Ignore:
Timestamp:
Dec 19, 2025, 11:29:38 PM (7 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/Graph
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at

    r29ba9a rd2be22  
    2525AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/CreateAdjacency/pre/ethane.xyz $file], 0)
    2626AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    27 AT_CHECK([../../molecuilder -i $file -o pdb --select-all-atoms --create-adjacency], 0, [stdout], [stderr])
     27AT_CHECK([../../molecuilder -i $file -o pdb --select-all-atoms --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency], 0, [stdout], [stderr])
    2828AT_CHECK([fgrep "I detected 7 bonds in the molecule" stdout], 0, [ignore], [ignore])
    2929AT_CHECK([fgrep "CONECT" ethane.pdb], 0, [stdout], [ignore])
    … …  
    3333AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/CreateAdjacency/pre/ethane.xyz $file], 0)
    3434AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    35 AT_CHECK([../../molecuilder -i $file -o pdb --select-atom-by-element 6 --create-adjacency], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file -o pdb --select-atom-by-element 6 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency], 0, [stdout], [stderr])
    3636AT_CHECK([fgrep "CONECT" ethane.pdb], 0, [stdout], [ignore])
    3737AT_CHECK([fgrep "1" stdout], 0, [stdout], [ignore])
    … …  
    4646AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/CreateAdjacency/pre/ethane.xyz $file], 0)
    4747AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    48 AT_CHECK([../../molecuilder -i $file -o pdb --select-all-atoms --create-adjacency --undo], 0, [stdout], [stderr])
     48AT_CHECK([../../molecuilder -i $file -o pdb --select-all-atoms --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency --undo], 0, [stdout], [stderr])
    4949AT_CHECK([fgrep "I detected 7 bonds in the molecule" stdout], 0, [ignore], [ignore])
    5050AT_CHECK([fgrep "CONECT" ethane.pdb], 1, [ignore], [ignore])
    … …  
    5353AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/CreateAdjacency/pre/ethane.xyz $file], 0)
    5454AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    55 AT_CHECK([../../molecuilder -i $file -o pdb --select-atom-by-element 6 --create-adjacency --undo], 0, [stdout], [stderr])
     55AT_CHECK([../../molecuilder -i $file -o pdb --select-atom-by-element 6 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency --undo], 0, [stdout], [stderr])
    5656AT_CHECK([fgrep "CONECT" ethane.pdb], 1, [ignore], [ignore])
    5757
    … …  
    6565AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/CreateAdjacency/pre/ethane.xyz $file], 0)
    6666AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    67 AT_CHECK([../../molecuilder -i $file -o pdb --select-all-atoms --create-adjacency --undo --redo], 0, [stdout], [stderr])
     67AT_CHECK([../../molecuilder -i $file -o pdb --select-all-atoms --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency --undo --redo], 0, [stdout], [stderr])
    6868AT_CHECK([fgrep "I detected 7 bonds in the molecule" stdout], 0, [ignore], [ignore])
    6969AT_CHECK([fgrep "CONECT" ethane.pdb], 0, [stdout], [ignore])
    … …  
    7373AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/CreateAdjacency/pre/ethane.xyz $file], 0)
    7474AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    75 AT_CHECK([../../molecuilder -i $file -o pdb --select-atom-by-element 6 --create-adjacency --undo --redo], 0, [stdout], [stderr])
     75AT_CHECK([../../molecuilder -i $file -o pdb --select-atom-by-element 6 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency --undo --redo], 0, [stdout], [stderr])
    7676AT_CHECK([fgrep "CONECT" ethane.pdb], 0, [stdout], [ignore])
    7777AT_CHECK([fgrep "1" stdout], 0, [stdout], [ignore])

  • tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at

    r29ba9a rd2be22  
    2424AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/DepthFirstSearch/pre/test.conf $file], 0)
    2525AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --create-adjacency -D 2.], 0, [stdout], [stderr])
     26AT_CHECK([../../molecuilder -i $file -v 3 --select-all-atoms --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency -D 2.], 0, [stdout], [stderr])
    2727AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [stdout], [ignore])
    2828

  • tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at

    r29ba9a rd2be22  
    2424AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    2525AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 -I], 0, [stdout], [stderr])
     26AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    2727AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    2828file=water-bounced.xyz
    2929AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    3030AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    31 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 -I], 0, [stdout], [stderr])
     31AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    3232AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    3333file=water-wrapped.xyz
    3434AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    3535AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    36 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 -I], 0, [stdout], [stderr])
     36AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    3737AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    3838
    … …  
    4545AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    4646AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    47 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 -I], 0, [stdout], [stderr])
     47AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    4848AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    4949file=water-bounced.xyz
    5050AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    5151AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    52 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 -I], 0, [stdout], [stderr])
     52AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    5353AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    5454file=water-wrapped.xyz
    5555AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    5656AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    57 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 -I], 0, [stdout], [stderr])
     57AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    5858AT_CHECK([fgrep "I scanned 2 molecules." stdout], 0, [ignore], [ignore])
    5959
    … …  
    6666AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    6767AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    68 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 -I], 0, [stdout], [stderr])
     68AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    6969AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    7070file=water-bounced.xyz
    7171AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    7272AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    73 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 -I], 0, [stdout], [stderr])
     73AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    7474AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    7575file=water-wrapped.xyz
    7676AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    7777AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    78 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 -I], 0, [stdout], [stderr])
     78AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    7979AT_CHECK([fgrep "I scanned 2 molecules." stdout], 0, [ignore], [ignore])
    8080

  • tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at

    r29ba9a rd2be22  
    2424AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection/pre/test.conf $file], 0)
    2525AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $file  -v 3 -I], 0, [stdout], [stderr])
     26AT_CHECK([../../molecuilder -i $file  -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I], 0, [stdout], [stderr])
    2727AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
    2828
    … …  
    3636AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection/pre/test.conf $file], 0)
    3737AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    38 AT_CHECK([../../molecuilder -i $file  -v 3 -I --undo], 0, [stdout], [stderr])
     38AT_CHECK([../../molecuilder -i $file  -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --undo], 0, [stdout], [stderr])
    3939AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
    4040
    … …  
    4848AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection/pre/test.conf $file], 0)
    4949AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    50 AT_CHECK([../../molecuilder -i $file  -v 3 -I --undo --redo], 0, [stdout], [stderr])
     50AT_CHECK([../../molecuilder -i $file  -v 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --undo --redo], 0, [stdout], [stderr])
    5151AT_CHECK([grep -c "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
    5252
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