From e28674d0dc65eb88aeba806cbf326376a203e667 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Wed, 3 Feb 2021 19:36:01 -0800
Subject: [PATCH] model format improvements
- add a source format to the mmcif format
- add pdb format
- allow undefined in typeguard .is helpers
---
src/mol-model-formats/structure/cif-core.ts | 4 ++--
src/mol-model-formats/structure/cube.ts | 4 ++--
src/mol-model-formats/structure/gro.ts | 4 ++--
src/mol-model-formats/structure/mmcif.ts | 20 +++++++++++++------
src/mol-model-formats/structure/mol.ts | 4 ++--
src/mol-model-formats/structure/mol2.ts | 4 ++--
src/mol-model-formats/structure/pdb.ts | 17 +++++++++++++++-
src/mol-model-formats/structure/psf.ts | 4 ++--
src/mol-model-formats/volume/ccp4.ts | 4 ++--
src/mol-model-formats/volume/cube.ts | 4 ++--
.../volume/density-server.ts | 4 ++--
src/mol-model-formats/volume/dsn6.ts | 4 ++--
src/mol-model-formats/volume/dx.ts | 4 ++--
13 files changed, 52 insertions(+), 29 deletions(-)
diff --git a/src/mol-model-formats/structure/cif-core.ts b/src/mol-model-formats/structure/cif-core.ts
index e3e3bd296..75af4d45f 100644
--- a/src/mol-model-formats/structure/cif-core.ts
+++ b/src/mol-model-formats/structure/cif-core.ts
@@ -251,8 +251,8 @@ type CifCoreFormat = ModelFormat<CifCoreFormat.Data>
namespace CifCoreFormat {
export type Data = { db: CifCore_Database, frame: CifFrame }
- export function is(x: ModelFormat): x is CifCoreFormat {
- return x.kind === 'cifCore';
+ export function is(x?: ModelFormat): x is CifCoreFormat {
+ return x?.kind === 'cifCore';
}
export function fromFrame(frame: CifFrame, db?: CifCore_Database): CifCoreFormat {
diff --git a/src/mol-model-formats/structure/cube.ts b/src/mol-model-formats/structure/cube.ts
index 9983693f0..1c04f685d 100644
--- a/src/mol-model-formats/structure/cube.ts
+++ b/src/mol-model-formats/structure/cube.ts
@@ -69,8 +69,8 @@ export { CubeFormat };
type CubeFormat = ModelFormat<CubeFile>
namespace MolFormat {
- export function is(x: ModelFormat): x is CubeFormat {
- return x.kind === 'cube';
+ export function is(x?: ModelFormat): x is CubeFormat {
+ return x?.kind === 'cube';
}
export function create(cube: CubeFile): CubeFormat {
diff --git a/src/mol-model-formats/structure/gro.ts b/src/mol-model-formats/structure/gro.ts
index af13e6c01..33f0efac5 100644
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -106,8 +106,8 @@ export { GroFormat };
type GroFormat = ModelFormat<GroFile>
namespace GroFormat {
- export function is(x: ModelFormat): x is GroFormat {
- return x.kind === 'gro';
+ export function is(x?: ModelFormat): x is GroFormat {
+ return x?.kind === 'gro';
}
export function fromGro(gro: GroFile): GroFormat {
diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts
index 67caefba3..9ccb7d28d 100644
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -79,14 +79,22 @@ export { MmcifFormat };
type MmcifFormat = ModelFormat<MmcifFormat.Data>
namespace MmcifFormat {
- export type Data = { db: mmCIF_Database, frame: CifFrame }
- export function is(x: ModelFormat): x is MmcifFormat {
- return x.kind === 'mmCIF';
+ export type Data = {
+ db: mmCIF_Database,
+ frame: CifFrame,
+ /**
+ * Original source format. Some formats, including PDB, are converted
+ * to mmCIF before further processing.
+ */
+ source?: ModelFormat
+ }
+ export function is(x?: ModelFormat): x is MmcifFormat {
+ return x?.kind === 'mmCIF';
}
- export function fromFrame(frame: CifFrame, db?: mmCIF_Database): MmcifFormat {
+ export function fromFrame(frame: CifFrame, db?: mmCIF_Database, source?: ModelFormat): MmcifFormat {
if (!db) db = CIF.schema.mmCIF(frame);
- return { kind: 'mmCIF', name: db._name, data: { db, frame } };
+ return { kind: 'mmCIF', name: db._name, data: { db, frame, source } };
}
}
diff --git a/src/mol-model-formats/structure/mol.ts b/src/mol-model-formats/structure/mol.ts
index 51f45c0d0..fb66c34e8 100644
--- a/src/mol-model-formats/structure/mol.ts
+++ b/src/mol-model-formats/structure/mol.ts
@@ -81,8 +81,8 @@ export { MolFormat };
type MolFormat = ModelFormat<MolFile>
namespace MolFormat {
- export function is(x: ModelFormat): x is MolFormat {
- return x.kind === 'mol';
+ export function is(x?: ModelFormat): x is MolFormat {
+ return x?.kind === 'mol';
}
export function create(mol: MolFile): MolFormat {
diff --git a/src/mol-model-formats/structure/mol2.ts b/src/mol-model-formats/structure/mol2.ts
index 43772c8ad..ec9565fe0 100644
--- a/src/mol-model-formats/structure/mol2.ts
+++ b/src/mol-model-formats/structure/mol2.ts
@@ -99,8 +99,8 @@ export { Mol2Format };
type Mol2Format = ModelFormat<Mol2File>
namespace Mol2Format {
- export function is(x: ModelFormat): x is Mol2Format {
- return x.kind === 'mol2';
