actual tests

bjornwallner · Mar 25, 2024 · 540a70f · 540a70f
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diff --git a/run_test.sh b/run_test.sh
@@ -1,21 +1,38 @@
 #!/bin/bash
 set -euo pipefail
 
+which DockQ
+
 # Test that cython version behaves the same as nocython
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
-coverage run -a src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
-coverage run -a src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+diff test testdata/1A2K.dockq
+coverage run -a --source='DockQ.DockQ' src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+diff test testdata/1A2K.dockq
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
+diff test testdata/1A2K.dockq
+coverage run -a --source='DockQ.DockQ' 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
+
 # Multiple interfaces
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short > test
+diff test testdata/dimer_dimer.dockq
+
 # Test on structures with slightly different sequences
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/model.pdb examples/native.pdb --allowed_mismatches 1
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/model.pdb examples/native.pdb --allowed_mismatches 1 > test
+diff test testdata/model.dockq
+
 # Test various mapping strategies
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping AB*:BA*
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping :ABC
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping ABCDEFGH:BADCFEHG
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping AB*:BA* > test
+diff test testdata/1EXB_AB.BA.dockq
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping :ABC > test
+diff test testdata/1EXB_.ABC.dockq
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping ABCDEFGH:BADCFEHG > test
+diff test testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
+
 # Test that cif parsing behaves same as pdb parsing
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE > test
+diff test testdata/1EXB_DH.AE.dockq
+coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE > test
+diff test testdata/1EXB_DH.AE_cif.dockq
 
 coverage report
diff --git a/src/DockQ/DockQ.py b/src/DockQ/DockQ.py
@@ -3,6 +3,7 @@
 import sys
 import gzip
 import hashlib
+import warnings
 import traceback
 import itertools
 import math
@@ -22,7 +23,7 @@
     from .operations import residue_distances, get_fnat_stats
     from .parsers import PDBParser, MMCIFParser
 except ImportError:
-    print(
+    warnings.warn(
         """WARNING: It looks like cython is not working,
          falling back on native python. This will make DockQ slower"""
     )

diff --git a/testdata/1A2K.dockq b/testdata/1A2K.dockq
@@ -0,0 +1,37 @@
+****************************************************************
+*                       DockQ                                  *
+*   Scoring function for protein-protein docking models        *
+*   Statistics on CAPRI data:                                  *
+*    0.00 <= DockQ <  0.23 - Incorrect                         *
+*    0.23 <= DockQ <  0.49 - Acceptable quality                *
+*    0.49 <= DockQ <  0.80 - Medium quality                    *
+*            DockQ >= 0.80 - High quality                      *
+*   Ref: S. Basu and B. Wallner, DockQ: A quality measure for  *
+*   protein-protein docking models                             *
+*                            doi:10.1371/journal.pone.0161879  *
+*   For comments, please email: [email protected]          *
+****************************************************************
+Model  : examples/1A2K_r_l_b.model.pdb
+Native : examples/1A2K_r_l_b.pdb
+Total DockQ over 3 native interfaces: 1.959
+Native chains: A, B
+	Model chains: B, A
+	DockQ_F1: 0.996
+	DockQ: 0.994
+	irms: 0.000
+	Lrms: 0.000
+	fnat: 0.983
+Native chains: A, C
+	Model chains: B, C
+	DockQ_F1: 0.567
+	DockQ: 0.511
+	irms: 1.237
+	Lrms: 6.864
+	fnat: 0.333
+Native chains: B, C
+	Model chains: A, C
+	DockQ_F1: 0.500
+	DockQ: 0.453
+	irms: 2.104
+	Lrms: 8.131
+	fnat: 0.500
diff --git a/testdata/1EXB_.ABC.dockq b/testdata/1EXB_.ABC.dockq
@@ -0,0 +1,3 @@
+Total DockQ over 2 native interfaces: 0.998 with ABC:ABC model:native mapping
+DockQ 0.995 DockQ_F1 0.998 Fnat 0.985 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AC:AC examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb A C
