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Deep CNS scripts checking and example cleaning #763

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merged 11 commits into from
Dec 22, 2023
Merged

Deep CNS scripts checking and example cleaning #763

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877a136
A deep dive into CNS outputs to identify and solve reported error mes…
amjjbonvin Dec 20, 2023
0f7bf62
Updated print_coorheader to check for existence of a variable
amjjbonvin Dec 20, 2023
a150f3b
Removed unnecessary warning
amjjbonvin Dec 20, 2023
7ef29e2
Corrected example config files
amjjbonvin Dec 20, 2023
b97e8b6
Merge branch 'main' into deepCNS
rvhonorato Dec 21, 2023
aa15e63
Updated alascan integration test
amjjbonvin Dec 21, 2023
8289ca9
updates alascan integration test
amjjbonvin Dec 21, 2023
75682b7
updates alascan integration test
amjjbonvin Dec 21, 2023
39df951
consistent verbosity definition for param/topo file
amjjbonvin Dec 21, 2023
cb3f33b
two more cleaned config files
amjjbonvin Dec 21, 2023
a0515fc
added seletopclusts to all examples (where possible)
amjjbonvin Dec 22, 2023
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8 changes: 5 additions & 3 deletions examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-full.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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"
Expand All @@ -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
Expand All @@ -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
Expand All @@ -62,7 +64,7 @@ reference_fname = "data/4G6M-matched.pdb"
[clustfcc]

[seletopclusts]

top_models = 4

[caprieval]
reference_fname = "data/4G6M-matched.pdb"
Expand Down
10 changes: 8 additions & 2 deletions examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-test.cfg
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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"

Expand Down
15 changes: 4 additions & 11 deletions examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-full-mpi.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@ mode = "mpi"
# 5 nodes x 50 tasks = ncores = 250
ncores = 250


# molecules to be docked
molecules = [
"data/4G6K_fv.pdb",
Expand All @@ -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
Expand Down Expand Up @@ -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"
Expand All @@ -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
Expand All @@ -87,7 +80,7 @@ reference_fname = "data/4G6M-matched.pdb"
[clustfcc]

[seletopclusts]

top_models = 4

[caprieval]
reference_fname = "data/4G6M-matched.pdb"
Expand Down
17 changes: 5 additions & 12 deletions examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-full.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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",
Expand All @@ -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
Expand Down Expand Up @@ -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"
Expand All @@ -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
Expand All @@ -92,7 +85,7 @@ reference_fname = "data/4G6M-matched.pdb"
[clustfcc]

[seletopclusts]

top_models = 4

[caprieval]
reference_fname = "data/4G6M-matched.pdb"
Expand Down
27 changes: 10 additions & 17 deletions examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-test.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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"

Expand Down
7 changes: 4 additions & 3 deletions examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-full-mpi.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -76,7 +77,7 @@ reference_fname = "data/4G6M-matched.pdb"
[clustfcc]

[seletopclusts]

top_models = 4

[caprieval]
reference_fname = "data/4G6M-matched.pdb"
Expand Down
8 changes: 5 additions & 3 deletions examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-full.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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"
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -64,7 +66,7 @@ reference_fname = "data/4G6M-matched.pdb"
[clustfcc]

[seletopclusts]

top_models = 4

[caprieval]
reference_fname = "data/4G6M-matched.pdb"
Expand Down
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