From 87e0c05ec0a342bf8f0daa5105a41eb968d28caf Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 27 Aug 2019 09:54:27 -0700
Subject: [PATCH] tweaked cellpack loader: baseUrl, binary membrane file
---
src/apps/viewer/extensions/cellpack/model.ts | 12 ++++++------
src/apps/viewer/extensions/cellpack/state.ts | 7 +++++--
src/apps/viewer/extensions/cellpack/util.ts | 2 +-
3 files changed, 12 insertions(+), 9 deletions(-)
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index 32f92dcef..d96a0307e 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -21,7 +21,7 @@ import { StateTransforms } from '../../../../mol-plugin/state/transforms';
import { distinctColors } from '../../../../mol-util/color/distinct';
import { ModelIndexColorThemeProvider } from '../../../../mol-theme/color/model-index';
import { Hcl } from '../../../../mol-util/color/spaces/hcl';
-import { ParseCellPack, StructureFromCellpack } from './state';
+import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl } from './state';
import { formatMolScript } from '../../../../mol-script/language/expression-formatter';
import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
import { getMatFromResamplePoints } from './curve';
@@ -31,7 +31,7 @@ import { ThemeRegistryContext } from '../../../../mol-theme/theme';
import { ColorTheme } from '../../../../mol-theme/color';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
- return `${baseUrl}/cellPACK_database_1.1.0/results/${fileName}`
+ return `${baseUrl}/results/${fileName}`
}
async function getModel(id: string, baseUrl: string) {
@@ -177,7 +177,7 @@ export const LoadCellPackModel = StateAction.build({
['influenza_model1.json', 'influenza_model1'],
['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
]),
- baseUrl: PD.Text('https://cdn.jsdelivr.net/gh/mesoscope/cellPACK_data@master'),
+ baseUrl: PD.Text(DefaultCellPackBaseUrl),
preset: PD.Group({
traceOnly: PD.Boolean(false),
representation: PD.Select('spacefill', [
@@ -210,7 +210,7 @@ export const LoadCellPackModel = StateAction.build({
if (isHiv) {
for (let i = 0, il = packings.length; i < il; ++i) {
if (packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0') {
- const url = `${params.baseUrl}/cellPACK_database_1.1.0/extras/rna_allpoints.json`
+ const url = `${params.baseUrl}/extras/rna_allpoints.json`
const data = await ctx.fetch({ url, type: 'string' }).runInContext(taskCtx);
const { points } = await (new Response(data)).json() as { points: number[] }
@@ -257,8 +257,8 @@ export const LoadCellPackModel = StateAction.build({
}
if (isHiv) {
- const url = `${params.baseUrl}/cellPACK_database_1.1.0/membranes/hiv_lipids.bcif`
- tree.apply(StateTransforms.Data.Download, { url }, { state: { isGhost: true } })
+ const url = `${params.baseUrl}/membranes/hiv_lipids.bcif`
+ tree.apply(StateTransforms.Data.Download, { url, isBinary: true }, { state: { isGhost: true } })
.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
.apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
.apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
diff --git a/src/apps/viewer/extensions/cellpack/state.ts b/src/apps/viewer/extensions/cellpack/state.ts
index 105ed330d..61ae4062b 100644
--- a/src/apps/viewer/extensions/cellpack/state.ts
+++ b/src/apps/viewer/extensions/cellpack/state.ts
@@ -10,6 +10,9 @@ import { Task } from '../../../../mol-task';
import { CellPack as _CellPack, Cell, CellPacking } from './data';
import { createStructureFromCellPack } from './model';
+// export const DefaultCellPackBaseUrl = 'https://cdn.jsdelivr.net/gh/mesoscope/cellPACK_data@master/cellPACK_database_1.1.0/'
+export const DefaultCellPackBaseUrl = 'https://mgldev.scripps.edu/projects/autoPACK/web/cellpackproject/'
+
export class CellPack extends PSO.Create<_CellPack>({ name: 'CellPack', typeClass: 'Object' }) { }
export { ParseCellPack }
@@ -51,13 +54,13 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
if (!a) {
return {
packing: PD.Numeric(0, {}, { description: 'Packing Index' }),
- baseUrl: PD.Text('https://cdn.jsdelivr.net/gh/mesoscope/cellPACK_data@master/')
+ baseUrl: PD.Text(DefaultCellPackBaseUrl)
};
}
const options = a.data.packings.map((d, i) => [i, d.name] as [number, string])
return {
packing: PD.Select(0, options),
- baseUrl: PD.Text('https://cdn.jsdelivr.net/gh/mesoscope/cellPACK_data@master/')
+ baseUrl: PD.Text(DefaultCellPackBaseUrl)
}
}
})({
diff --git a/src/apps/viewer/extensions/cellpack/util.ts b/src/apps/viewer/extensions/cellpack/util.ts
index 2995456bd..f71e10701 100644
--- a/src/apps/viewer/extensions/cellpack/util.ts
+++ b/src/apps/viewer/extensions/cellpack/util.ts
@@ -37,7 +37,7 @@ export async function getFromPdb(id: string) {
}
function getCellPackDataUrl(id: string, baseUrl: string) {
- const url = `${baseUrl}/cellPACK_database_1.1.0/other/${id}`
+ const url = `${baseUrl}/other/${id}`
return url.endsWith('.pdb') ? url : `${url}.pdb`
}
--
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