| Next changeset 1:511c4bd8aa6d (2019-06-13) |
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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc |
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added:
antechamber.xml macros.xml test-data/LigA.mol2 test-data/LigA.pdb test-data/LigA_output.mol2 test-data/LigA_output.pdb test-data/LigA_output.txt test-data/LigA_prmchk.mol2 |
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| diff -r 000000000000 -r c01897428864 antechamber.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/antechamber.xml Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,148 @@ +<tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@"> + <description>Amber's molecular input file processor</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <command detect_errors="exit_code"> + <![CDATA[ + antechamber -i '$input1' + -o '$output1' + -fi '$input1.ext' + -fo '$selected_output_format' + -c '$allparams.c' + -pf '$extraparams.pf' + #if '$extraparams.usenc' + -nc '$allparams.nc' + #end if + -at '$allparams.at' + -j '$allparams.j' + -rn '$allparams.resname' + -m '$allparams.m' + ]]> + </command> + <inputs> + <param type="data" name="input1" label="Molecular input (PDB or mol2)" format="pdb,mol2"/> + <param name="selected_output_format" type="select" label="Select an output file format (mol2 recommended!):"> + <option value="pdb">pdb</option> + <option value="mol2" selected="true">mol2</option> + </param> + <section name="allparams" title="General Parameters" expanded="true"> + <param name="nc" type="integer" value="0" label="Net charge" min="-50" max="50" help="Specify the net charge for the molecule. Default is 0. (-nc)"/> + <param name="m" type="integer" value="1" label="Multiplicity" min="1" max="10" help="Multiplicity, 2S+1. Default is 1. (-m)"/> + <param name="resname" type="text" value="MOL" label="Residue name" help="From 1-3 characters allowed. Default is MOL. (-rn)"/> + <param name="c" type="select" label="Charge method" help="Charge method to use for the calculations. AM1-BCC or RESP recommended (-c)"> + <option value="resp">RESP</option> + <option selected="True" value="bcc">AM1-BCC</option> + <option value="cm1">CM1</option> + <option value="cm2">CM2</option> + <option value="esp">ESP (Kollman)</option> + <option value="mul">Mulliken</option> + <option value="gas">Gasteiger</option> + </param> + <param name="at" type="select" label="Atom type" help="Create atom type for the specified forcefield (-at)"> + <option selected="True" value="gaff">gaff</option> + <option value="gaff2">gaff2</option> + <option value="amber">amber for PARM94/99/99SB</option> + <option value="bcc">bcc</option> + <option value="sybyl">sybyl</option> + </param> + <param name="j" type="select" label="Atom type and bond type prediction index" help="Specify how to run predictions (-j)"> + <option value="0">0 - No assignment</option> + <option value="1">1 - atom type</option> + <option value="2">2 - full bond types</option> + <option value="3">3 - part bond types</option> + <option selected="True" value="4">4 - atom and full bond type (default)</option> + <option value="5">5 - atom and part bond type</option> + </param> + </section> + <section name="extraparams" title="Additional Parameters" expanded="false"> + <param name="pf" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="remove intermediate files (recommended)" help="(-pf)"/> + <param name="usenc" type="boolean" checked="true" truevalue="True" falsevalue="False" label="use netcharge (recommended)" help="Can choose to let the charge be inferred by setting this to False."