000 + 31.1720 -0.2380 28.7070 C 0 0 2 0 0 0 0 0 0 0 0 0 + 31.0931 -0.3224 29.8074 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2760 -1.6690 28.1770 C 0 0 1 0 0 0 0 0 0 0 0 0 + 32.0203 -2.2068 28.7837 H 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0500 -2.3690 28.4310 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.8610 -1.9480 27.9670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9320 -2.9010 27.5800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.1542 -3.9573 27.7316 H 0 0 0 0 0 0 0 0 0 0 0 0 + 26.7240 -2.5350 27.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.0814 -3.2823 26.5373 H 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3460 -1.1830 27.0310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.1280 -0.8570 26.5840 O 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0516 0.1675 26.5105 H 0 0 0 0 0 0 0 0 0 0 0 0 + 27.2840 -0.2150 27.4260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0045 0.8381 27.3950 H 0 0 0 0 0 0 0 0 0 0 0 0 + 28.5550 -0.5630 27.8540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.6080 0.4570 28.1910 S 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4700 0.4800 28.4200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6800 1.3800 27.3730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8675 1.6111 26.6842 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.9320 1.9870 27.2050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0953 2.6824 26.3817 H 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9760 1.6980 28.0990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1910 2.2510 27.9230 O 0 0 0 0 0 0 0 0 0 0 0 0 + 36.9000 1.6860 28.4118 H 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7830 0.7840 29.1430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6032 0.5288 29.8140 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.5190 0.2030 29.3110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.3474 -0.4750 30.1470 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.6300 -1.8400 26.7020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6480 -2.7670 26.4480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1205 -3.2805 27.2854 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0730 -3.0500 25.1480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.8424 -3.8019 24.9727 H 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4960 -2.3520 24.0600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.4550 -1.4710 24.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.9433 -1.0029 23.4540 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.0470 -1.1710 25.6230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.2786 -0.4184 25.7997 H 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9110 -2.5720 22.7850 O 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0020 -3.4000 22.3460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3997 -4.0684 23.1191 H 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8354 -2.7288 22.0713 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6550 -4.3840 21.2060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0771 -5.2015 21.6765 H 0 0 0 0 0 0 0 0 0 0 0 0 + 34.5750 -4.8437 20.8101 H 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8000 -4.0120 20.0540 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4248 -4.9327 19.8505 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5970 -3.2410 20.3190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8950 -2.1972 20.4989 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.1253 -3.6247 21.2365 H 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5570 -3.2640 19.1770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7656 -2.5506 19.4575 H 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0729 -4.2549 19.1109 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.1870 -2.9120 17.8130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5113 -1.8555 17.8003 H 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4559 -3.0304 16.9933 H 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4130 -3.8420 17.