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Fix parameter name in seletopclusts #184

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Merged
sverhoeven merged 4 commits into from
Feb 20, 2026
Merged

Fix parameter name in seletopclusts #184

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0bb8cbb
top_clusters in scenarios
VGPReys Feb 16, 2026
9c3ebbc
top_clusters in catalog schemes
VGPReys Feb 16, 2026
b75b8b5
fix reference fname
VGPReys Feb 18, 2026
9e8a31e
modify coloring scheme
VGPReys Feb 18, 2026
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2 changes: 1 addition & 1 deletion app/catalogs/haddock3.easy.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2186,7 +2186,7 @@
"schema": {
"type": "object",
"properties": {
"top_cluster": {
"top_clusters": {
"default": 1000,
"title": "Number of clusters to consider",
"description": "Number of clusters to consider (ranked by score)",
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2 changes: 1 addition & 1 deletion app/catalogs/haddock3.expert.json
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Expand Up @@ -8798,7 +8798,7 @@
"schema": {
"type": "object",
"properties": {
"top_cluster": {
"top_clusters": {
"default": 1000,
"title": "Number of clusters to consider",
"description": "Number of clusters to consider (ranked by score)",
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2 changes: 1 addition & 1 deletion app/catalogs/haddock3.guru.json
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Original file line number Diff line number Diff line change
Expand Up @@ -9220,7 +9220,7 @@
"schema": {
"type": "object",
"properties": {
"top_cluster": {
"top_clusters": {
"default": 1000,
"title": "Number of clusters to consider",
"description": "Number of clusters to consider (ranked by score)",
Expand Down
9 changes: 6 additions & 3 deletions app/routes/scenarios.antibody-antigen.tsx
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Expand Up @@ -116,10 +116,11 @@ ${unambig_line}

[clustfcc]
min_population = 10
plot_matrix = true

[seletopclusts]
## select all the clusters
top_cluster = 500
## select top 500 clusters
top_clusters = 500
## select the best 10 models of each cluster
top_models = 10

Expand All @@ -146,7 +147,9 @@ ${unambig_line}
[clustfcc]

[seletopclusts]
top_cluster = 500
top_clusters = 500
## select the best 10 models of each cluster
top_models = 4

[caprieval]
${ref_line}
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6 changes: 3 additions & 3 deletions app/routes/scenarios.protein-glycan.tsx
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Expand Up @@ -115,9 +115,11 @@ ${ref_line}
[clustrmsd]
criterion = 'maxclust'
n_clusters = 50 # the number of clusters to be formed
plot_matrix = true

[seletopclusts]
top_models = 5
top_clusters = 50
top_models = 20

[caprieval]
${ref_line}
Expand All @@ -135,8 +137,6 @@ ${ref_line}
[clustrmsd]
criterion = 'distance'
linkage = 'average'
# full example, 4 models should be present in a cluster
min_population = 4
clust_cutoff = 2.5

[seletopclusts]
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5 changes: 3 additions & 2 deletions app/routes/scenarios.protein-ligand.tsx
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Expand Up @@ -142,8 +142,9 @@ ${ref_line}
[ilrmsdmatrix]

[clustrmsd]
criterion = 'maxclust'
n_clusters = 4 # the number of clusters to be formed
criterion = 'distance'
clust_cutoff = 2.5
plot_matrix = true

[seletopclusts]
top_models = 4
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13 changes: 11 additions & 2 deletions app/routes/scenarios.scoring.tsx
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Expand Up @@ -29,6 +29,7 @@
import { Label } from "~/components/ui/label";
import { ActionButtons, handleActionButton } from "~/scenarios/actions";
import { FormErrors } from "~/scenarios/FormErrors";
import { ReferenceStructureInput } from "~/scenarios/ReferenceStructureInput";
import { PDBFilesInput } from "~/scenarios/PDBFilesInput.client";
import {
moleculeFieldDescription,
Expand All @@ -49,7 +50,7 @@
const fieldDescriptions = {
molecules: moleculeFieldDescription,
...getModuleDescriptions(`clustfcc`, ["clust_cutoff", "min_population"]),
...getModuleDescriptions(`seletopclusts`, ["top_models", "top_cluster"]),
...getModuleDescriptions(`seletopclusts`, ["top_models", "top_clusters"]),
} as {
// TODO do fancy typescipt so cast is not needed
molecules: Description;
Expand Down Expand Up @@ -109,6 +110,9 @@
undefined,
2,
);
const ref_line = data.reference_fname

Check failure on line 113 in app/routes/scenarios.scoring.tsx

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GitHub Actions / build (20.x) 

Property 'reference_fname' does not exist on type '{ molecules: File[]; clust_cutoff: number; min_population: number; top_models: number; top_cluster: number; }'.
? `reference_fname = "${data.reference_fname.name}"`

Check failure on line 114 in app/routes/scenarios.scoring.tsx

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GitHub Actions / build (20.x) 

Property 'reference_fname' does not exist on type '{ molecules: File[]; clust_cutoff: number; min_population: number; top_models: number; top_cluster: number; }'.
: "";

// easy is not allowed to set tolerance
const tolerance_line =
Expand Down Expand Up @@ -136,16 +140,18 @@
${tolerance_line}

[caprieval]
${ref_line}

[clustfcc]
min_population = ${data.min_population}
clust_cutoff = ${data.clust_cutoff}

[seletopclusts]
top_models = ${data.top_models}
top_cluster = ${data.top_cluster}
top_clusters = ${data.top_cluster}

[caprieval]
${ref_line}
# ===================================================================================
`;
}
Expand Down Expand Up @@ -285,6 +291,9 @@
/>
</div>
</details>
<ReferenceStructureInput>

Check failure on line 294 in app/routes/scenarios.scoring.tsx

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GitHub Actions / build (20.x) 

Property 'children' is missing in type '{}' but required in type '{ label?: string | undefined; children: ReactNode; }'.

</ReferenceStructureInput>
<FormErrors errors={errors ?? actionData?.errors} />
<ActionButtons />
</form>
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8 changes: 4 additions & 4 deletions app/scenarios/ResiduesSelect.tsx
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Expand Up @@ -164,17 +164,17 @@ export function PickIn3D({
<ToggleGroup type="single" defaultValue={value} onValueChange={onChange}>
<ToggleGroupItem
value="act"
className="data-[state=on]:bg-green-100"
className="data-[state=on]:bg-red-100"
aria-label="Picking in 3D viewer will select active"
title="Picking in 3D viewer will select active"
>
A
</ToggleGroupItem>
<ToggleGroupItem
value="pass"
className="data-[state=on]:bg-yellow-100"
aria-label="Picking in 3D will viwer select passive"
title="Picking in 3D will viwer select passive"
className="data-[state=on]:bg-green-100"
aria-label="Picking in 3D viewer will select passive"
title="Picking in 3D viewer will select passive"
>
P
</ToggleGroupItem>
Expand Down
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