/> + </section> + </inputs> + <outputs> + <data format="mol2" name="output1" label="${tool.name}: structure output"> + <change_format> + <when input="selected_output_format" value="pdb" format="pdb"/> + <when input="selected_output_format" value="mol2" format="mol2"/> + <!-- <when input="selected_format" value="xyz" format="xyz"/> <when input="selected_format" value="tinker" format="tinker"/> <when input="selected_format" value="moldy" format="moldy"/> --> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input1" value="LigA.mol2"/> + <section name="allparams"> + <param name="nc" value="-2"/> + <param name="c" value="AM1-BCC"/> + <param name="at" value="gaff2"/> + <param name="j" value="5 - atom and part bond type"/> + </section> + <output name="output1" file="LigA_output.mol2" compare="diff" lines_diff="0"> + <assert_contents> + <has_text text=" 1 C 49.2110 26.9920 85.5530 c2 1 MOL"/> + </assert_contents> + </output> + </test> + <test> + <param name="input1" value="LigA.pdb" ftype="pdb"/> + <param name="selected_output_format" value="pdb"/> + <section name="allparams"> + <param name="nc" value="-2"/> + <param name="c" value="AM1-BCC"/> + <param name="at" value="gaff2"/> + <param name="j" value="5 - atom and part bond type"/> + </section> + <output name="output1" file="LigA_output.pdb" compare="diff" lines_diff="0"> + <assert_contents> + <has_text text="ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C"/> + </assert_contents> + </output> + </test> + </tests> + <help> + <![CDATA[ +.. class:: infomark + +**What it does** + +Antechamber sets up parameters for the input molecules provided. + +.. class:: infomark + +**How it works** + +- Select an input file (PDB, mol2) +- Specify the correct charge, or keep the default charge of 0 +- Adjust other parameters as needed. +- Click on Execute + +.. class:: infomark + +**Outputs created** + +- A mol2 or PDB output is created with the forcefield compatible atom names. + +.. class:: infomark + +**User guide and documentation** + +- AmberTools `userguide`_ + + +.. _`userguide`: http://ambermd.org/doc12/Amber19.pdf + +.. class:: infomark + +**Feature requests** + +Go to Galaxy Computational Chemistry and make a `feature request`_ + +.. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new + + +]]> + </help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r c01897428864 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,20 @@ +<macros> + <token name="@VERSION@">19.