From ab2031f79bffb19f21fff5f6a74084765cbb3b63 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 30 Oct 2017 17:27:23 +0100
Subject: [PATCH] data model (part 2 of ???)
---
src/mol-base/utils/bit-flags.ts | 13 ++
src/mol-data/model.ts | 4 +-
src/mol-data/model/properties/basic.ts | 28 ----
src/mol-data/model/properties/conformation.ts | 20 ++-
src/mol-data/model/properties/hierarchy.ts | 62 +++++++++
.../model/properties/macromolecule.ts | 72 ----------
.../model/properties/secondary-structure.ts | 128 ++++++++++++++++++
src/mol-data/model/properties/symmetry.ts | 0
src/mol-data/model/properties/transforms.ts | 9 ++
src/mol-data/query.ts | 2 +-
src/mol-data/{ => query}/selection.ts | 2 +-
11 files changed, 232 insertions(+), 108 deletions(-)
create mode 100644 src/mol-base/utils/bit-flags.ts
delete mode 100644 src/mol-data/model/properties/basic.ts
create mode 100644 src/mol-data/model/properties/hierarchy.ts
delete mode 100644 src/mol-data/model/properties/macromolecule.ts
create mode 100644 src/mol-data/model/properties/secondary-structure.ts
delete mode 100644 src/mol-data/model/properties/symmetry.ts
create mode 100644 src/mol-data/model/properties/transforms.ts
rename src/mol-data/{ => query}/selection.ts (94%)
diff --git a/src/mol-base/utils/bit-flags.ts b/src/mol-base/utils/bit-flags.ts
new file mode 100644
index 000000000..e5cd20290
--- /dev/null
+++ b/src/mol-base/utils/bit-flags.ts
@@ -0,0 +1,13 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+interface BitFlags<Flags> { '@type': Flags }
+
+namespace BitFlags {
+ export function has<F>(flags: BitFlags<F>, flag: F) { return ((flags as any) & (flag as any)) !== 0; }
+}
+
+export default BitFlags
\ No newline at end of file
diff --git a/src/mol-data/model.ts b/src/mol-data/model.ts
index 2d238f801..3572e7618 100644
--- a/src/mol-data/model.ts
+++ b/src/mol-data/model.ts
@@ -6,7 +6,7 @@
import * as Formats from './model/formats'
//import CommonProperties from './model/properties/common'
-import MacromoleculeProperties from './model/properties/macromolecule'
+import HierarchyProperties from './model/properties/hierarchy'
import Conformation from './model/properties/conformation'
import Segmentation from '../mol-base/collections/integer/segmentation'
@@ -23,7 +23,7 @@ interface Model extends Readonly<{
sourceData: Formats.RawData,
//common: CommonProperties,
- macromolecule: MacromoleculeProperties,
+ macromolecule: HierarchyProperties,
conformation: Conformation,
// used for diffing.
diff --git a/src/mol-data/model/properties/basic.ts b/src/mol-data/model/properties/basic.ts
deleted file mode 100644
index 1837912b6..000000000
--- a/src/mol-data/model/properties/basic.ts
+++ /dev/null
@@ -1,28 +0,0 @@
-/**
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import Column from '../../../mol-base/collections/column'
-
-export type Table<Data> = { [E in keyof Data]: Column<Data[E]> }
-
-export interface ElementSymbol extends String { '@type': 'element-symbol' }
-export function ElementSymbol(s: string): ElementSymbol {
- // TODO: optimize?
- return s.toUpperCase() as any;
-}
-
-
-export interface Atoms extends Table<{
- name: string,
- elementSymbol: ElementSymbol,
-
-}> { }
-
-interface Common {
-
-}
-
-export default Common
\ No newline at end of file
diff --git a/src/mol-data/model/properties/conformation.ts b/src/mol-data/model/properties/conformation.ts
index 7c18e8ab5..ac90abac4 100644
--- a/src/mol-data/model/properties/conformation.ts
+++ b/src/mol-data/model/properties/conformation.ts
@@ -4,13 +4,25 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-interface Conformation {
+import { SecondaryStructureFlag as SSF } from './secondary-structure'
+import BitFlags from '../../../mol-base/utils/bit-flags'
+import Segmentation from '../../../mol-base/collections/integer/segmentation'
+
+interface Positions {
x: ArrayLike<number>,
y: ArrayLike<number>,
- z: ArrayLike<number>,
+ z: ArrayLike<number>
+}
- // Assign a secondary structure type to each residue.