+ export function is(x?: ModelFormat): x is Mol2Format {
+ return x?.kind === 'mol2';
}
export function create(mol2: Mol2File): Mol2Format {
diff --git a/src/mol-model-formats/structure/pdb.ts b/src/mol-model-formats/structure/pdb.ts
index 87c6006e9..8f794c328 100644
--- a/src/mol-model-formats/structure/pdb.ts
+++ b/src/mol-model-formats/structure/pdb.ts
@@ -13,12 +13,27 @@ import { createModels } from './basic/parser';
import { Column } from '../../mol-data/db';
import { AtomPartialCharge } from './property/partial-charge';
import { Trajectory } from '../../mol-model/structure';
+import { ModelFormat } from '../format';
+
+export { PdbFormat };
+
+type PdbFormat = ModelFormat<PdbFile>
+
+namespace PdbFormat {
+ export function is(x?: ModelFormat): x is PdbFormat {
+ return x?.kind === 'pdb';
+ }
+
+ export function create(pdb: PdbFile): PdbFormat {
+ return { kind: 'pdb', name: pdb.id || '', data: pdb };
+ }
+}
export function trajectoryFromPDB(pdb: PdbFile): Task<Trajectory> {
return Task.create('Parse PDB', async ctx => {
await ctx.update('Converting to mmCIF');
const cif = await pdbToMmCif(pdb);
- const format = MmcifFormat.fromFrame(cif);
+ const format = MmcifFormat.fromFrame(cif, undefined, PdbFormat.create(pdb));
const models = await createModels(format.data.db, format, ctx);
const partial_charge = cif.categories['atom_site']?.getField('partial_charge');
if (partial_charge) {
diff --git a/src/mol-model-formats/structure/psf.ts b/src/mol-model-formats/structure/psf.ts
index 344795f79..362cf9f22 100644
--- a/src/mol-model-formats/structure/psf.ts
+++ b/src/mol-model-formats/structure/psf.ts
@@ -103,8 +103,8 @@ export { PsfFormat };
type PsfFormat = ModelFormat<PsfFile>
namespace PsfFormat {
- export function is(x: ModelFormat): x is PsfFormat {
- return x.kind === 'psf';
+ export function is(x?: ModelFormat): x is PsfFormat {
+ return x?.kind === 'psf';
}
export function fromPsf(psf: PsfFile): PsfFormat {
diff --git a/src/mol-model-formats/volume/ccp4.ts b/src/mol-model-formats/volume/ccp4.ts
index c86cb08b1..753713c95 100644
--- a/src/mol-model-formats/volume/ccp4.ts
+++ b/src/mol-model-formats/volume/ccp4.ts
@@ -98,8 +98,8 @@ export { Ccp4Format };
type Ccp4Format = ModelFormat<Ccp4File>
namespace Ccp4Format {
- export function is(x: ModelFormat): x is Ccp4Format {
- return x.kind === 'ccp4';
+ export function is(x?: ModelFormat): x is Ccp4Format {
+ return x?.kind === 'ccp4';
}
export function create(ccp4: Ccp4File): Ccp4Format {
diff --git a/src/mol-model-formats/volume/cube.ts b/src/mol-model-formats/volume/cube.ts
index 224812fd5..6ff8ea4c0 100644
--- a/src/mol-model-formats/volume/cube.ts
+++ b/src/mol-model-formats/volume/cube.ts
@@ -71,8 +71,8 @@ export { CubeFormat };
type CubeFormat = ModelFormat<CubeFile>
namespace CubeFormat {
- export function is(x: ModelFormat): x is CubeFormat {
- return x.kind === 'cube';
+ export function is(x?: ModelFormat): x is CubeFormat {
+ return x?.kind === 'cube';
}
export function create(cube: CubeFile): CubeFormat {
diff --git a/src/mol-model-formats/volume/density-server.ts b/src/mol-model-formats/volume/density-server.ts
index 5e8a3ab5d..65b88fb50 100644
--- a/src/mol-model-formats/volume/density-server.ts
+++ b/src/mol-model-formats/volume/density-server.ts
@@ -62,8 +62,8 @@ export { DscifFormat };
type DscifFormat = ModelFormat<DensityServer_Data_Database>
namespace DscifFormat {
- export function is(x: ModelFormat): x is DscifFormat {
- return x.kind === 'dscif';
+ export function is(x?: ModelFormat): x is DscifFormat {
+ return x?.kind === 'dscif';
}
export function create(dscif: DensityServer_Data_Database): DscifFormat {
diff --git a/src/mol-model-formats/volume/dsn6.ts b/src/mol-model-formats/volume/dsn6.ts
index 75196b04a..ae1973438 100644
--- a/src/mol-model-formats/volume/dsn6.ts
+++ b/src/mol-model-formats/volume/dsn6.ts
@@ -60,8 +60,8 @@ export { Dsn6Format };
type Dsn6Format = ModelFormat<Dsn6File>
namespace Dsn6Format {
- export function is(x: ModelFormat): x is Dsn6Format {
- return x.kind === 'dsn6';
+ export function is(x?: ModelFormat): x is Dsn6Format {
+ return x?.kind === 'dsn6';
}
export function create(dsn6: Dsn6File): Dsn6Format {
diff --git a/src/mol-model-formats/volume/dx.ts b/src/mol-model-formats/volume/dx.ts
index e850511c4..d27e7c94c 100644
--- a/src/mol-model-formats/volume/dx.ts
+++ b/src/mol-model-formats/volume/dx.ts
@@ -48,8 +48,8 @@ export { DxFormat };
type DxFormat = ModelFormat<DxFile>
namespace DxFormat {
- export function is(x: ModelFormat): x is DxFormat {
- return x.kind === 'dx';
+ export function is(x?: ModelFormat): x is DxFormat {
+ return x?.kind === 'dx';
}
export function create(dx: DxFile): DxFormat {
--
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