From 1d765bfb4ea9967832cb7243deee7dd98ad7c134 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 31 Oct 2017 15:48:24 +0100
Subject: [PATCH] date model part ?? + 1 of ???
---
src/mol-data/model.ts | 8 +-
src/mol-data/model/builders/mmcif.ts | 2 +-
src/mol-data/model/constants.ts | 317 ++++++++++++++++++
.../model/data/secondary-structure.ts | 128 -------
src/mol-data/model/properties/computed.ts | 7 +
.../{data => properties}/conformation.ts | 11 +-
.../keys.ts => properties/format-specific.ts} | 2 +
.../hierarchy.ts} | 35 +-
.../model/{data => properties}/transforms.ts | 0
src/mol-data/model/utils/hierarchy-keys.ts | 14 +
src/mol-data/structure/atom.ts | 16 +
src/mol-io/reader/cif/schema/mmcif.ts | 2 +-
12 files changed, 393 insertions(+), 149 deletions(-)
create mode 100644 src/mol-data/model/constants.ts
delete mode 100644 src/mol-data/model/data/secondary-structure.ts
create mode 100644 src/mol-data/model/properties/computed.ts
rename src/mol-data/model/{data => properties}/conformation.ts (62%)
rename src/mol-data/model/{common/keys.ts => properties/format-specific.ts} (75%)
rename src/mol-data/model/{data/macromolecule.ts => properties/hierarchy.ts} (65%)
rename src/mol-data/model/{data => properties}/transforms.ts (100%)
create mode 100644 src/mol-data/model/utils/hierarchy-keys.ts
diff --git a/src/mol-data/model.ts b/src/mol-data/model.ts
index db02acf8a..a6177c117 100644
--- a/src/mol-data/model.ts
+++ b/src/mol-data/model.ts
@@ -5,8 +5,8 @@
*/
import * as Formats from './model/formats'
-import MacromoleculeData from './model/data/macromolecule'
-import ConformationData from './model/data/conformation'
+import HierarchyProperties from './model/properties/hierarchy'
+import ConformationProperties from './model/properties/conformation'
import Segmentation from '../mol-base/collections/integer/segmentation'
/**
@@ -21,8 +21,8 @@ interface Model extends Readonly<{
sourceData: Formats.RawData,
- macromolecule: MacromoleculeData,
- conformation: ConformationData,
+ hierarchy: HierarchyProperties,
+ conformation: ConformationProperties,
// used for diffing.
version: {
diff --git a/src/mol-data/model/builders/mmcif.ts b/src/mol-data/model/builders/mmcif.ts
index 24ad91e49..b3dad75ba 100644
--- a/src/mol-data/model/builders/mmcif.ts
+++ b/src/mol-data/model/builders/mmcif.ts
@@ -48,7 +48,7 @@ function createModel(raw: RawData, data: mmCIF, bounds: Interval): Model {
sourceData: raw,
model_num: 0, // TODO: fix
//common: 0 as any,
- macromolecule: 0 as any,
+ hierarchy: 0 as any,
conformation: 0 as any,
version: { data: 0, conformation: 0 },
atomCount: Interval.size(bounds),
diff --git a/src/mol-data/model/constants.ts b/src/mol-data/model/constants.ts
new file mode 100644
index 000000000..5db57c733
--- /dev/null
+++ b/src/mol-data/model/constants.ts
@@ -0,0 +1,317 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import BitFlags from '../../mol-base/utils/bit-flags'
+
+export const enum EntityType {
+ Unknown = 'unknown',
