From 06bf2c39a1a24ed98213851e237c0ca2ba0cc4fe Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 2 May 2020 12:59:31 -0700
Subject: [PATCH] add pdb-dev download bcif encoding
---
src/apps/viewer/index.ts | 5 ++++-
src/mol-plugin-state/actions/structure.ts | 15 ++++++++++-----
2 files changed, 14 insertions(+), 6 deletions(-)
diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts
index cd677bf98..b38e48623 100644
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -150,7 +150,10 @@ export class Viewer {
source: {
name: 'pdb-dev' as const,
params: {
- id: pdbDev,
+ provider: {
+ id: pdbDev,
+ encoding: 'bcif',
+ },
options: params.source.params.options,
}
}
diff --git a/src/mol-plugin-state/actions/structure.ts b/src/mol-plugin-state/actions/structure.ts
index 7a46fd102..24a43eb67 100644
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.ts
@@ -32,7 +32,7 @@ export const PdbDownloadProvider = {
encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
}, { label: 'RCSB PDB', isFlat: true }),
'pdbe': PD.Group({
- variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'archival', string][]),
+ variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'updtaed-bcif' | 'archival', string][]),
}, { label: 'PDBe', isFlat: true }),
};
export type PdbDownloadProvider = keyof typeof PdbDownloadProvider;
@@ -55,7 +55,10 @@ const DownloadStructure = StateAction.build({
options
}, { isFlat: true, label: 'PDB' }),
'pdb-dev': PD.Group({
- id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
+ provider: PD.Group({
+ id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
+ encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
+ }, { pivot: 'id' }),
options
}, { isFlat: true, label: 'PDBDEV' }),
'bcif-static': PD.Group({
@@ -104,13 +107,15 @@ const DownloadStructure = StateAction.build({
asTrajectory = !!src.params.options.asTrajectory;
break;
case 'pdb-dev':
- downloadParams = getDownloadParams(src.params.id,
+ downloadParams = getDownloadParams(src.params.provider.id,
id => {
const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
- return `https://pdb-dev.wwpdb.org/cif/${nId.toUpperCase()}.cif`;
+ return src.params.provider.encoding === 'bcif'
+ ? `https://pdb-dev.wwpdb.org/bcif/${nId.toUpperCase()}.bcif`
+ : `https://pdb-dev.wwpdb.org/cif/${nId.toUpperCase()}.cif`;
},
id => id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`,
- false
+ src.params.provider.encoding === 'bcif'
);
asTrajectory = !!src.params.options.asTrajectory;
break;
--
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