+DockQ 1.000 DockQ_F1 1.000 Fnat 1.000 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping BC:BC examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb B C
diff --git a/testdata/1EXB_AB.BA.dockq b/testdata/1EXB_AB.BA.dockq
@@ -0,0 +1,17 @@
+Total DockQ over 16 native interfaces: 0.852 with ABCDFHEG:BADCEGFH model:native mapping
+DockQ 0.995 DockQ_F1 0.998 Fnat 0.985 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
+DockQ 0.995 DockQ_F1 0.998 Fnat 0.985 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.742 DockQ_F1 0.772 Fnat 0.609 iRMS 0.850 LRMS 3.426 Fnonnat 0.176 clashes 0 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
+DockQ 0.824 DockQ_F1 0.853 Fnat 0.800 iRMS 0.625 LRMS 3.994 Fnonnat 0.000 clashes 0 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
+DockQ 1.000 DockQ_F1 1.000 Fnat 1.000 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
+DockQ 0.995 DockQ_F1 0.998 Fnat 0.985 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
+DockQ 0.552 DockQ_F1 0.606 Fnat 0.304 iRMS 1.458 LRMS 3.757 Fnonnat 0.000 clashes 0 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
+DockQ 0.694 DockQ_F1 0.751 Fnat 0.400 iRMS 0.793 LRMS 2.831 Fnonnat 0.000 clashes 0 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
+DockQ 0.687 DockQ_F1 0.737 Fnat 0.600 iRMS 1.161 LRMS 3.757 Fnonnat 0.000 clashes 0 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
+DockQ 0.477 DockQ_F1 0.502 Fnat 0.087 iRMS 1.425 LRMS 3.994 Fnonnat 0.000 clashes 0 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
+DockQ 0.775 DockQ_F1 0.812 Fnat 0.609 iRMS 0.711 LRMS 2.831 Fnonnat 0.125 clashes 0 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
+DockQ 0.914 DockQ_F1 0.914 Fnat 1.000 iRMS 0.547 LRMS 3.426 Fnonnat 0.000 clashes 0 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
+DockQ 0.992 DockQ_F1 0.996 Fnat 0.976 iRMS 0.001 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
+DockQ 0.992 DockQ_F1 0.996 Fnat 0.976 iRMS 0.001 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
+DockQ 0.992 DockQ_F1 0.996 Fnat 0.976 iRMS 0.001 LRMS 0.001 Fnonnat 0.000 clashes 0 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
+DockQ 1.000 DockQ_F1 0.996 Fnat 1.000 iRMS 0.001 LRMS 0.001 Fnonnat 0.024 clashes 0 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
diff --git a/testdata/1EXB_ABCDEFGH.BADCFEHG.dockq b/testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
@@ -0,0 +1,17 @@
+Total DockQ over 16 native interfaces: 0.852 with ABCDEFGH:BADCFEHG model:native mapping
+DockQ 0.995 DockQ_F1 0.998 Fnat 0.985 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
+DockQ 0.995 DockQ_F1 0.998 Fnat 0.985 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.742 DockQ_F1 0.772 Fnat 0.609 iRMS 0.850 LRMS 3.426 Fnonnat 0.176 clashes 0 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
+DockQ 0.824 DockQ_F1 0.853 Fnat 0.800 iRMS 0.625 LRMS 3.994 Fnonnat 0.000 clashes 0 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
+DockQ 1.000 DockQ_F1 1.000 Fnat 1.000 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
+DockQ 0.995 DockQ_F1 0.998 Fnat 0.985 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
+DockQ 0.552 DockQ_F1 0.606 Fnat 0.304 iRMS 1.458 LRMS 3.757 Fnonnat 0.000 clashes 0 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
+DockQ 0.694 DockQ_F1 0.751 Fnat 0.400 iRMS 0.793 LRMS 2.831 Fnonnat 0.000 clashes 0 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
+DockQ 0.687 DockQ_F1 0.737 Fnat 0.600 iRMS 1.161 LRMS 3.757 Fnonnat 0.000 clashes 0 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
+DockQ 0.477 DockQ_F1 0.502 Fnat 0.087 iRMS 1.425 LRMS 3.994 Fnonnat 0.000 clashes 0 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
+DockQ 0.914 DockQ_F1 0.914 Fnat 1.000 iRMS 0.547 LRMS 3.426 Fnonnat 0.000 clashes 0 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
+DockQ 0.775 DockQ_F1 0.812 Fnat 0.609 iRMS 0.711 LRMS 2.831 Fnonnat 0.125 clashes 0 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
+DockQ 1.000 DockQ_F1 0.996 Fnat 1.000 iRMS 0.001 LRMS 0.001 Fnonnat 0.024 clashes 0 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
+DockQ 0.992 DockQ_F1 0.996 Fnat 0.976 iRMS 0.001 LRMS 0.001 Fnonnat 0.000 clashes 0 mapping EH:FG examples/1EXB_r_l_b.model.pdb E H -> examples/1EXB_r_l_b.pdb F G
+DockQ 0.992 DockQ_F1 0.996 Fnat 0.976 iRMS 0.001 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