+ Polymer = 'polymer',
+ NonPolymer = 'non-polymer',
+ Macrolide = 'macrolide',
+ Water = 'water'
+}
+
+export const enum MoleculeType {
+ Unknown,
+ Water,
+ Ion,
+ Protein,
+ RNA,
+ DNA,
+ Saccharide
+}
+
+export const enum BackboneType {
+ Unknown,
+ Protein,
+ RNA,
+ DNA,
+ CgProtein,
+ CgRNA,
+ CgDNA
+}
+
+const _chemCompNonPolymer = ['NON-POLYMER'];
+const _chemCompOther = ['OTHER'];
+const _chemCompSaccharide = [
+ 'D-SACCHARIDE', 'D-SACCHARIDE 1,4 AND 1,4 LINKING', 'D-SACCHARIDE 1,4 AND 1,6 LINKING',
+ 'L-SACCHARIDE', 'L-SACCHARIDE 1,4 AND 1,4 LINKING', 'L-SACCHARIDE 1,4 AND 1,6 LINKING',
+ 'SACCHARIDE'
+];
+
+export const ChemComp = {
+ Protein: [
+ 'D-BETA-PEPTIDE, C-GAMMA LINKING', 'D-GAMMA-PEPTIDE, C-DELTA LINKING',
+ 'D-PEPTIDE COOH CARBOXY TERMINUS', 'D-PEPTIDE NH3 AMINO TERMINUS', 'D-PEPTIDE LINKING',
+ 'L-BETA-PEPTIDE, C-GAMMA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING',
+ 'L-PEPTIDE COOH CARBOXY TERMINUS', 'L-PEPTIDE NH3 AMINO TERMINUS', 'L-PEPTIDE LINKING',
+ 'PEPTIDE LINKING', 'PEPTIDE-LIKE'
+ ],
+ RNA: [
+ 'RNA OH 3 PRIME TERMINUS', 'RNA OH 5 PRIME TERMINUS', 'RNA LINKING'
+ ],
+ DNA: [
+ 'DNA OH 3 PRIME TERMINUS', 'DNA OH 5 PRIME TERMINUS', 'DNA LINKING',
+ 'L-DNA LINKING', 'L-RNA LINKING'
+ ],
+ Saccharide: _chemCompSaccharide,
+ Other: _chemCompOther,
+ NonPolymer: _chemCompNonPolymer,
+ Hetero: _chemCompNonPolymer.concat(_chemCompOther, _chemCompSaccharide)
+}
+
+export interface SecondaryStructureType extends BitFlags<SecondaryStructureType.Flag> { }
+export namespace SecondaryStructureType {
+ export const Helix = ['h', 'g', 'i']
+ export const Sheet = ['e', 'b']
+ export const Turn = ['s', 't', 'l', '']
+
+ export const is: (ss: SecondaryStructureType, f: Flag) => boolean = BitFlags.has
+
+ export const enum Flag {
+ 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 const SecondaryStructureMmcif: { [value: string]: number } = {
+ HELX_LH_27_P: Flag.Helix | Flag.LeftHanded | Flag.Helix27, // left-handed 2-7 helix (protein)
+ HELX_LH_3T_P: Flag.Helix | Flag.LeftHanded | Flag.Helix3Ten, // left-handed 3-10 helix (protein)
+ HELX_LH_AL_P: Flag.Helix | Flag.LeftHanded | Flag.HelixAlpha, // left-handed alpha helix (protein)
+ HELX_LH_A_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixA, // left-handed A helix (nucleic acid)
+ HELX_LH_B_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixB, // left-handed B helix (nucleic acid)
+ HELX_LH_GA_P: Flag.Helix | Flag.LeftHanded | Flag.HelixGamma, // left-handed gamma helix (protein)
+ HELX_LH_N: Flag.DoubleHelix | Flag.LeftHanded, // left-handed helix with type not specified (nucleic acid)
+ HELX_LH_OM_P: Flag.Helix | Flag.LeftHanded | Flag.HelixOmega, // left-handed omega helix (protein)
+ HELX_LH_OT_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixOther, // left-handed helix with type that does not conform to an accepted category (nucleic acid)
+ HELX_LH_OT_P: Flag.Helix | Flag.LeftHanded | Flag.HelixOther, // left-handed helix with type that does not conform to an accepted category (protein)