- secondaryStructureType: ArrayLike<any>
+interface SecondaryStructure {
+ ofResidue: ArrayLike<BitFlags<SSF>>,
+ // atom segmentation
+ segments: Segmentation
+}
+
+interface Conformation {
+ positions: Positions,
+ secondaryStructureType: SecondaryStructure
}
export default Conformation
diff --git a/src/mol-data/model/properties/hierarchy.ts b/src/mol-data/model/properties/hierarchy.ts
new file mode 100644
index 000000000..427b2a1bc
--- /dev/null
+++ b/src/mol-data/model/properties/hierarchy.ts
@@ -0,0 +1,62 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Column from '../../../mol-base/collections/column'
+import { Shape as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
+
+export interface ElementSymbol extends String { '@type': 'element-symbol' }
+export function ElementSymbol(s: string): ElementSymbol {
+ // TODO: optimize?
+ return s.toUpperCase() as any;
+}
+
+type Key = { key: Column<number> }
+
+type _Atoms = Pick<mmCIF['atom_site'],
+ | 'type_symbol'
+ | 'label_atom_id'
+ | 'auth_atom_id'
+ | 'label_alt_id'
+ | 'pdbx_formal_charge'
+ | 'occupancy'
+ | 'B_iso_or_equiv'>
+ & Key
+export interface Atoms extends _Atoms {
+ source_row: Column<number>
+}
+
+type _Residues = Pick<mmCIF['atom_site'],
+ | 'group_PDB'
+ | 'label_comp_id'
+ | 'auth_comp_id'
+ | 'label_seq_id'
+ | 'auth_seq_id'
+ | 'pdbx_PDB_ins_code'>
+ & Key
+export interface Residues extends _Residues { }
+
+type _Chains = Pick<mmCIF['atom_site'],
+ | 'label_asym_id'
+ | 'auth_asym_id'
+ | 'auth_comp_id'
+ | 'label_entity_id'
+ | 'pdbx_PDB_model_num'>
+ & Key
+export interface Chains extends _Chains {
+ enityDataIndex: Column<number>
+}
+
+type _EntityData = mmCIF['entity']
+export interface EntityData extends _EntityData { }
+
+export interface Macromolecule {
+ atoms: Atoms,
+ residues: Residues,
+ chains: Chains,
+ entityData: EntityData
+}
+
+export default Macromolecule
\ No newline at end of file
diff --git a/src/mol-data/model/properties/macromolecule.ts b/src/mol-data/model/properties/macromolecule.ts
deleted file mode 100644
index 1285ba4d3..000000000
--- a/src/mol-data/model/properties/macromolecule.ts
+++ /dev/null
@@ -1,72 +0,0 @@
-/**
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import Column from '../../../mol-base/collections/column'
-import { Shape as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
-
-export type Table<Data> = { [E in keyof Data]: Column<Data[E]> }
-
-export interface ElementSymbol extends String { '@type': 'element-symbol' }
-export function ElementSymbol(s: string): ElementSymbol {
- // TODO: optimize?