+DockQ 0.992 DockQ_F1 0.996 Fnat 0.976 iRMS 0.001 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
diff --git a/testdata/1EXB_DH.AE.dockq b/testdata/1EXB_DH.AE.dockq
@@ -0,0 +1,23 @@
+****************************************************************
+*                       DockQ                                  *
+*   Scoring function for protein-protein docking models        *
+*   Statistics on CAPRI data:                                  *
+*    0.00 <= DockQ <  0.23 - Incorrect                         *
+*    0.23 <= DockQ <  0.49 - Acceptable quality                *
+*    0.49 <= DockQ <  0.80 - Medium quality                    *
+*            DockQ >= 0.80 - High quality                      *
+*   Ref: S. Basu and B. Wallner, DockQ: A quality measure for  *
+*   protein-protein docking models                             *
+*                            doi:10.1371/journal.pone.0161879  *
+*   For comments, please email: [email protected]          *
+****************************************************************
+Model  : examples/1EXB_r_l_b.model.pdb
+Native : examples/1EXB_r_l_b.pdb
+Total DockQ over 1 native interfaces: 0.775
+Native chains: A, E
+	Model chains: D, H
+	DockQ_F1: 0.812
+	DockQ: 0.775
+	irms: 0.711
+	Lrms: 2.831
+	fnat: 0.609
diff --git a/testdata/1EXB_DH.AE_cif.dockq b/testdata/1EXB_DH.AE_cif.dockq
@@ -0,0 +1,23 @@
+****************************************************************
+*                       DockQ                                  *
+*   Scoring function for protein-protein docking models        *
+*   Statistics on CAPRI data:                                  *
+*    0.00 <= DockQ <  0.23 - Incorrect                         *
+*    0.23 <= DockQ <  0.49 - Acceptable quality                *
+*    0.49 <= DockQ <  0.80 - Medium quality                    *
+*            DockQ >= 0.80 - High quality                      *
+*   Ref: S. Basu and B. Wallner, DockQ: A quality measure for  *
+*   protein-protein docking models                             *
+*                            doi:10.1371/journal.pone.0161879  *
+*   For comments, please email: [email protected]          *
+****************************************************************
+Model  : examples/1EXB_r_l_b.model.pdb
+Native : examples/1EXB.cif.gz
+Total DockQ over 1 native interfaces: 0.775
+Native chains: A, E
+	Model chains: D, H
+	DockQ_F1: 0.812
+	DockQ: 0.775
+	irms: 0.711
+	Lrms: 2.831
+	fnat: 0.609
diff --git a/testdata/dimer_dimer.dockq b/testdata/dimer_dimer.dockq
@@ -0,0 +1,5 @@
+Total DockQ over 4 native interfaces: 1.000 with ABLH:ABLH model:native mapping
+DockQ 1.000 DockQ_F1 1.000 Fnat 1.000 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AB:AB examples/dimer_dimer.model.pdb A B -> examples/dimer_dimer.pdb A B
+DockQ 1.000 DockQ_F1 1.000 Fnat 1.000 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AL:AL examples/dimer_dimer.model.pdb A L -> examples/dimer_dimer.pdb A L
+DockQ 1.000 DockQ_F1 1.000 Fnat 1.000 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping AH:AH examples/dimer_dimer.model.pdb A H -> examples/dimer_dimer.pdb A H
+DockQ 1.000 DockQ_F1 1.000 Fnat 1.000 iRMS 0.000 LRMS 0.000 Fnonnat 0.000 clashes 0 mapping LH:LH examples/dimer_dimer.model.pdb L H -> examples/dimer_dimer.pdb L H
diff --git a/testdata/model.dockq b/testdata/model.dockq
@@ -0,0 +1,23 @@
+****************************************************************
+*                       DockQ                                  *
+*   Scoring function for protein-protein docking models        *
+*   Statistics on CAPRI data:                                  *
+*    0.00 <= DockQ <  0.23 - Incorrect                         *
+*    0.23 <= DockQ <  0.49 - Acceptable quality                *
+*    0.49 <= DockQ <  0.80 - Medium quality                    *
+*            DockQ >= 0.80 - High quality                      *
+*   Ref: S. Basu and B. Wallner, DockQ: A quality measure for  *
+*   protein-protein docking models                             *
+*                            doi:10.1371/journal.pone.0161879  *
+*   For comments, please email: [email protected]          *
+****************************************************************
+Model  : examples/model.pdb
+Native : examples/native.pdb
+Total DockQ over 1 native interfaces: 0.700
+Native chains: A, B
+	Model chains: A, B
+	DockQ_F1: 0.731
+	DockQ: 0.700
+	irms: 1.232
+	Lrms: 1.516
+	fnat: 0.533