+ HELX_LH_P: Flag.Helix | Flag.LeftHanded, // left-handed helix with type not specified (protein)
+ HELX_LH_PI_P: Flag.Helix | Flag.LeftHanded | Flag.HelixPi, // left-handed pi helix (protein)
+ HELX_LH_PP_P: Flag.Helix | Flag.LeftHanded | Flag.HelixPolyproline, // left-handed polyproline helix (protein)
+ HELX_LH_Z_N: Flag.DoubleHelix | Flag.LeftHanded | Flag.DoubleHelixZ, // left-handed Z helix (nucleic acid)
+ HELX_N: Flag.DoubleHelix, // helix with handedness and type not specified (nucleic acid)
+ HELX_OT_N: Flag.DoubleHelix, // helix with handedness and type that do not conform to an accepted category (nucleic acid)
+ HELX_OT_P: Flag.Helix, // helix with handedness and type that do not conform to an accepted category (protein)
+ HELX_P: Flag.Helix, // helix with handedness and type not specified (protein)
+ HELX_RH_27_P: Flag.Helix | Flag.RightHanded | Flag.Helix27, // right-handed 2-7 helix (protein)
+ HELX_RH_3T_P: Flag.Helix | Flag.RightHanded | Flag.Helix3Ten, // right-handed 3-10 helix (protein)
+ HELX_RH_AL_P: Flag.Helix | Flag.RightHanded | Flag.HelixAlpha, // right-handed alpha helix (protein)
+ HELX_RH_A_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixA, // right-handed A helix (nucleic acid)
+ HELX_RH_B_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixB, // right-handed B helix (nucleic acid)
+ HELX_RH_GA_P: Flag.Helix | Flag.RightHanded | Flag.HelixGamma, // right-handed gamma helix (protein)
+ HELX_RH_N: Flag.DoubleHelix | Flag.RightHanded, // right-handed helix with type not specified (nucleic acid)
+ HELX_RH_OM_P: Flag.Helix | Flag.RightHanded | Flag.HelixOmega, // right-handed omega helix (protein)
+ HELX_RH_OT_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixOther, // right-handed helix with type that does not conform to an accepted category (nucleic acid)
+ HELX_RH_OT_P: Flag.Helix | Flag.RightHanded | Flag.HelixOther, // right-handed helix with type that does not conform to an accepted category (protein)
+ HELX_RH_P: Flag.Helix | Flag.RightHanded, // right-handed helix with type not specified (protein)
+ HELX_RH_PI_P: Flag.Helix | Flag.RightHanded | Flag.HelixPi, // right-handed pi helix (protein)
+ HELX_RH_PP_P: Flag.Helix | Flag.RightHanded | Flag.HelixPolyproline, // right-handed polyproline helix (protein)
+ HELX_RH_Z_N: Flag.DoubleHelix | Flag.RightHanded | Flag.DoubleHelixZ, // right-handed Z helix (nucleic acid)
+ STRN: Flag.Beta | Flag.BetaStrand, // beta strand (protein)
+ TURN_OT_P: Flag.Turn | Flag.TurnOther, // turn with type that does not conform to an accepted category (protein)
+ TURN_P: Flag.Turn, // turn with type not specified (protein)
+ TURN_TY1P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn1, // type I prime turn (protein)
+ TURN_TY1_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn1, // type I turn (protein)
+ TURN_TY2P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn2, // type II prime turn (protein)