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="19.0">ambertools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1002/jcc.20290</citation> + <citation type="bibtex"> + @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. + Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, + J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url = + {http://ambermd.org/CiteAmber.php}, }</citation> + <yield/> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r c01897428864 test-data/LigA.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.mol2 Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,61 @@ +@<TRIPOS>MOLECULE +LigA +24 24 1 0 0 +SMALL +USER_CHARGES + + +@<TRIPOS>ATOM + 1 C 49.2110 26.9920 85.5530 C.2 1 <1> -0.3000 + 2 H 49.1050 28.0330 85.7020 H 1 <1> 0.1500 + 3 H 48.8320 26.6060 84.6410 H 1 <1> 0.1500 + 4 C 49.8460 26.1960 86.4430 C.2 1 <1> -0.1733 + 5 C 50.0590 24.7460 86.2630 C.2 1 <1> 1.0500 + 6 O 50.4810 24.0440 87.2160 O.co2 1 <1> -0.9000 + 7 O 49.8330 24.2110 85.1490 O.co2 1 <1> -0.9000 + 8 O 50.3730 26.8140 87.5890 O.3 1 <1> -0.3567 + 9 C 51.7280 27.3660 87.5930 C.3 1 <1> 0.3382 + 10 H 51.8840 27.9250 88.5040 H 1 <1> 0.0800 + 11 C 51.8170 28.2920 86.3980 C.2 1 <1> -0.2882 + 12 H 51.3990 29.2560 86.5300 H 1 <1> 0.1500 + 13 C 52.1840 27.8630 85.1670 C.2 1 <1> -0.2500 + 14 C 52.8190 26.5610 85.0450 C.2 1 <1> -0.1500 + 15 H 53.0370 26.2220 84.0630 H 1 <1> 0.1500 + 16 C 53.1170 25.8090 86.1190 C.2 1 <1> -0.2882 + 17 H 53.5700 24.8590 86.0130 H 1 <1> 0.1500 + 18 C 52.7610 26.1980 87.5410 C.3 1 <1> 0.3382 + 19 H 52.3530 25.3480 88.0710 H 1 <1> 0.0800 + 20 O 54.0020 26.6280 88.1730 O.3 1 <1> -0.6800 + 21 H 54.4570 27.1880 87.5220 H 1 <1> 0.4000 + 22 C 51.9410 28.6780 83.9640 C.2 1 <1> 1.0500 + 23 O 51.9100 29.9280 84.0860 O.co2 1 <1> -0.9000 + 24 O 51.8570 28.1570 82.8230 O.co2 1 <1> -0.9000 +@<TRIPOS>BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 2 + 4 4 5 1 + 5 4 8 1 + 6 5 6 ar + 7 5 7 ar + 8 8 9 1 + 9 9 10 1 + 10 9 11 1 + 11 9 18 1 + 12 11 12 1 + 13 11 13 2 + 14 13 14 1 + 15 13 22 1 + 16 14 15 1 + 17 14 16 2 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 18 20 1 + 22 20 21 1 + 23 22 23 ar + 24 22 24 ar +@<TRIPOS>SUBSTRUCTURE + 1 **** 13 GROUP 4 **** **** 0 + +# MOE 2016.08 (io_trps.svl 2016.04) |
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| diff -r 000000000000 -r c01897428864 test-data/LigA.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.pdb Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,26 @@ +CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 +ATOM 1 C <1> X 1 49.211 26.992 85.553 0.00 0.00 +ATOM 2 H <1> X 1 49.105 28.033 85.702 0.00 0.00 +ATOM 3 H <1> X 1 48.832 26.606 84.641 0.00 0.00 +ATOM 4 C <1> X 1 49.846 26.196 86.443 0.00 0.00 +ATOM 5 C <1> X 1 50.059 24.746 86.263 0.00 0.00 +ATOM 6 O <1> X 1 50.481 24.044 87.216 0.00 0.00 +ATOM 7 O <1> X 1 49.833 24.211 85.149 0.00 0.00 +ATOM 8 O <1> X 1 50.373 26.814 87.589 0.00 0.00 +ATOM 9 C <1> X 1 51.728 27.366 87.593 0.00 0.00 +ATOM 10 H <1> X 1 51.884 27.925 88.504 0.00 0.00 +ATOM 11 C <1> X 1 51.817 28.292 86.398 0.00 0.00 +ATOM 12 H <1> X 1 51.399 29.256 86.530 0.00 0.00 +ATOM 13 C <1> X 1 52.184 27.863 85.167 0.00 0.00 +ATOM 14 C <1> X 1 52.819 26.561 85.045 0.00 0.00 +ATOM 15 H <1> X 1 53.037 26.222 84.063 0.00 0.00 +ATOM 16 C <1> X 1 53.117 25.809 86.119 0.00 0.00 +ATOM 17 H <1> X 1 53.570 24.859 86.013 0.00 0.00 +ATOM 18 C <1> X 1 52.761 26.198 87.541 0.00 0.00 +ATOM 19 H <1> X 1 52.353 25.348 88.071 0.00 0.00 +ATOM 20 O <1> X 1 54.002 26.628 88.173 0.00 0.00 +ATOM 21 H <1> X 1 54.457 27.188 87.522 0.00 0.00 +ATOM 22 C <1> X 1 51.941 28.678 83.964 0.00 0.00 +ATOM 23 O <1> X 1 51.910 29.928 84.086 0.00 0.00 +ATOM 24 O <1> X 1 51.857 28.157 82.823 0.00 0.00 +END |