- return s.toUpperCase() as any;
-}
-
-export interface Atoms extends Table<{
- // unique number for each atom
- key: number,
-
- id: number,
- type_symbol: ElementSymbol,
- label_atom_id: string,
- auth_atom_id: string,
- label_alt_id: string,
- auth_alt_id: string,
- pdbx_formal_charge: string,
- occupancy: number,
- B_iso_or_equiv: number
-}> { }
-
-export interface Residues extends Table<{
- // unique number for each residue
- key: number,
-
- group_PDB: string,
-
- label_comp_id: string,
- auth_comp_id: string,
- label_seq_id: number,
- auth_seq_id: number,
- pdbx_PDB_ins_code: string
-}> { }
-
-export interface Chains extends Table<{
- // unique number for each chain
- key: number,
-
- label_asym_id: string,
- auth_asym_id: string
-}> { }
-
-export interface Entities extends Table<{
- // unique number for each entity
- // row index to the EntityData table
- key: number,
- label_entity_id: string,
- pdbx_PDB_model_num: number
-}> { }
-
-type _EntityData = mmCIF['entity']
-export interface EntityData extends _EntityData { }
-
-export interface Macromolecule {
- atoms: Atoms,
- residues: Residues,
- chains: Chains,
- entities: Entities
-}
-
-export default Macromolecule
\ No newline at end of file
diff --git a/src/mol-data/model/properties/secondary-structure.ts b/src/mol-data/model/properties/secondary-structure.ts
new file mode 100644
index 000000000..75d1f4b89
--- /dev/null
+++ b/src/mol-data/model/properties/secondary-structure.ts
@@ -0,0 +1,128 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+const enum SSF {
+ None = 0x0,
+
+ // category
+ DoubleHelix = 0x1,
+ Helix = 0x2,
+ Beta = 0x4,
+ Turn = 0x8,
+
+ // category variant
+ LeftHanded = 0x10, // helix
+ RightHanded = 0x20,
+
+ ClassicTurn = 0x40, // turn
+ InverseTurn = 0x80,
+
+ // sub-category
+ HelixOther = 0x100, // protein
+ Helix27 = 0x200,
+ Helix3Ten = 0x400,
+ HelixAlpha = 0x800,
+ HelixGamma = 0x1000,
+ HelixOmega = 0x2000,
+ HelixPi = 0x4000,
+ HelixPolyproline = 0x8000,
+
+ DoubleHelixOther = 0x10000, // nucleic
+ DoubleHelixZ = 0x20000,
+ DoubleHelixA = 0x40000,
+ DoubleHelixB = 0x80000,
+
+ BetaOther = 0x100000, // protein
+ BetaStrand = 0x200000, // single strand
+ BetaSheet = 0x400000, // multiple hydrogen bonded strands
+ BetaBarell = 0x800000, // closed series of sheets
+
+ TurnOther = 0x1000000, // protein
+ Turn1 = 0x2000000,
+ Turn2 = 0x4000000,
+ Turn3 = 0x8000000,
+
+ NA = 0x10000000, // not applicable/available
+}
+export { SSF as SecondaryStructureFlag }
+
+export const SecondaryStructureMmcif: { [value: string]: number } = {
+ HELX_LH_27_P: SSF.Helix | SSF.LeftHanded | SSF.Helix27, // left-handed 2-7 helix (protein)
+ HELX_LH_3T_P: SSF.Helix | SSF.LeftHanded | SSF.Helix3Ten, // left-handed 3-10 helix (protein)
+ HELX_LH_AL_P: SSF.Helix | SSF.LeftHanded | SSF.HelixAlpha, // left-handed alpha helix (protein)
+ HELX_LH_A_N: SSF.DoubleHelix | SSF.LeftHanded | SSF.DoubleHelixA, // left-handed A helix (nucleic acid)
+ HELX_LH_B_N: SSF.DoubleHelix | SSF.LeftHanded | SSF.DoubleHelixB, // left-handed B helix (nucleic acid)
+ HELX_LH_GA_P: SSF.Helix | SSF.LeftHanded | SSF.HelixGamma, // left-handed gamma helix (protein)
+ HELX_LH_N: SSF.DoubleHelix | SSF.LeftHanded, // left-handed helix with type not specified (nucleic acid)
