Changeset d2be22 for tests/regression/Molecules

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/Molecules

Files:

• ForceAnnealing/testsuite-molecules-force-annealing.at (modified) (1 diff)
• Remove/testsuite-molecules-remove.at (modified) (3 diffs)
• SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) (1 diff)
• SaveBonds/testsuite-molecules-save-bonds.at (modified) (1 diff)
• SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified) (1 diff)
• StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (modified) (3 diffs)
• StretchBond/testsuite-molecules-stretch-bond.at (modified) (3 diffs)

tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at

@@ -25 +25 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/ForceAnnealing/pre/test.forces .], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-all-atoms --step-world-time 1 --force-annealing --forces-file test.forces --steps 1], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-all-atoms --step-world-time 1 --force-annealing --forces-file test.forces --steps 1], 0, [stdout], [stderr])
 AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/ForceAnnealing/post/test.conf], 0, [ignore], [ignore])
 

tests/regression/Molecules/Remove/testsuite-molecules-remove.at

@@ -24 +24 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Remove/pre/water_box.pdb $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 2 --remove-molecule], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-molecule-by-id 0 2 --remove-molecule], 0, [ignore], [ignore])
 AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/Remove/post/id0_2_missing.pdb], 0, [ignore], [ignore])
 
@@ -36 +36 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Remove/pre/water_box.pdb $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 2 --remove-molecule --undo], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-molecule-by-id 0 2 --remove-molecule --undo], 0, [ignore], [ignore])
 AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/Remove/post/water_box.pdb], 0, [ignore], [ignore])
 
@@ -48 +48 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Remove/pre/water_box.pdb $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 2 --remove-molecule --undo --redo], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-molecule-by-id 0 2 --remove-molecule --undo --redo], 0, [ignore], [ignore])
 AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/Remove/post/id0_2_missing.pdb], 0, [ignore], [ignore])
 

tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at

@@ -23 +23 @@
 file=test.conf
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/SaveAdjacency/pre/test.conf $file], 0)
-AT_CHECK([../../molecuilder -i $file  -v 1 --select-all-atoms --create-adjacency --select-molecule-by-id 0 -J test.adj], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file  -v 1 --select-all-atoms --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency --select-molecule-by-id 0 -J test.adj], 0, [stdout], [stderr])
 AT_CHECK([file=test.adj; ../../adjacencymatcher $file $file ${abs_top_srcdir}/tests/regression/Molecules/SaveAdjacency/post/$file], 0, [ignore], [ignore])
 

tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at

@@ -23 +23 @@
 file=test.conf
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/SaveBonds/pre/test.conf $file], 0)
-AT_CHECK([../../molecuilder -i $file  -v 1 --select-all-atoms --create-adjacency --select-molecule-by-id 0 -j test.dbond], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file  -v 1 --select-all-atoms --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --create-adjacency --select-molecule-by-id 0 -j test.dbond], 0, [stdout], [stderr])
 AT_CHECK([file=test.dbond; diff $file ${abs_top_srcdir}/tests/regression/Molecules/SaveBonds/post/test.dbond], 0, [ignore], [ignore])
 

tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at

@@ -23 +23 @@
 file=test.xyz
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/SaveSelectedMolecules/pre/test.xyz $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-order 1 -s testsave.xyz], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-molecule-by-order 1 -s testsave.xyz], 0, [stdout], [stderr])
 AT_CHECK([file=testsave.xyz; diff -I '.*Created by.*' $file ${abs_top_srcdir}/tests/regression/Molecules/SaveSelectedMolecules/post/testsave.xyz], 0, [ignore], [ignore])
 

tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at

@@ -24 +24 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file $file], 0)
 AT_CHECK([chmod +w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atom-by-id 2 3 --stretch-bond 2.], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --select-atom-by-id 2 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --stretch-bond 2.], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/post/$file], 0, [ignore], [ignore])
 
@@ -35 +35 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file $file], 0)
 AT_CHECK([chmod +w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atom-by-id 2 3 --stretch-bond 2. --undo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --select-atom-by-id 2 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --stretch-bond 2. --undo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file], 0, [ignore], [ignore])
 
@@ -46 +46 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file $file], 0)
 AT_CHECK([chmod +w $file], 0)
-AT_CHECK([../../molecuilder -i $file --select-atom-by-id 2 3 --stretch-bond 2. --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --select-atom-by-id 2 3 --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat --stretch-bond 2. --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/post/$file], 0, [ignore], [ignore])
 

tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond.at

@@ -24 +24 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file $file], 0)
 AT_CHECK([chmod +w $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-atom-by-element 6 --stretch-bond 2.], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-atom-by-element 6 --stretch-bond 2.], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/post/$file], 0, [ignore], [ignore])
 
@@ -35 +35 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file $file], 0)
 AT_CHECK([chmod +w $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-atom-by-element 6 --stretch-bond 2. --undo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-atom-by-element 6 --stretch-bond 2. --undo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file], 0, [ignore], [ignore])
 
@@ -46 +46 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/pre/$file $file], 0)
 AT_CHECK([chmod +w $file], 0)
-AT_CHECK([../../molecuilder -i $file -I --select-atom-by-element 6 --stretch-bond 2. --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file --bond-table ${abs_top_srcdir}/data/bondtables/bondtable.dat -I --select-atom-by-element 6 --stretch-bond 2. --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/StretchBond/post/$file], 0, [ignore], [ignore])