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Commit 1d765bfb authored by David Sehnal's avatar David Sehnal
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date model part ?? + 1 of ???

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src/mol-data/model.ts
+ 4
− 4
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......@@ -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: {
......
src/mol-data/model/builders/mmcif.ts
+ 1
− 1
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......@@ -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),
......
src/mol-data/model/constants.ts 0 → 100644
+ 317
− 0
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/**
* 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
src/mol-data/model/data/secondary-structure.ts deleted 100644 → 0
+ 0
− 128
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/**
* 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
src/mol-data/model/properties/computed.ts 0 → 100644
+ 7
− 0
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/**
* 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
src/mol-data/model/data/conformation.ts → src/mol-data/model/properties/conformation.ts
+ 5
− 6
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......@@ -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
src/mol-data/model/common/keys.ts → src/mol-data/model/properties/format-specific.ts
+ 2
− 0
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......@@ -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
src/mol-data/model/data/macromolecule.ts → src/mol-data/model/properties/hierarchy.ts
+ 26
− 9
View file @ 1d765bfb
......@@ -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
src/mol-data/model/utils/hierarchy-keys.ts 0 → 100644
+ 14
− 0
View file @ 1d765bfb
/**
* 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
src/mol-data/structure/atom.ts
+ 16
− 0
View file @ 1d765bfb
......@@ -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
src/mol-io/reader/cif/schema/mmcif.ts
+ 1
− 1
View file @ 1d765bfb
......@@ -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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