+ TURN_TY2_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn2, // type II turn (protein)
+ TURN_TY3P_P: Flag.Turn | Flag.InverseTurn | Flag.Turn3, // type III prime turn (protein)
+ TURN_TY3_P: Flag.Turn | Flag.ClassicTurn | Flag.Turn3, // type III turn (protein)
+ }
+
+ export const SecondaryStructurePdb: { [value: string]: number } = {
+ 1: Flag.Helix | Flag.RightHanded | Flag.HelixAlpha, // Right-handed alpha (default)
+ 2: Flag.Helix | Flag.RightHanded | Flag.HelixOmega, // Right-handed omega
+ 3: Flag.Helix | Flag.RightHanded | Flag.HelixPi, // Right-handed pi
+ 4: Flag.Helix | Flag.RightHanded | Flag.HelixGamma, // Right-handed gamma
+ 5: Flag.Helix | Flag.RightHanded | Flag.Helix3Ten, // Right-handed 310
+ 6: Flag.Helix | Flag.LeftHanded | Flag.HelixAlpha, // Left-handed alpha
+ 7: Flag.Helix | Flag.LeftHanded | Flag.HelixOmega, // Left-handed omega
+ 8: Flag.Helix | Flag.LeftHanded | Flag.HelixGamma, // Left-handed gamma
+ 9: Flag.Helix | Flag.Helix27, // 27 ribbon/helix
+ 10: Flag.Helix | Flag.HelixPolyproline, // Polyproline
+ }
+
+ export const SecondaryStructureStride: { [value: string]: number } = {
+ H: Flag.Helix | Flag.HelixAlpha, // Alpha helix
+ G: Flag.Helix | Flag.Helix3Ten, // 3-10 helix
+ I: Flag.Helix | Flag.HelixPi, // PI-helix
+ E: Flag.Beta | Flag.BetaSheet, // Extended conformation
+ B: Flag.Beta | Flag.BetaStrand, // Isolated bridge
+ b: Flag.Beta | Flag.BetaStrand, // Isolated bridge
+ T: Flag.Turn, // Turn
+ C: Flag.NA, // Coil (none of the above)
+ }
+
+ export const SecondaryStructureDssp: { [value: string]: number } = {
+ H: Flag.Helix | Flag.HelixAlpha, // alpha-helix
+ B: Flag.Beta | Flag.BetaStrand, // residue in isolated beta-bridge
+ E: Flag.Beta | Flag.BetaSheet, // extended strand, participates in beta ladder
+ G: Flag.Helix | Flag.Helix3Ten, // 3-helix (310 helix)
+ I: Flag.Helix | Flag.HelixPi, // 5 helix (pi-helix)
+ T: Flag.Turn, // hydrogen bonded turn
+ S: Flag.Turn, // bend
+ }
+}
+
+export const VdwRadii = {
+ 'H': 1.1,
+ 'HE': 1.4,
+ 'LI': 1.81,
+ 'BE': 1.53,
+ 'B': 1.92,
+ 'C': 1.7,
+ 'N': 1.55,
+ 'O': 1.52,
+ 'F': 1.47,
+ 'NE': 1.54,
+ 'NA': 2.27,
+ 'MG': 1.73,
+ 'AL': 1.84,
+ 'SI': 2.1,
+ 'P': 1.8,
+ 'S': 1.8,
+ 'CL': 1.75,
+ 'AR': 1.88,
+ 'K': 2.75,
+ 'CA': 2.31,
+ 'SC': 2.3,
+ 'TI': 2.15,
+ 'V': 2.05,
+ 'CR': 2.05,
+ 'MN': 2.05,
+ 'FE': 2.05,
+ 'CO': 2.0,
+ 'NI': 2.0,
+ 'CU': 2.0,
+ 'ZN': 2.1,
+ 'GA': 1.87,
+ 'GE': 2.11,
+ 'AS': 1.85,
+ 'SE': 1.9,
+ 'BR': 1.83,
+ 'KR': 2.02,
+ 'RB': 3.03,
+ 'SR': 2.49,
+ 'Y': 2.4,
+ 'ZR': 2.3,
+ 'NB': 2.15,
+ 'MO': 2.1,
+ 'TC': 2.05,
+ 'RU': 2.05,
+ 'RH': 2.0,
+ 'PD': 2.05,
+ 'AG': 2.1,
+ 'CD': 2.2,
+ 'IN': 2.2,
+ 'SN': 1.93,
+ 'SB': 2.17,
+ 'TE': 2.06,
+ 'I': 1.98,
+ 'XE': 2.16,
+ 'CS': 3.43,
+ 'BA': 2.68,
+ 'LA': 2.5,
+ 'CE': 2.48,
+ 'PR': 2.47,
+ 'ND': 2.45,
+ 'PM': 2.43,
+ 'SM': 2.42,
+ 'EU': 2.4,
+ 'GD': 2.38,
+ 'TB': 2.37,
+ 'DY': 2.35,
+ 'HO': 2.33,
+ 'ER': 2.32,
+ 'TM': 2.3,
+ 'YB': 2.28,