+ HELX_LH_OM_P: SSF.Helix | SSF.LeftHanded | SSF.HelixOmega, // left-handed omega helix (protein)
+ HELX_LH_OT_N: SSF.DoubleHelix | SSF.LeftHanded | SSF.DoubleHelixOther, // left-handed helix with type that does not conform to an accepted category (nucleic acid)
+ HELX_LH_OT_P: SSF.Helix | SSF.LeftHanded | SSF.HelixOther, // left-handed helix with type that does not conform to an accepted category (protein)
+ HELX_LH_P: SSF.Helix | SSF.LeftHanded, // left-handed helix with type not specified (protein)
+ HELX_LH_PI_P: SSF.Helix | SSF.LeftHanded | SSF.HelixPi, // left-handed pi helix (protein)
+ HELX_LH_PP_P: SSF.Helix | SSF.LeftHanded | SSF.HelixPolyproline, // left-handed polyproline helix (protein)
+ HELX_LH_Z_N: SSF.DoubleHelix | SSF.LeftHanded | SSF.DoubleHelixZ, // left-handed Z helix (nucleic acid)
+ HELX_N: SSF.DoubleHelix, // helix with handedness and type not specified (nucleic acid)
+ HELX_OT_N: SSF.DoubleHelix, // helix with handedness and type that do not conform to an accepted category (nucleic acid)
+ HELX_OT_P: SSF.Helix, // helix with handedness and type that do not conform to an accepted category (protein)
+ HELX_P: SSF.Helix, // helix with handedness and type not specified (protein)
+ HELX_RH_27_P: SSF.Helix | SSF.RightHanded | SSF.Helix27, // right-handed 2-7 helix (protein)
+ HELX_RH_3T_P: SSF.Helix | SSF.RightHanded | SSF.Helix3Ten, // right-handed 3-10 helix (protein)
+ HELX_RH_AL_P: SSF.Helix | SSF.RightHanded | SSF.HelixAlpha, // right-handed alpha helix (protein)
+ HELX_RH_A_N: SSF.DoubleHelix | SSF.RightHanded | SSF.DoubleHelixA, // right-handed A helix (nucleic acid)
+ HELX_RH_B_N: SSF.DoubleHelix | SSF.RightHanded | SSF.DoubleHelixB, // right-handed B helix (nucleic acid)
+ HELX_RH_GA_P: SSF.Helix | SSF.RightHanded | SSF.HelixGamma, // right-handed gamma helix (protein)
+ HELX_RH_N: SSF.DoubleHelix | SSF.RightHanded, // right-handed helix with type not specified (nucleic acid)
+ HELX_RH_OM_P: SSF.Helix | SSF.RightHanded | SSF.HelixOmega, // right-handed omega helix (protein)
+ HELX_RH_OT_N: SSF.DoubleHelix | SSF.RightHanded | SSF.DoubleHelixOther, // right-handed helix with type that does not conform to an accepted category (nucleic acid)
+ HELX_RH_OT_P: SSF.Helix | SSF.RightHanded | SSF.HelixOther, // right-handed helix with type that does not conform to an accepted category (protein)
+ HELX_RH_P: SSF.Helix | SSF.RightHanded, // right-handed helix with type not specified (protein)
+ HELX_RH_PI_P: SSF.Helix | SSF.RightHanded | SSF.HelixPi, // right-handed pi helix (protein)
+ HELX_RH_PP_P: SSF.Helix | SSF.RightHanded | SSF.HelixPolyproline, // right-handed polyproline helix (protein)
+ HELX_RH_Z_N: SSF.DoubleHelix | SSF.RightHanded | SSF.DoubleHelixZ, // right-handed Z helix (nucleic acid)
+ STRN: SSF.Beta | SSF.BetaStrand, // beta strand (protein)
+ TURN_OT_P: SSF.Turn | SSF.TurnOther, // turn with type that does not conform to an accepted category (protein)
+ TURN_P: SSF.Turn, // turn with type not specified (protein)
+ TURN_TY1P_P: SSF.Turn | SSF.InverseTurn | SSF.Turn1, // type I prime turn (protein)
+ TURN_TY1_P: SSF.Turn | SSF.ClassicTurn | SSF.Turn1, // type I turn (protein)
+ TURN_TY2P_P: SSF.Turn | SSF.InverseTurn | SSF.Turn2, // type II prime turn (protein)
+ TURN_TY2_P: SSF.Turn | SSF.ClassicTurn | SSF.Turn2, // type II turn (protein)
