ignore new headers in test

bjornwallner · May 16, 2024 · 5d09aac · 5d09aac
1 parent ac37693
commit 5d09aac
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Showing 2 changed files with 24 additions and 41 deletions.
diff --git a/run_test.sh b/run_test.sh
@@ -10,18 +10,18 @@ else
 fi
 
 $binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
-diff test testdata/1A2K.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
 
 $binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
-diff test testdata/1A2K.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
 
 # Multiple interfaces
 $binary examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb --short > test
 diff test testdata/dimer_dimer.dockq
 
 # Test on structures with slightly different sequences
 $binary examples/model.pdb examples/native.pdb --allowed_mismatches 1 > test
-diff test testdata/model.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/model.dockq)
 
 # lowmem test
 $binary examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short > test
@@ -37,21 +37,21 @@ diff test testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
 
 # Test that cif parsing behaves same as pdb parsing
 $binary examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE > test
-diff test testdata/1EXB_DH.AE.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/1EXB_DH.AE.dockq)
 $binary examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE > test
-diff test testdata/1EXB_DH.AE_cif.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/1EXB_DH.AE_cif.dockq)
 
 # Peptide measures
 $binary examples/6qwn-assembly1.cif.gz examples/6qwn-assembly2.cif.gz --capri_peptide > test
-diff test testdata/6q2n_peptide.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/6q2n_peptide.dockq)
 
 # Small molecule test
-$binary examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG
+$binary examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG > test
 
 # Test that cython version behaves the same as nocython
 python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
-diff test testdata/1A2K.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
 python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
-diff test testdata/1A2K.dockq
+diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
 
 coverage combine
diff --git a/src/DockQ/DockQ.py b/src/DockQ/DockQ.py
@@ -170,7 +170,6 @@ def calc_sym_corrected_lrmsd(
     sample_chains,
     ref_chains,
     alignments,
-    low_memory=False,
 ):
     import networkx as nx
     is_het_sample_0 = bool(sample_chains[0].is_het)
@@ -592,7 +591,6 @@ def run_on_chains(
             model_chains,
             native_chains,
             alignments=tuple(alignments),
-            low_memory=low_memory,
         )
     return info
 
@@ -981,38 +979,23 @@ def print_results(info, short=False, verbose=False, capri_peptide=False, small_m
 
 def print_header(verbose=False, capri_peptide=False, small_molecule=False):
     reference = (
-        "*   Ref: S. Basu and B. Wallner, DockQ: A quality measure for  *\n"
-        "*   protein-protein docking models                             *\n"
-        "*                            doi:10.1371/journal.pone.0161879  *\n"
+        "*   Ref: Mirabello and Wallner, 'DockQ v2: Improved automatic  *\n"
+        "*   quality measure for protein multimers, nucleic acids       *\n"
+        "*   and small molecules'                                       *\n"
+        "*                                                              *\n"
         "*   For comments, please email: [email protected]          *"
     )
-    if not capri_peptide:
-        header = (
-            "****************************************************************\n"
-            "*                       DockQ                                  *\n"
-            "*   Scoring function for protein-protein docking models        *\n"
-            "*   Statistics on CAPRI data:                                  *\n"
-            "*    0.00 <= DockQ <  0.23 - Incorrect                         *\n"
-            "*    0.23 <= DockQ <  0.49 - Acceptable quality                *\n"
-            "*    0.49 <= DockQ <  0.80 - Medium quality                    *\n"
-            "*            DockQ >= 0.80 - High quality                      *"
-        )
-    elif not small_molecule:
-        header = (
-            "****************************************************************\n"
-            "*                DockQ-CAPRI peptide                           *\n"
-            "*   Do not trust any thing you read....                        *\n"
-            "*   OBS THE DEFINITION OF Fnat and iRMS are different for      *\n"
-            "*   peptides in CAPRI                                          *\n"
-            "*                                                              *"
-        )
-    else:
-        header = (
-            "****************************************************************\n"
-            "*                DockQ-small molecules                         *\n"
-            "*   LRMSD is reported for small molecule ligands               *\n"
-            "*   DockQ is reported for macromolecules                       *"
-        )
+
+    header = (
+        "****************************************************************\n"
+        "*                       DockQ                                  *\n"
+        "*   Scoring function for biomolecular models                   *\n"
+        "*   DockQ score legend (proteins and nucleic acids only):      *\n"
+        "*    0.00 <= DockQ <  0.23 - Incorrect                         *\n"
+        "*    0.23 <= DockQ <  0.49 - Acceptable quality                *\n"
+        "*    0.49 <= DockQ <  0.80 - Medium quality                    *\n"
+        "*            DockQ >= 0.80 - High quality                      *"
+    )
 
     if verbose:
         notice = (