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| diff -r 000000000000 -r c01897428864 test-data/LigA_output.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.mol2 Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,59 @@ +@<TRIPOS>MOLECULE +MOL + 24 24 1 0 0 +SMALL +bcc + + +@<TRIPOS>ATOM + 1 C 49.2110 26.9920 85.5530 c2 1 MOL -0.311000 + 2 H 49.1050 28.0330 85.7020 ha 1 MOL 0.109500 + 3 H1 48.8320 26.6060 84.6410 ha 1 MOL 0.109500 + 4 C1 49.8460 26.1960 86.4430 ce 1 MOL 0.022900 + 5 C2 50.0590 24.7460 86.2630 ce 1 MOL 0.384200 + 6 O 50.4810 24.0440 87.2160 o 1 MOL -0.575500 + 7 O1 49.8330 24.2110 85.1490 o 1 MOL -0.575500 + 8 O2 50.3730 26.8140 87.5890 os 1 MOL -0.351900 + 9 C3 51.7280 27.3660 87.5930 c3 1 MOL 0.157300 + 10 H2 51.8840 27.9250 88.5040 h1 1 MOL 0.051700 + 11 C4 51.8170 28.2920 86.3980 c2 1 MOL -0.174200 + 12 H3 51.3990 29.2560 86.5300 ha 1 MOL 0.141000 + 13 C5 52.1840 27.8630 85.1670 ce 1 MOL -0.149200 + 14 C6 52.8190 26.5610 85.0450 ce 1 MOL -0.081000 + 15 H4 53.0370 26.2220 84.0630 ha 1 MOL 0.142000 + 16 C7 53.1170 25.8090 86.1190 c2 1 MOL -0.248200 + 17 H5 53.5700 24.8590 86.0130 ha 1 MOL 0.104000 + 18 C8 52.7610 26.1980 87.5410 c3 1 MOL 0.131300 + 19 H6 52.3530 25.3480 88.0710 h1 1 MOL 0.151700 + 20 O3 54.0020 26.6280 88.1730 oh 1 MOL -0.611800 + 21 H7 54.4570 27.1880 87.5220 ho 1 MOL 0.374000 + 22 C9 51.9410 28.6780 83.9640 ce 1 MOL 0.376200 + 23 O4 51.9100 29.9280 84.0860 o 1 MOL -0.587000 + 24 O5 51.8570 28.1570 82.8230 o 1 MOL -0.587000 +@<TRIPOS>BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 2 + 4 4 5 1 + 5 4 8 1 + 6 5 6 2 + 7 5 7 1 + 8 8 9 1 + 9 9 10 1 + 10 9 11 1 + 11 9 18 1 + 12 11 12 1 + 13 11 13 2 + 14 13 14 1 + 15 13 22 1 + 16 14 15 1 + 17 14 16 2 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 18 20 1 + 22 20 21 1 + 23 22 23 2 + 24 22 24 1 +@<TRIPOS>SUBSTRUCTURE + 1 MOL 1 TEMP 0 **** **** 0 ROOT |
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| diff -r 000000000000 -r c01897428864 test-data/LigA_output.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.pdb Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,24 @@ +ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C +ATOM 2 H MOL 1 49.105 28.033 85.702 1.00 0.00 H +ATOM 3 H1 MOL 1 48.832 26.606 84.641 1.00 0.00 H +ATOM 4 C1 MOL 1 49.846 26.196 86.443 1.00 0.00 C +ATOM 5 C2 MOL 1 50.059 24.746 86.263 1.00 0.00 C +ATOM 6 O MOL 1 50.481 24.044 87.216 1.00 0.00 O +ATOM 7 O1 MOL 1 49.833 24.211 85.149 1.00 0.00 O +ATOM 8 O2 MOL 1 50.373 26.814 87.589 1.00 0.00 O +ATOM 9 C3 MOL 1 51.728 27.366 87.593 1.00 0.00 C +ATOM 10 H2 MOL 1 51.884 27.925 88.504 1.00 0.00 H +ATOM 11 C4 MOL 1 51.817 28.292 86.398 1.00 0.00 C +ATOM 12 H3 MOL 1 51.399 29.256 86.530 1.00 0.00 H +ATOM 13 C5 MOL 1 52.184 