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Added boolean to retain molecule name #557

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merged 5 commits into from
Jun 18, 2024
Merged

Added boolean to retain molecule name #557

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c05cdb6
added boolean to retain mole name or print default message
wverastegui Jun 11, 2024
5d78262
Implemented tests
wverastegui Jun 12, 2024
a3e607f
update
wverastegui Jun 12, 2024
b4eb0e6
testing empty line
wverastegui Jun 13, 2024
8e93f3b
Merge branch 'master' into wverastegui/issue534
hechth Jun 17, 2024
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26 changes: 26 additions & 0 deletions tools/xtb/test-data/initial_mol_molname.xyz
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
24
Benzophenone
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
0 tools/xtb/test-data/initial_mol.xyz → .../xtb/test-data/initial_mol_no_molname.xyz
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52 changes: 41 additions & 11 deletions tools/xtb/xtb_molecular_optimization.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy1" profile="21.09">
<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy2" profile="21.09">
<description>Semiempirical quantum mechanical molecular optimization method</description>
<macros>
<import>macros.xml</import>
Expand All @@ -10,7 +10,18 @@
<command detect_errors="exit_code"><![CDATA[
ln -s '${coordinates}' 'mol.${coordinates.ext}' &&
xtb 'mol.${coordinates.ext}' --opt '${opt_level}' &&
cp 'xtbopt.${coordinates.ext}' '${output}'

#if $replace_second_line == "FALSE":
cp 'xtbopt.${coordinates.ext}' '${output}'
#end if

#if $replace_second_line == "TRUE":
cp 'xtbopt.${coordinates.ext}' '${output}' &&
awk 'NR==FNR{if(NR==2) line=$0; next} {if(FNR==2) print line; else print $0}' '${coordinates}' '${output}' > final &&
mv final '${output}'
#end if


]]></command>
<inputs>
<param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/>
Expand All @@ -24,29 +35,48 @@
<option value="vtight">vtight</option>
<option value="extreme">extreme</option>
</param>
<param type="boolean" name="replace_second_line" label = "Keep molecule name" truevalue="TRUE" falsevalue="FALSE" checked="false" help = "If YES, the molecule name from the coordinates file is preserved, if it exists. Otherwise, the energy, gnorm, and xtb version are printed." />
</inputs>
<outputs>
<data name="output" format_source="coordinates" />
</outputs>
<tests>
<test>
<param name="coordinates" value="initial_mol.xyz" ftype="xyz"/>
<param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
<param name="replace_second_line" value="TRUE" />
<output name="output">
<assert_contents>
<has_text text="xtb"/>
<has_n_lines n="26"/>
<has_text text="Benzophenone"/>
</assert_contents>
</output>
</test>
<!-- <test>
<param name="coordinates" value="initial_mol.coord" ftype="coord"/>
<output name="output" file="optimized_mol.coord" ftype="coord">
<test>
<param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
<param name="replace_second_line" value="FALSE" />
<output name="output">
<assert_contents>
<has_text text="energy"/>
</assert_contents>
</output>
</test>
<test>
<param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
<param name="replace_second_line" value="TRUE" />
<output name="output">
<assert_contents>
<has_text text="$coord"/>
<has_n_lines min="26"/>
<not_has_text text="energy"/>
</assert_contents>
</output>
</test> -->
</test>
<test>
<param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
<param name="replace_second_line" value="FALSE" />
<output name="output">
<assert_contents>
<has_text text="energy"/>
</assert_contents>
</output>
</test>
</tests>
<help>
<![CDATA[
Expand Down