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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pdb commit 678c8fe83eb51fb36538c0719fceb9a97999c10f |
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get_pdb.xml test-data/1AKI.pdb |
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| diff -r 000000000000 -r 538790c6c21b get_pdb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_pdb.xml Fri May 31 06:22:47 2019 -0400 |
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| @@ -0,0 +1,29 @@ +<tool id="get_pdb" name="Get PDB file" version="0.1.0"> + <description>from Protein Data Bank</description> + <requirements> + <requirement type="package" version="1.20.1">wget</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + wget https://files.rcsb.org/download/${pdb_id}.pdb -O '$output' + ]]></command> + <inputs> + <param name="pdb_id" type="text" label="PDB accession code"> + <validator type="regex" message="Invalid accession code">^[0-9][a-zA-Z0-9]{3}$</validator> + </param> + </inputs> + <outputs> + <data name="output" format="pdb" /> + </outputs> + <tests> + <test> + <param name="pdb_id" value="1AKI"/> + <output name="output" file="1AKI.pdb"/> + </test> + </tests> + <help><![CDATA[ + Download a protein structure in PDB format from the Protein Data Bank using its four-letter accession code. + ]]></help> + <citations> + <citation type="doi">10.1093/nar/28.1.235</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 538790c6c21b test-data/1AKI.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1AKI.pdb Fri May 31 06:22:47 2019 -0400 |
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| b'@@ -0,0 +1,1436 @@\n+HEADER HYDROLASE 19-MAY-97 1AKI \n+TITLE THE STRUCTURE OF THE ORTHORHOMBIC FORM OF HEN EGG-WHITE \n+TITLE 2 LYSOZYME AT 1.5 ANGSTROMS RESOLUTION \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: LYSOZYME; \n+COMPND 3 CHAIN: A; \n+COMPND 4 EC: 3.2.1.17 \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; \n+SOURCE 3 ORGANISM_COMMON: CHICKEN; \n+SOURCE 4 ORGANISM_TAXID: 9031; \n+SOURCE 5 CELL: EGG \n+KEYWDS HYDROLASE, GLYCOSIDASE \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR D.CARTER,J.HE,J.R.RUBLE,B.WRIGHT \n+REVDAT 2 24-FEB-09 1AKI 1 VERSN \n+REVDAT 1 19-NOV-97 1AKI 0 \n+JRNL AUTH P.J.ARTYMIUK,C.C.F.BLAKE,D.W.RICE,K.S.WILSON \n+JRNL TITL THE STRUCTURES OF THE MONOCLINIC AND ORTHORHOMBIC \n+JRNL TITL 2 FORMS OF HEN EGG-WHITE LYSOZYME AT 6 ANGSTROMS \n+JRNL TITL 3 RESOLUTION \n+JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 38 778 1982 \n+JRNL REFN ISSN 0108-7681 \n+REMARK 1 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 1.50 ANGSTROMS. \n+REMARK 3 \n+REMARK 3 REFINEMENT. \n+REMARK 3 PROGRAM : GPRLSA, X-PLOR \n+REMARK 3 AUTHORS : FUREY \n+REMARK 3 \n+REMARK 3 DATA USED IN REFINEMENT. \n+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 \n+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 \n+REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 \n+REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 \n+REMARK 3 NUMBER OF REFLECTIONS : 16327 \n+REMARK 3 \n+REMARK 3 FIT TO DATA USED IN REFINEMENT. \n+REMARK 3 CROSS-VALIDATION METHOD : NULL \n+REMARK 3 FREE R VALUE TEST SET SELECTION : NULL \n+REMARK 3 R VALUE (WORKING + TEST SET) : NULL \n+REMARK 3 R VALUE (WORKING SET) : 0.212 \n+REMARK 3 FREE R VALUE : NULL \n+REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL \n+REMARK 3 FREE R VALUE TEST SET COUNT : NULL \n+REMARK 3 \n+REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. \n+REMARK 3 R VALUE (WORKING + TEST SET,'..b'OH A 169 22.984 29.224 13.124 0.75 22.56 O \n+HETATM 1043 O HOH A 170 30.778 7.794 -3.514 0.65 21.58 O \n+HETATM 1044 O HOH A 171 42.965 14.657 4.991 0.63 23.91 O \n+HETATM 1045 O HOH A 172 36.927 17.948 -13.093 0.62 23.36 O \n+HETATM 1046 O HOH A 173 35.412 25.852 -11.575 0.58 23.42 O \n+HETATM 1047 O HOH A 174 37.428 32.540 -5.787 0.62 21.98 O \n+HETATM 1048 O HOH A 175 37.317 8.592 7.456 0.64 22.92 O \n+HETATM 1049 O HOH A 176 9.314 36.705 -11.546 0.69 23.77 O \n+HETATM 1050 O HOH A 177 39.972 23.760 -2.655 0.86 18.96 O \n+HETATM 1051 O HOH A 178 22.128 30.274 -0.543 0.76 18.78 O \n+HETATM 1052 O HOH A 179 22.244 15.813 10.000 0.68 19.66 O \n+HETATM 1053 O HOH A 180 40.729 9.223 0.292 0.64 20.15 O \n+HETATM 1054 O HOH A 181 12.500 15.267 4.097 0.56 20.12 O \n+HETATM 1055 O HOH A 182 20.372 28.618 -2.353 0.64 20.17 O \n+HETATM 1056 O HOH A 183 22.793 15.462 -6.673 0.63 20.60 O \n+HETATM 1057 O HOH A 184 23.138 31.809 15.121 0.55 20.90 O \n+HETATM 1058 O HOH A 185 22.671 38.691 8.245 0.48 21.16 O \n+HETATM 1059 O HOH A 186 33.966 33.112 6.837 0.59 19.45 O \n+HETATM 1060 O HOH A 187 19.572 25.423 -1.420 0.53 19.94 O \n+HETATM 1061 O HOH A 188 14.790 15.672 7.259 0.52 21.22 O \n+HETATM 1062 O HOH A 189 19.112 28.022 -14.647 0.49 19.83 O \n+HETATM 1063 O HOH A 190 17.302 39.059 -12.453 0.52 20.14 O \n+HETATM 1064 O HOH A 191 16.198 14.502 5.577 0.46 20.78 O \n+HETATM 1065 O HOH A 192 17.345 46.346 -7.080 0.50 18.13 O \n+HETATM 1066 O HOH A 193 14.992 31.300 -4.242 0.46 17.90 O \n+HETATM 1067 O HOH A 194 28.196 44.775 -3.148 0.44 18.15 O \n+HETATM 1068 O HOH A 195 29.479 13.863 -9.107 0.44 18.30 O \n+HETATM 1069 O HOH A 196 23.613 44.811 2.608 0.45 17.66 O \n+HETATM 1070 O HOH A 197 40.572 22.184 -6.358 0.42 18.06 O \n+HETATM 1071 O HOH A 198 12.475 31.860 -6.226 0.47 17.85 O \n+HETATM 1072 O HOH A 199 16.684 13.594 -5.832 0.31 18.51 O \n+HETATM 1073 O HOH A 200 27.534 38.059 -12.862 0.48 18.19 O \n+HETATM 1074 O HOH A 201 25.892 35.973 11.563 0.46 18.15 O \n+HETATM 1075 O HOH A 202 24.790 25.182 16.063 0.46 17.64 O \n+HETATM 1076 O HOH A 203 12.580 21.214 5.006 0.51 17.97 O \n+HETATM 1077 O HOH A 204 19.687 23.750 -4.851 0.37 18.08 O \n+HETATM 1078 O HOH A 205 27.098 35.956 -12.358 0.39 18.71 O \n+HETATM 1079 O HOH A 206 37.255 9.634 10.002 0.46 18.39 O \n+HETATM 1080 O HOH A 207 43.755 23.843 8.038 0.38 17.96 O \n+CONECT 48 981 \n+CONECT 238 889 \n+CONECT 513 630 \n+CONECT 601 724 \n+CONECT 630 513 \n+CONECT 724 601 \n+CONECT 889 238 \n+CONECT 981 48 \n+MASTER 290 0 0 8 2 0 0 6 1079 1 8 10 \n+END \n' |