27.863 85.167 1.00 0.00 C +ATOM 14 C6 MOL 1 52.819 26.561 85.045 1.00 0.00 C +ATOM 15 H4 MOL 1 53.037 26.222 84.063 1.00 0.00 H +ATOM 16 C7 MOL 1 53.117 25.809 86.119 1.00 0.00 C +ATOM 17 H5 MOL 1 53.570 24.859 86.013 1.00 0.00 H +ATOM 18 C8 MOL 1 52.761 26.198 87.541 1.00 0.00 C +ATOM 19 H6 MOL 1 52.353 25.348 88.071 1.00 0.00 H +ATOM 20 O3 MOL 1 54.002 26.628 88.173 1.00 0.00 O +ATOM 21 H7 MOL 1 54.457 27.188 87.522 1.00 0.00 H +ATOM 22 C9 MOL 1 51.941 28.678 83.964 1.00 0.00 C +ATOM 23 O4 MOL 1 51.910 29.928 84.086 1.00 0.00 O +ATOM 24 O5 MOL 1 51.857 28.157 82.823 1.00 0.00 O |
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| diff -r 000000000000 -r c01897428864 test-data/LigA_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.txt Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,21 @@ +Remark line goes here +MASS + +BOND + +ANGLE + +DIHE + +IMPROPER +c2-ha-c2-ha 1.1 180.0 2.0 Using the default value +c2-c2-c2-os 1.1 180.0 2.0 Using the default value +c2-o -c2-o 1.1 180.0 2.0 Using the default value +c2-c3-c2-ha 1.1 180.0 2.0 Using the default value +c2-c2-c2-c2 1.1 180.0 2.0 Using the default value +c2-c2-c2-ha 1.1 180.0 2.0 Using the default value + +NONBON + + + |
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| diff -r 000000000000 -r c01897428864 test-data/LigA_prmchk.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_prmchk.mol2 Thu Jun 13 03:52:54 2019 -0400 |
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| @@ -0,0 +1,59 @@ +@<TRIPOS>MOLECULE +MOL + 24 24 1 0 0 +SMALL +bcc + + +@<TRIPOS>ATOM + 1 C 49.2110 26.9920 85.5530 c2 1 MOL -0.412000 + 2 H 49.1050 28.0330 85.7020 ha 1 MOL 0.190500 + 3 H1 48.8320 26.6060 84.6410 ha 1 MOL 0.190500 + 4 C1 49.8460 26.1960 86.4430 c2 1 MOL 0.290000 + 5 C2 50.0590 24.7460 86.2630 c2 1 MOL 0.448000 + 6 O 50.4810 24.0440 87.2160 o 1 MOL -0.224000 + 7 O1 49.8330 24.2110 85.1490 o 1 MOL -0.224000 + 8 O2 50.3730 26.8140 87.5890 os 1 MOL -0.260000 + 9 C3 51.7280 27.3660 87.5930 c3 1 MOL -0.040000 + 10 H2 51.8840 27.9250 88.5040 h1 1 MOL 0.169000 + 11 C4 51.8170 28.2920 86.3980 c2 1 MOL -0.190000 + 12 H3 51.3990 29.2560 86.5300 ha 1 MOL 0.188000 + 13 C5 52.1840 27.8630 85.1670 c2 1 MOL 0.171000 + 14 C6 52.8190 26.5610 85.0450 c2 1 MOL -0.190000 + 15 H4 53.0370 26.2220 84.0630 ha 1 MOL 0.188000 + 16 C7 53.1170 25.8090 86.1190 c2 1 MOL -0.040000 + 17 H5 53.5700 24.8590 86.0130 ha 1 MOL 0.169000 + 18 C8 52.7610 26.1980 87.5410 c3 1 MOL -0.003000 + 19 H6 52.3530 25.3480 88.0710 h1 1 MOL 0.221000 + 20 O3 54.0020 26.6280 88.1730 oh 1 MOL -0.280000 + 21 H7 54.4570 27.1880 87.5220 ho 1 MOL 0.215000 + 22 C9 51.9410 28.6780 83.9640 c2 1 MOL 0.366000 + 23 O4 51.9100 29.9280 84.0860 o 1 MOL -0.472500 + 24 O5 51.8570 28.1570 82.8230 o 1 MOL -0.472500 +@<TRIPOS>BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 1 + 4 4 5 1 + 5 4 8 1 + 6 5 6 1 + 7 5 7 1 + 8 8 9 1 + 9 9 10 1 + 10 9 11 1 + 11 9 18 1 + 12 11 12 1 + 13 11 13 1 + 14 13 14 1 + 15 13 22 1 + 16 14 15 1 + 17 14 16 1 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 18 20 1 + 22 20 21 1 + 23 22 23 1 + 24 22 24 1 +@<TRIPOS>SUBSTRUCTURE + 1 MOL 1 TEMP 0 **** **** 0 ROOT |