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Merge pull request #394 from wverastegui/xtb
Molecular optimization tool
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name: xtb_molecular_optimization | ||
owner: recetox | ||
description: Performs semiempirical molecular optimization. | ||
long_description: | | ||
The xtb molecular optimization tool is based on the Semiempirical Tight Binding method GFNn-xTB implemented in the | ||
xtb (extended tight binding) program package. It handles coord and XYZ input formats, and optimize calculations at three | ||
convergence levels. | ||
categories: | ||
- Metabolomics | ||
remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/xtb" | ||
homepage_url: "https://github.com/grimme-lab/xtb" | ||
type: unrestricted |
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<macros> | ||
<token name="@TOOL_VERSION@">6.6.1</token> | ||
<xml name="creator"> | ||
<creator> | ||
<person | ||
givenName="Wudmir" | ||
familyName="Rojas" | ||
url="https://github.com/wverastegui" | ||
identifier="0000-0001-7036-9987" /> | ||
<person | ||
givenName="Helge" | ||
familyName="Hecht" | ||
url="https://github.com/hechth" | ||
identifier="0000-0001-6744-996X" /> | ||
<organization | ||
url="https://www.recetox.muni.cz/" | ||
email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" | ||
name="RECETOX MUNI"/> | ||
</creator> | ||
</xml> | ||
<token name="@HELP@"><![CDATA[ | ||
XTB Molecular Optimization handles coord and XYZ input formats, as well as, several levels of optimization. | ||
Documentation | ||
The xTB molecular optimization tool is based on the Semiempirical Tight Binding method GFNn-xTB implemented in the xtb (extended tight binding) | ||
program package. Detailed documentation for the xtb program can be found in https://xtb-docs.readthedocs.io/en/latest/optimization.html. | ||
]]> | ||
</token> | ||
</macros> |
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$coord | ||
-5.99455141918216 -0.78682526666358 0.39370554088116 o | ||
-3.63830860571141 0.01577921314370 -0.52394546541572 c | ||
-6.35936304761218 -2.10863199931285 2.70896019470081 c | ||
-3.55829760157918 1.30103864253559 -2.83710252323663 c | ||
-1.37182778317785 -0.42798517278855 0.80154623317728 c | ||
-5.79337117591535 1.74470854216158 -4.15870138601214 o | ||
-1.24576415337952 2.14009593929399 -3.80929102550083 c | ||
0.95939505639800 0.38378447872495 -0.17733189956940 c | ||
0.99635809940287 1.69597250539800 -2.49145271771405 c | ||
3.28572350531010 -0.11846693077585 1.30693458804557 c | ||
5.61705972845345 -0.10469082732464 0.32679033879514 c | ||
7.86643852955582 -0.65707667092152 1.94484943605965 c | ||
-5.32333959684569 -3.93320036751666 2.66940822690469 h | ||
-5.70103915744816 -0.93681282920432 4.32059422314034 h | ||
-8.40293177644150 -2.50316901968901 2.95745918013747 h | ||
-1.40671212744523 -1.41886306642894 2.59009642143871 h | ||
-5.80002301187533 2.67033419270594 -5.83513412327771 h | ||
-1.18548188999223 3.15210097101181 -5.58646506248980 h | ||
2.73579430567572 2.42368713887178 -3.27655833360389 h | ||
3.06831051462959 -0.59798493499297 3.28804786844385 h | ||
5.93406128592112 0.25488625973914 -1.65921733226687 h | ||
8.01034117397408 0.76605717654990 3.48047867975194 h | ||
9.61237539369864 -0.57937113266178 0.78425523913359 h | ||
7.69517265084765 -2.57395816033127 2.78205480121556 h | ||
$end |
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24 | ||
|
||
O -3.17218 -0.41637 0.20834 | ||
C -1.92531 0.00835 -0.27726 | ||
C -3.36523 -1.11584 1.43352 | ||
C -1.88297 0.68848 -1.50133 | ||
C -0.72594 -0.22648 0.42416 | ||
O -3.06572 0.92326 -2.20069 | ||
C -0.65923 1.13249 -2.01579 | ||
C 0.50769 0.20309 -0.09384 | ||
C 0.52725 0.89747 -1.31842 | ||
C 1.73873 -0.06269 0.69160 | ||
C 2.97242 -0.05540 0.17293 | ||
C 4.16274 -0.34771 1.02917 | ||
H -2.81699 -2.08136 1.41259 | ||
H -3.01686 -0.49574 2.28636 | ||
H -4.44664 -1.32462 1.56502 | ||
H -0.74440 -0.75083 1.37062 | ||
H -3.06924 1.41308 -3.08782 | ||
H -0.62733 1.66802 -2.95623 | ||
H 1.44772 1.28256 -1.73388 | ||
H 1.62368 -0.31644 1.73996 | ||
H 3.14017 0.13488 -0.87802 | ||
H 4.23889 0.40538 1.84179 | ||
H 5.08665 -0.30659 0.41501 | ||
H 4.07211 -1.36208 1.47220 |
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<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy0" profile="21.09"> | ||
<description>Semiempirical quantum mechanical molecular optimization method</description> | ||
<macros> | ||
<import>macros.xml</import> | ||
</macros> | ||
<expand macro="creator"/> | ||
<requirements> | ||
<requirement type="package" version="@TOOL_VERSION@">xtb</requirement> | ||
</requirements> | ||
<command detect_errors="exit_code"><![CDATA[ | ||
ln -s '${coordinates}' 'mol.${coordinates.ext}' && | ||
xtb 'mol.${coordinates.ext}' --opt '${opt_level}' && | ||
cp 'xtbopt.${coordinates.ext}' '${output}' | ||
]]></command> | ||
<inputs> | ||
<param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/> | ||
<param type="select" label="Optimization Levels" name="opt_level" help="Geometry optimization convergence levels." > | ||
<option value="crude">crude</option> | ||
<option value="sloppy">sloppy</option> | ||
<option value="loose">loose</option> | ||
<option value="lax">lax</option> | ||
<option value="normal">normal</option> | ||
<option value="tight">tight</option> | ||
<option value="vtight">vtight</option> | ||
<option value="extreme">extreme</option> | ||
</param> | ||
</inputs> | ||
<outputs> | ||
<data name="output" format_source="coordinates" /> | ||
</outputs> | ||
<tests> | ||
<test> | ||
<param name="coordinates" value="initial_mol.xyz" ftype="xyz"/> | ||
<output name="output"> | ||
<assert_contents> | ||
<has_text text="xtb"/> | ||
<has_n_lines n="26"/> | ||
</assert_contents> | ||
</output> | ||
</test> | ||
<!-- <test> | ||
<param name="coordinates" value="initial_mol.coord" ftype="coord"/> | ||
<output name="output" file="optimized_mol.coord" ftype="coord"> | ||
<assert_contents> | ||
<has_text text="$coord"/> | ||
<has_n_lines min="26"/> | ||
</assert_contents> | ||
</output> | ||
</test> --> | ||
</tests> | ||
<help> | ||
<![CDATA[ | ||
@HELP@ | ||
]]> | ||
</help> | ||
<citations> | ||
<citation type="doi">https://doi.org/10.1002/wcms.1493</citation> | ||
</citations> | ||
</tool> |