Molecular optimization tool

tools/xtb/.shed.yml

@@ -0,0 +1,13 @@
+
+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

tools/xtb/macros.xml

@@ -0,0 +1,29 @@
+<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>

tools/xtb/test-data/initial_mol.coord

@@ -0,0 +1,26 @@
+$coord
+   -5.99455141918216     -0.78682526666358      0.39370554088116      o
+   -3.63830860571141      0.01577921314370     -0.52394546541572      c
+   -6.35936304761218     -2.10863199931285      2.70896019470081      c
+   -3.55829760157918      1.30103864253559     -2.83710252323663      c
+   -1.37182778317785     -0.42798517278855      0.80154623317728      c
+   -5.79337117591535      1.74470854216158     -4.15870138601214      o
+   -1.24576415337952      2.14009593929399     -3.80929102550083      c
+    0.95939505639800      0.38378447872495     -0.17733189956940      c
+    0.99635809940287      1.69597250539800     -2.49145271771405      c
+    3.28572350531010     -0.11846693077585      1.30693458804557      c
+    5.61705972845345     -0.10469082732464      0.32679033879514      c
+    7.86643852955582     -0.65707667092152      1.94484943605965      c
+   -5.32333959684569     -3.93320036751666      2.66940822690469      h
+   -5.70103915744816     -0.93681282920432      4.32059422314034      h
+   -8.40293177644150     -2.50316901968901      2.95745918013747      h
+   -1.40671212744523     -1.41886306642894      2.59009642143871      h
+   -5.80002301187533      2.67033419270594     -5.83513412327771      h
+   -1.18548188999223      3.15210097101181     -5.58646506248980      h
+    2.73579430567572      2.42368713887178     -3.27655833360389      h
+    3.06831051462959     -0.59798493499297      3.28804786844385      h
+    5.93406128592112      0.25488625973914     -1.65921733226687      h
+    8.01034117397408      0.76605717654990      3.48047867975194      h
+    9.61237539369864     -0.57937113266178      0.78425523913359      h
+    7.69517265084765     -2.57395816033127      2.78205480121556      h
+$end

tools/xtb/test-data/initial_mol.xyz

@@ -0,0 +1,26 @@
+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

tools/xtb/test-data/optimized_mol.coord

@@ -0,0 +1,26 @@
+$coord
+       -6.01017061243307       -0.68612283164446        0.35007418473419      o
+       -3.67340416824736       -0.01780235186512       -0.50264798768195      c
+       -6.18185939323380       -2.03532755404815        2.62763902402684      c
+       -3.62010456101484        1.32817902543340       -2.79740326913722      c
+       -1.41615154813136       -0.55640186936880        0.69775742002271      c
+       -5.85736808211654        1.84324256792891       -3.95891917900420      o
+       -1.31850197161190        2.07482922016929       -3.78998744408611      c
+        0.91486326485543        0.20147128127821       -0.29806581088636      c
+        0.92554197356825        1.52602500877368       -2.56716850590522      c
+        3.19780378318462       -0.43949298521511        1.09477447257175      c
+        5.56147824281210        0.19654913582679        0.51528708227513      c
+        7.81078775156755       -0.53015854875032        2.04691043221776      c
+       -5.21258483806113       -3.86095199184170        2.50948681670029      h
+       -5.41393198556303       -0.95368717724628        4.21717541562350      h
+       -8.19183266429923       -2.35380031796021        2.93315140178243      h
+       -1.42269889797059       -1.58657955561497        2.45756855657697      h
+       -5.53858330186178        2.76625429839504       -5.49868388531298      h
+       -1.28955517445069        3.10583036101135       -5.55664900242085      h
+        2.68066393791624        2.13530318917370       -3.40195963843741      h
+        2.88221148475170       -1.55026295035729        2.78705958349957      h
+        5.97084437203676        1.31202384457661       -1.14629602260902      h
+        8.79823041312269        1.15417354914201        2.70654267076514      h
+        9.13646813425649       -1.61207338357599        0.89891618869828      h
+        7.26787273818478       -1.65981128269585        3.67541859872572      h
+$end

tools/xtb/test-data/optimized_mol.xyz

@@ -0,0 +1,26 @@
+24
+ energy: -35.631472601995 gnorm: 0.000208709513 xtb: 6.6.1 (8d0f1dd)
+O           -3.18044520106779       -0.36308106035026        0.18525128009828
+C           -1.94388186977512       -0.00942067611874       -0.26599024242786
+C           -3.27129774395325       -1.07704901836458        1.39048703460945
+C           -1.91567700024810        0.70284200518838       -1.48032237276738
+C           -0.74939519500948       -0.29443493091702        0.36923692321706
+O           -3.09958593129294        0.97540167452119       -2.09497033043045
+C           -0.69772156119433        1.09795302459165       -2.00557524884203
+C            0.48412457431048        0.10661486595053       -0.15772996967053
+C            0.48977545385570        0.80753887008807       -1.35848722712852
+C            1.69220450470073       -0.23256934099220        0.57932947241604
+C            2.94300730873844        0.10400903448845        0.27267808308720
+C            4.13329006100010       -0.28054877278294        1.08317892116181
+H           -2.75837706330488       -2.04312642253260        1.32796455990487
+H           -2.86493004534637       -0.50466793800864        2.23163327575353
+H           -4.33492932496560       -1.24558040766386        1.55215681782140
+H           -0.75285929027887       -0.83958169463296        1.30048874838021
+H           -2.93089212177776        1.46383811085295       -2.90977888311486
+H           -0.68240389752710        1.64353544779937       -2.94045219665132
+H            1.41854601710713        1.12995528663813       -1.80023942004511
+H            1.52519968931286       -0.82036329765314        1.47484818962671
+H            3.15963487773523        0.69429322224961       -0.60659352714192
+H            4.65582408065385        0.61076084355871        1.43223958217964
+H            4.83480843982276       -0.85307530799215        0.47568718276182
+H            3.84599123850420       -0.87833351791759        1.94494934720223

tools/xtb/xtb_molecular_optimization.xml

@@ -0,0 +1,49 @@
+<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 '${coordinates}' 'mol.${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,coord" 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" file="optimized_mol.xyz" ftype="xyz">
+                <assert_contents>
+                    <has_text text=" energy" n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests> 
+    <help>
+        <![CDATA[
+        @HELP@
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">https://doi.org/10.1002/wcms.1493</citation>
+    </citations>
+</tool>