Merge pull request #763 from haddocking/deepCNS

Deep CNS scripts checking and example cleaning
haddocking · Dec 22, 2023 · 09f9d70 · 09f9d70
2 parents 18a5528 + a0515fc
commit 09f9d70
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Showing 98 changed files with 1,550 additions and 1,591 deletions.
diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-full.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-full.cfg
@@ -4,7 +4,7 @@
 # directory in which the scoring will be done
 run_dir = "run1-CDR-NMR-CSP-full"
 
-# compute mode
+# execution mode
 mode = "hpc"
 # in which queue the jobs should run, if nothing is defined
 #  it will take the system's default
@@ -14,7 +14,7 @@ concat = 5
 #  Limit the number of concurrent submissions to the queue
 queue_limit = 100
 
-
+# molecules to be docked
 molecules =  [
     "data/4G6K_fv.pdb",
     "data/4I1B-matched.pdb"
@@ -26,6 +26,7 @@ molecules =  [
 [topoaa]
 
 [rigidbody]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig-CDR-NMR-CSP.tbl"
 # Restraints to keep the antibody chains together
@@ -51,6 +52,7 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [emref]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig-CDR-NMR-CSP.tbl"
 # Restraints to keep the antibody chains together
@@ -62,7 +64,7 @@ reference_fname = "data/4G6M-matched.pdb"
 [clustfcc]
 
 [seletopclusts]
-
+top_models = 4
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-test.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-test.cfg
@@ -4,7 +4,11 @@
 # directory in which the scoring will be done
 run_dir = "run1-CDR-NMR-CSP-test"
 
+# execution mode
+mode = "local"
+ncores = 40
 
+# molecules to be docked
 molecules =  [
     "data/4G6K_fv.pdb",
     "data/4I1B-matched.pdb"
@@ -16,6 +20,7 @@ molecules =  [
 [topoaa]
 
 [rigidbody]
+tolerance = 20
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig-CDR-NMR-CSP.tbl"
 # Restraints to keep the antibody chains together
@@ -32,7 +37,7 @@ select = 5
 reference_fname = "data/4G6M-matched.pdb"
 
 [flexref]
-tolerance = 1
+tolerance = 20
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig-CDR-NMR-CSP.tbl"
 # Restraints to keep the antibody chains together
@@ -42,6 +47,7 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [emref]
+tolerance = 20
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig-CDR-NMR-CSP.tbl"
 # Restraints to keep the antibody chains together
@@ -51,10 +57,10 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [clustfcc]
+threshold = 1
 
 [seletopclusts]
 
-
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"
 

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-full-mpi.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-full-mpi.cfg
@@ -9,7 +9,6 @@ mode = "mpi"
 #  5 nodes x 50 tasks = ncores = 250
 ncores = 250
 
-
 # molecules to be docked
 molecules =  [
     "data/4G6K_fv.pdb",
@@ -22,6 +21,7 @@ molecules =  [
 [topoaa]
 
 [rigidbody]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -49,18 +49,10 @@ sampling = 10000
 reference_fname = "data/4G6M-matched.pdb"
 
 [clustfcc]
-threshold = 4
 
 [seletopclusts]
-## select all the clusters
-
-## select the best 4 models of each cluster
+## select the best 20 models of each cluster
 top_models = 20
-##select all the models
-#top_models = NaN
-
-#[seletop]
-#select = 500
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"
@@ -76,6 +68,7 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [emref]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -87,7 +80,7 @@ reference_fname = "data/4G6M-matched.pdb"
 [clustfcc]
 
 [seletopclusts]
-
+top_models = 4
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-full.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-full.cfg
@@ -4,7 +4,7 @@
 # directory in which the scoring will be done
 run_dir = "run1-CDR-acc-cltsel-full"
 
-# compute mode
+# execution mode
 mode = "hpc"
 # in which queue the jobs should run, if nothing is defined
 #  it will take the system's default
@@ -14,7 +14,6 @@ concat = 5
 #  Limit the number of concurrent submissions to the queue
 queue_limit = 250
 