+ TURN_TY3P_P: SSF.Turn | SSF.InverseTurn | SSF.Turn3, // type III prime turn (protein)
+ TURN_TY3_P: SSF.Turn | SSF.ClassicTurn | SSF.Turn3, // type III turn (protein)
+}
+
+export const SecondaryStructurePdb: { [value: string]: number } = {
+ 1: SSF.Helix | SSF.RightHanded | SSF.HelixAlpha, // Right-handed alpha (default)
+ 2: SSF.Helix | SSF.RightHanded | SSF.HelixOmega, // Right-handed omega
+ 3: SSF.Helix | SSF.RightHanded | SSF.HelixPi, // Right-handed pi
+ 4: SSF.Helix | SSF.RightHanded | SSF.HelixGamma, // Right-handed gamma
+ 5: SSF.Helix | SSF.RightHanded | SSF.Helix3Ten, // Right-handed 310
+ 6: SSF.Helix | SSF.LeftHanded | SSF.HelixAlpha, // Left-handed alpha
+ 7: SSF.Helix | SSF.LeftHanded | SSF.HelixOmega, // Left-handed omega
+ 8: SSF.Helix | SSF.LeftHanded | SSF.HelixGamma, // Left-handed gamma
+ 9: SSF.Helix | SSF.Helix27, // 27 ribbon/helix
+ 10: SSF.Helix | SSF.HelixPolyproline, // Polyproline
+}
+
+export const SecondaryStructureStride: { [value: string]: number } = {
+ H: SSF.Helix | SSF.HelixAlpha, // Alpha helix
+ G: SSF.Helix | SSF.Helix3Ten, // 3-10 helix
+ I: SSF.Helix | SSF.HelixPi, // PI-helix
+ E: SSF.Beta | SSF.BetaSheet, // Extended conformation
+ B: SSF.Beta | SSF.BetaStrand, // Isolated bridge
+ b: SSF.Beta | SSF.BetaStrand, // Isolated bridge
+ T: SSF.Turn, // Turn
+ C: SSF.NA, // Coil (none of the above)
+}
+
+export const SecondaryStructureDssp: { [value: string]: number } = {
+ H: SSF.Helix | SSF.HelixAlpha, // alpha-helix
+ B: SSF.Beta | SSF.BetaStrand, // residue in isolated beta-bridge
+ E: SSF.Beta | SSF.BetaSheet, // extended strand, participates in beta ladder
+ G: SSF.Helix | SSF.Helix3Ten, // 3-helix (310 helix)
+ I: SSF.Helix | SSF.HelixPi, // 5 helix (pi-helix)
+ T: SSF.Turn, // hydrogen bonded turn
+ S: SSF.Turn, // bend
+}
\ No newline at end of file
diff --git a/src/mol-data/model/properties/symmetry.ts b/src/mol-data/model/properties/symmetry.ts
deleted file mode 100644
index e69de29bb..000000000
diff --git a/src/mol-data/model/properties/transforms.ts b/src/mol-data/model/properties/transforms.ts
new file mode 100644
index 000000000..f43641255
--- /dev/null
+++ b/src/mol-data/model/properties/transforms.ts
@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// TODO: symmetry and assebmlies descriptors
+
+//import Column from '../../../mol-base/collections/column'
\ No newline at end of file
diff --git a/src/mol-data/query.ts b/src/mol-data/query.ts
index d99fbd941..89aaef1c2 100644
--- a/src/mol-data/query.ts
+++ b/src/mol-data/query.ts
@@ -5,7 +5,7 @@
*/
import Structure from './structure'
-import Selection from './selection'
+import Selection from './query/selection'
interface Query { (s: Structure): Selection }
diff --git a/src/mol-data/selection.ts b/src/mol-data/query/selection.ts
similarity index 94%
rename from src/mol-data/selection.ts
rename to src/mol-data/query/selection.ts
index 6364aa263..a509c40fe 100644
--- a/src/mol-data/selection.ts
+++ b/src/mol-data/query/selection.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Structure from './structure'
+import Structure from './../structure'
type Selection =
| Structure // each atom is interpreted as a singleton structure
--
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