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9393 -3.6069 16.6782 H 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0839 -4.8933 17.5339 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4340 -3.6740 18.7760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2956 -4.3392 18.6161 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.8078 -2.6408 18.8276 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 3 1 0 0 0 0 + 1 17 1 0 0 0 0 + 1 18 1 0 0 0 0 + 1 2 1 1 0 0 0 + 3 5 1 0 0 0 0 + 3 30 1 0 0 0 0 + 3 4 1 1 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 16 2 0 0 0 0 + 7 9 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 11 1 0 0 0 0 + 9 10 1 0 0 0 0 + 11 12 1 0 0 0 0 + 11 14 2 0 0 0 0 + 12 13 1 0 0 0 0 + 14 16 1 0 0 0 0 + 14 15 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 19 1 0 0 0 0 + 18 28 2 0 0 0 0 + 19 21 2 0 0 0 0 + 19 20 1 0 0 0 0 + 21 23 1 0 0 0 0 + 21 22 1 0 0 0 0 + 23 24 1 0 0 0 0 + 23 26 2 0 0 0 0 + 24 25 1 0 0 0 0 + 26 28 1 0 0 0 0 + 26 27 1 0 0 0 0 + 28 29 1 0 0 0 0 + 30 31 1 0 0 0 0 + 30 38 2 0 0 0 0 + 31 33 2 0 0 0 0 + 31 32 1 0 0 0 0 + 33 35 1 0 0 0 0 + 33 34 1 0 0 0 0 + 35 36 2 0 0 0 0 + 35 40 1 0 0 0 0 + 36 38 1 0 0 0 0 + 36 37 1 0 0 0 0 + 38 39 1 0 0 0 0 + 40 41 1 0 0 0 0 + 41 44 1 0 0 0 0 + 41 42 1 0 0 0 0 + 41 43 1 0 0 0 0 + 44 47 1 0 0 0 0 + 44 45 1 0 0 0 0 + 44 46 1 0 0 0 0 + 47 49 1 0 0 0 0 + 47 61 1 0 0 0 0 + 47 48 1 0 0 0 0 + 49 52 1 0 0 0 0 + 49 50 1 0 0 0 0 + 49 51 1 0 0 0 0 + 52 55 1 0 0 0 0 + 52 53 1 0 0 0 0 + 52 54 1 0 0 0 0 + 55 58 1 0 0 0 0 + 55 56 1 0 0 0 0 + 55 57 1 0 0 0 0 + 58 61 1 0 0 0 0 + 58 59 1 0 0 0 0 + 58 60 1 0 0 0 0 + 61 62 1 0 0 0 0 + 61 63 1 0 0 0 0 +M END +$$$$ |
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| diff -r 000000000000 -r 63f3f7b17aa4 test-data/1sj0_rdock.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1sj0_rdock.mol2 Fri May 12 09:56:42 2017 -0400 |
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| b'@@ -0,0 +1,7885 @@\n+@<TRIPOS>MOLECULE\n+A_1SJ0_PROTEIN\n+ 3920 3957 0 0 0\n+SMALL\n+USER_CHARGES\n+\n+@<TRIPOS>ATOM\n+ 1 N 10.2140 11.7660 7.2280 N.3 1 ALA3071 1.0000\n+ 2 HN1 10.1708 12.6773 6.7499 H 1 ALA3071 1.0000\n+ 3 HN2 11.1616 11.3736 7.1330 H 1 ALA3071 1.0000\n+ 4 CA 9.9000 11.9420 8.6390 C.3 1 ALA3071 1.0000\n+ 5 HA 9.1476 11.2332 8.9848 H 1 ALA3071 1.0000\n+ 6 C 9.3570 13.3360 8.9390 C.2 1 ALA3071 1.0000\n+ 7 O 9.2760 13.6980 10.1100 O.2 1 ALA3071 1.0000\n+ 8 CB 11.1290 11.7070 9.5050 C.3 1 ALA3071 1.0000\n+ 9 HB1 10.8667 11.8448 10.5540 H 1 ALA3071 1.0000\n+ 10 HB2 11.4927 10.6909 9.3524 H 1 ALA3071 1.0000\n+ 11 HB3 11.9091 12.4168 9.2298 H 1 ALA3071 1.0000\n+ 12 N 9.0170 14.0770 7.8960 N.am 2 LEU3082 1.0000\n+ 13 HN 9.0196 13.6375 6.9645 H 2 LEU3082 1.0000\n+ 14 CA 8.6390 15.4820 7.9950 C.3 2 LEU3082 1.0000\n+ 15 HA 8.7169 15.8758 9.0084 H 2 LEU3082 1.0000\n+ 16 C 7.2020 15.7470 7.5620 C.2 2 LEU3082 1.0000\n+ 17 O 6.8930 16.7930 6.9900 O.2 2 LEU3082 1.0000\n+ 18 CB 9.6310 16.3060 7.1530 C.3 2 LEU3082 1.0000\n+ 19 HB1 10.0119 17.1779 7.6848 H 2 LEU3082 1.0000\n+ 20 HB2 9.1882 16.6849 6.2319 H 2 LEU3082 1.0000\n+ 21 CG 10.8660 15.4950 6.7280 C.3 2 LEU3082 1.0000\n+ 22 HG 10.9979 14.6401 7.3913 H 2 LEU3082 1.0000\n+ 23 CD1 10.6940 14.9920 5.3060 C.3 2 LEU3082 1.0000\n+ 24 HD11 11.5738 14.4187 5.0139 H 2 LEU3082 1.0000\n+ 25 HD12 9.8110 14.3554 5.2495 H 2 LEU3082 1.0000\n+ 26 HD13 10.5735 15.8402 4.6321 H 2 LEU3082 1.0000\n+ 27 CD2 12.1340 16.3140 6.8740 C.3 2 LEU3082 1.0000\n+ 28 HD21 12.9913 15.7153 6.5664 H 2 LEU3082 1.0000\n+ 29 HD22 12.0677 17.2023 6.2459 H 2 LEU3082 1.0000\n+ 30 HD23 12.2556 16.6139 7.9149 H 2 LEU3082 1.0000\n+ 31 N 6.3360 14.7860 7.8520 N.am 3 SER3093 1.0000\n+ 32 HN 6.7091 13.9125 8.2503 H 3 SER3093 1.0000\n+ 33 CA 4.9010 14.8730 7.6500 C.3 3 SER3093 1.0000\n+ 34 HA 4.6011 15.9196 7.5965 H 3 SER3093 1.0000\n+ 35 C 4.1740 14.1970 8.8180 C.2 3 SER3093 1.0000\n+ 36 O 2.9580 14.3250 8.9390 O.2 3 SER3093 1.0000\n+ 37 CB 4.4560 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| b |
| diff -r 000000000000 -r 63f3f7b17aa4 test-data/1sj0_rdock.prm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1sj0_rdock.prm Fri May 12 09:56:42 2017 -0400 |
| b |
| @@ -0,0 +1,53 @@ +RBT_PARAMETER_FILE_V1.00 +TITLE 1sj0_ASTEX + +RECEPTOR_FILE 1sj0_rdock.mol2 +RECEPTOR_FLEX 3.0 + +################################################################## +### CAVITY DEFINITION: REFERENCE LIGAND METHOD +################################################################## +SECTION MAPPER + SITE_MAPPER RbtLigandSiteMapper + REF_MOL 1sj0_ligand.sd + RADIUS 6.0 + SMALL_SPHERE 1.0 + MIN_VOLUME 100 + MAX_CAVITIES 1 + VOL_INCR 0.0 + GRIDSTEP 0.5 +END_SECTION + +################################################################ +# CAVITY DEFINITION: TWO SPHERES METHOD +################################################################ +#SECTION MAPPER +# SITE_MAPPER RbtSphereSiteMapper +##HETATM 2815 O HOH 756 37.266 -20.992 -4.910 0.90 24.86 1CSE2940 +# CENTER (7.185,8.250,22.649) +# RADIUS 15.0 +# SMALL_SPHERE 1.5 +# LARGE_SPHERE 6.0 +# MAX_CAVITIES 1 +#END_SECTION + +################################# +#CAVITY RESTRAINT PENALTY +################################# +SECTION CAVITY + SCORING_FUNCTION RbtCavityGridSF + WEIGHT 1.0 +END_SECTION + +################################# +## PHARMACOPHORIC RESTRAINTS +################################# +#SECTION PHARMA +# SCORING_FUNCTION RbtPharmaSF +# WEIGHT 1.0 +# CONSTRAINTS_FILE pharma_cdk2.const +# OPTIONAL_FILE optional.const +# NOPT 3 +# WRITE_ERRORS TRUE +#END_SECTION + |