Changeset d2be22 for tests/regression/Fragmentation

Timestamp:

Dec 19, 2025, 11:29:38 PM (6 weeks ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.1, stable

Children:

25aa214

Parents:

29ba9a

git-author:

Frederik Heber <frederik.heber@…> (11/16/25 11:12:52)

git-committer:

Frederik Heber <frederik.heber@…> (12/19/25 23:29:38)

Message:

Actions relying on BondGraph fail if not bond table is loaded.

• this is to ensure to not stumble over missing optimal bond lengths from the table, like with StretchBondAction.
• TESTFIX: All regression tests that use these actions need to load the bond-table now.

Location:

tests/regression/Fragmentation

Files:

• FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) (1 diff)
• FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) (1 diff)
• StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) (1 diff)

tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at

@@ -29 +29 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule-MaxOrder/pre/test.conf $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i $file -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i $file -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 2, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 2, [ignore], [ignore])
 
 AT_CLEANUP

tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at

@@ -24 +24 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/pre/test.conf $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i $file -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
 #AT_CHECK([diff BondFragment0.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment0.conf], 0, [ignore], [ignore])
 #AT_CHECK([diff BondFragment1.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment1.conf], 0, [ignore], [ignore])

tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at

@@ -26 +26 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/StoreSaturatedFragment/pre/C6-0.Sheet.Aligned.xyz C6-0.Sheet.Aligned.xyz], 0)
 length="10.5"
-AT_CHECK([../../molecuilder -i C6-0.Sheet.Aligned.xyz --add-empty-boundary .6,.6,5 --select-all-atoms --create-adjacency --create-shape --shape-type cube --stretch $length,$length,2 --translation 10,10,4 --shape-name testfragment --select-shape-by-name testfragment --clear-atom-selection --select-atoms-inside-volume --store-saturated-fragment BondFragment --DoSaturate 1 --output-types xyz], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i C6-0.Sheet.Aligned.xyz --add-empty-boundary .6,.6,5 --select-all-atoms --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency --create-shape --shape-type cube --stretch $length,$length,2 --translation 10,10,4 --shape-name testfragment --select-shape-by-name testfragment --clear-atom-selection --select-atoms-inside-volume --store-saturated-fragment BondFragment --DoSaturate 1 --output-types xyz], 0, [ignore], [ignore])
 #AT_CHECK([diff -I '.*reated by.*' $file ${abs_top_srcdir}/tests/regression/Fragmentation/StoreSaturatedFragment/post/$file], 0, [ignore], [ignore])