-
 # molecules to be docked
 molecules =  [
     "data/4G6K_fv.pdb",
@@ -27,6 +26,7 @@ molecules =  [
 [topoaa]
 
 [rigidbody]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -54,18 +54,10 @@ sampling = 10000
 reference_fname = "data/4G6M-matched.pdb"
 
 [clustfcc]
-threshold = 4
 
 [seletopclusts]
-## select all the clusters
-
-## select the best 4 models of each cluster
+# select the best 20 models of each cluster
 top_models = 20
-##select all the models
-#top_models = NaN
-
-#[seletop]
-#select = 500
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"
@@ -81,6 +73,7 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [emref]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -92,7 +85,7 @@ reference_fname = "data/4G6M-matched.pdb"
 [clustfcc]
 
 [seletopclusts]
-
+top_models = 4
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-test.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-test.cfg
@@ -4,12 +4,10 @@
 # directory in which the scoring will be done
 run_dir = "run1-CDR-acc-cltsel-test"
 
-# compute mode
+# execution mode
 mode = "local"
-
 ncores = 40
 
-
 # molecules to be docked
 molecules =  [
     "data/4G6K_fv.pdb",
@@ -22,6 +20,8 @@ molecules =  [
 [topoaa]
 
 [rigidbody]
+tolerance = 20
+sampling = 100
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -43,30 +43,22 @@ rair_end_1_5 = 172
 rair_sta_1_6 = 212
 rair_end_1_6 = 215
 
-sampling = 20
-
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"
 
 [clustfcc]
-threshold = 4
+# only 2 members per cluster required for testing
+threshold = 2
 
 [seletopclusts]
-## select all the clusters
-
-## select the best 4 models of each cluster
-top_models = 10
-##select all the models
-#top_models = NaN
-
-#[seletop]
-#select = 500
+## select the best 2 models of each cluster
+top_models = 2
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"
 
 [flexref]
-tolerance = 5
+tolerance = 20
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -76,6 +68,7 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [emref]
+tolerance = 20
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -85,10 +78,10 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [clustfcc]
+threshold = 1
 
 [seletopclusts]
 
-
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"
 

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-full-mpi.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-full-mpi.cfg
@@ -4,12 +4,11 @@
 # directory in which the scoring will be done
 run_dir = "run1-CDR-acc-full"
 
-# compute mode
+# execution mode
 mode = "mpi"
 #  5 nodes x 50 tasks = ncores = 250
 ncores = 250
 
-
 # molecules to be docked
 molecules =  [
     "data/4G6K_fv.pdb",
@@ -22,6 +21,7 @@ molecules =  [
 [topoaa]
 
 [rigidbody]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -65,6 +65,7 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [emref]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -76,7 +77,7 @@ reference_fname = "data/4G6M-matched.pdb"
 [clustfcc]
 
 [seletopclusts]
-
+top_models = 4
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-full.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-full.cfg
@@ -4,7 +4,7 @@
 # directory in which the scoring will be done
 run_dir = "run1-CDR-acc-full"
 
-# compute mode
+# execution mode
 mode = "hpc"
 # in which queue the jobs should run, if nothing is defined
 #  it will take the system's default
@@ -14,7 +14,7 @@ concat = 5
 #  Limit the number of concurrent submissions to the queue
 queue_limit = 250
 
-
+# molecules to be docked
 molecules =  [
     "data/4G6K_fv.pdb",
     "data/4I1B-matched.pdb"
@@ -26,6 +26,7 @@ molecules =  [
 [topoaa]
 
 [rigidbody]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -53,6 +54,7 @@ unambig_fname = "data/unambig.tbl"
 reference_fname = "data/4G6M-matched.pdb"
 
 [emref]
+tolerance = 5
 # CDR to surface ambig restraints
 ambig_fname = "data/ambig.tbl"
 # Restraints to keep the antibody chains together
@@ -64,7 +66,7 @@ reference_fname = "data/4G6M-matched.pdb"
 [clustfcc]
 
 [seletopclusts]
-
+top_models = 4
 
 [caprieval]
 reference_fname = "data/4G6M-matched.pdb"