+ 'LU': 2.27,
+ 'HF': 2.25,
+ 'TA': 2.2,
+ 'W': 2.1,
+ 'RE': 2.05,
+ 'OS': 2.0,
+ 'IR': 2.0,
+ 'PT': 2.05,
+ 'AU': 2.1,
+ 'HG': 2.05,
+ 'TL': 1.96,
+ 'PB': 2.02,
+ 'BI': 2.07,
+ 'PO': 1.97,
+ 'AT': 2.02,
+ 'RN': 2.2,
+ 'FR': 3.48,
+ 'RA': 2.83,
+ 'AC': 2.0,
+ 'TH': 2.4,
+ 'PA': 2.0,
+ 'U': 2.3,
+ 'NP': 2.0,
+ 'PU': 2.0,
+ 'AM': 2.0,
+ 'CM': 2.0,
+ 'BK': 2.0,
+ 'CF': 2.0,
+ 'ES': 2.0,
+ 'FM': 2.0,
+ 'MD': 2.0,
+ 'NO': 2.0,
+ 'LR': 2.0,
+ 'RF': 2.0,
+ 'DB': 2.0,
+ 'SG': 2.0,
+ 'BH': 2.0,
+ 'HS': 2.0,
+ 'MT': 2.0,
+ 'DS': 2.0,
+ 'RG': 2.0,
+ 'CN': 2.0,
+ 'UUT': 2.0,
+ 'FL': 2.0,
+ 'UUP': 2.0,
+ 'LV': 2.0,
+ 'UUH': 2.0
+}
+export const DefaultVdwRadius = 2.0
\ No newline at end of file
diff --git a/src/mol-data/model/data/secondary-structure.ts b/src/mol-data/model/data/secondary-structure.ts
deleted file mode 100644
index 75d1f4b89..000000000
--- a/src/mol-data/model/data/secondary-structure.ts
+++ /dev/null
@@ -1,128 +0,0 @@
-/**
- * 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/computed.ts b/src/mol-data/model/properties/computed.ts
new file mode 100644
index 000000000..ad7120fc0
--- /dev/null
+++ b/src/mol-data/model/properties/computed.ts
@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// TODO: stuff like "residue type/flags", isRingAtom, rings, bonds??, wrap these in a computation?
\ No newline at end of file
diff --git a/src/mol-data/model/data/conformation.ts b/src/mol-data/model/properties/conformation.ts
similarity index 62%
rename from src/mol-data/model/data/conformation.ts
rename to src/mol-data/model/properties/conformation.ts
index ac90abac4..5cec094ae 100644
--- a/src/mol-data/model/data/conformation.ts
+++ b/src/mol-data/model/properties/conformation.ts
@@ -4,8 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { SecondaryStructureFlag as SSF } from './secondary-structure'
-import BitFlags from '../../../mol-base/utils/bit-flags'
+import { SecondaryStructureType } from '../constants'
import Segmentation from '../../../mol-base/collections/integer/segmentation'
interface Positions {
@@ -15,14 +14,14 @@ interface Positions {
}
interface SecondaryStructure {
- ofResidue: ArrayLike<BitFlags<SSF>>,
- // atom segmentation
+ ofResidue: ArrayLike<SecondaryStructureType>,
+ // atom segmentation??
segments: Segmentation
}
interface Conformation {
positions: Positions,
- secondaryStructureType: SecondaryStructure
+ secondaryStructure: SecondaryStructure
}
-export default Conformation
+export default Conformation
\ No newline at end of file
diff --git a/src/mol-data/model/common/keys.ts b/src/mol-data/model/properties/format-specific.ts
similarity index 75%
rename from src/mol-data/model/common/keys.ts
rename to src/mol-data/model/properties/format-specific.ts
index 1a7b5e35b..2a7bb4398 100644
--- a/src/mol-data/model/common/keys.ts
+++ b/src/mol-data/model/properties/format-specific.ts
@@ -3,3 +3,5 @@
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
+
+// TODO add access to things like MOL2 charge ...
\ No newline at end of file
diff --git a/src/mol-data/model/data/macromolecule.ts b/src/mol-data/model/properties/hierarchy.ts
similarity index 65%
rename from src/mol-data/model/data/macromolecule.ts
rename to src/mol-data/model/properties/hierarchy.ts
index f96f45163..1e7cfd5ef 100644
--- a/src/mol-data/model/data/macromolecule.ts
+++ b/src/mol-data/model/properties/hierarchy.ts
@@ -32,9 +32,7 @@ export const ResiduesSchema = {
auth_comp_id: mmCIF.atom_site.auth_comp_id,
label_seq_id: mmCIF.atom_site.label_seq_id,
auth_seq_id: mmCIF.atom_site.auth_seq_id,
- pdbx_PDB_ins_code: mmCIF.atom_site.pdbx_PDB_ins_code,
-
- key: Column.Type.int
+ pdbx_PDB_ins_code: mmCIF.atom_site.pdbx_PDB_ins_code
};
export interface Residues extends Table<typeof AtomsSchema> { }
@@ -44,10 +42,7 @@ export const ChainsSchema = {
auth_asym_id: mmCIF.atom_site.auth_asym_id,
auth_comp_id: mmCIF.atom_site.auth_comp_id,
label_entity_id: mmCIF.atom_site.label_entity_id,
- pdbx_PDB_model_num: mmCIF.atom_site.pdbx_PDB_model_num,
-
- key: Column.Type.int,
- entityIndex: Column.Type.int
+ pdbx_PDB_model_num: mmCIF.atom_site.pdbx_PDB_model_num
}
export interface Chains extends Table<typeof ChainsSchema> { }
@@ -55,11 +50,33 @@ export interface Chains extends Table<typeof ChainsSchema> { }
export const EntitySchema = mmCIF['entity']
export interface Entities extends Table<typeof EntitySchema> { }
-export interface Macromolecule {
+export interface HierarchyData {
atoms: Atoms,
residues: Residues,
chains: Chains,
entities: Entities
}
-export default Macromolecule
\ No newline at end of file
+export interface HierarchyKeys {
+ // indicate whether the keys form an increasing sequence (in other words, the residues are sorted).
+ // monotonous sequences enable for example faster secodnary structure assignment.
+ isMonotonous: number,
+
+ // assign a key to each residue index.
+ residue: ArrayLike<number>,
+ // assign a key to each chain index
+ chain: ArrayLike<number>,
+ // assigne a key to each chain index
+ // also index to the Entities table.
+ entity: ArrayLike<number>,
+
+ findEntity(id: string): number,
+ findChain(entityId: string, label_asym_id: string): number,
+ findResidue(entityId: string, label_asym_id: string, label_comp_id: string, label_seq_id: number, pdbx_PDB_ins_code: string): number
+}
+
+export interface Hierarchy extends HierarchyData {
+ keys: HierarchyKeys
+}
+
+export default Hierarchy
\ No newline at end of file
diff --git a/src/mol-data/model/data/transforms.ts b/src/mol-data/model/properties/transforms.ts
similarity index 100%
rename from src/mol-data/model/data/transforms.ts
rename to src/mol-data/model/properties/transforms.ts
diff --git a/src/mol-data/model/utils/hierarchy-keys.ts b/src/mol-data/model/utils/hierarchy-keys.ts
new file mode 100644
index 000000000..f65eb69ab
--- /dev/null
+++ b/src/mol-data/model/utils/hierarchy-keys.ts
@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { HierarchyData, HierarchyKeys } from '../properties/hierarchy'
+
+function create(data: HierarchyData): HierarchyKeys {
+
+ return 0 as any;
+}
+
+export default create;
\ No newline at end of file
diff --git a/src/mol-data/structure/atom.ts b/src/mol-data/structure/atom.ts
index 7a6ef43aa..a15da5213 100644
--- a/src/mol-data/structure/atom.ts
+++ b/src/mol-data/structure/atom.ts
@@ -5,6 +5,9 @@
*/
import Tuple from '../../mol-base/collections/integer/tuple'
+import Structure from '../structure'
+import Unit from './unit'
+import Model from '../model'
/** Atom pointer */
interface Atom { '@type': Tuple['@type'] }
@@ -17,6 +20,19 @@ namespace Atom {
export const index: (a: Atom) => number = Tuple.snd;
export const areEqual: (a: Atom, b: Atom) => boolean = Tuple.areEqual;
export const hashCode: (a: Atom) => number = Tuple.hashCode;
+
+ /** All the information required to access atom properties */
+ export interface Location {
+ structure: Structure,
+ unit: Unit,
+ model: Model,
+ atomIndex: number,
+ residueIndex: number,
+ chainIndex: number
+ }
+
+ export interface Property<T> { (location: Atom): T }
+ export interface Predicate extends Property<boolean> { }
}
export default Atom
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 839ee23e8..f9b7b9a6c 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -14,7 +14,7 @@ const entry = {
id: str
}
-type EntityType = 'polymer' | 'non-polymer' | 'water'
+type EntityType = 'polymer' | 'non-polymer' | 'water' | 'macrolide'
const entity = {
id: str,
--
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