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Commit 8a266e70 authored by Alexander Rose's avatar Alexander Rose
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fix handling of struct_conf mmCIF field (#425)

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CHANGELOG.md
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......@@ -6,6 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
- Fix case handling of ``struct_conf`` mmCIF enumeration field (#425)
## [v3.7.0] - 2022-04-13
- Fix ``xrayShaded`` for texture-mesh geometries
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src/mol-model-formats/structure/property/secondary-structure.ts
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/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2018-2022 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>
......@@ -92,7 +92,7 @@ function addHelices(cat: StructConf, coordinates: CoordinateType, map: Secondary
const element: SecondaryStructure.Helix = {
kind: 'helix',
flags: type,
type_id: conf_type_id.valueKind(i) === Column.ValueKind.Present ? conf_type_id.value(i) : 'HELIX_P',
type_id: conf_type_id.valueKind(i) === Column.ValueKind.Present ? conf_type_id.value(i) : 'helx_p',
helix_class: pdbx_PDB_helix_class.value(i),
details: details.valueKind(i) === Column.ValueKind.Present ? details.value(i) : void 0
};
......
src/mol-model/structure/model/properties/seconday-structure.ts
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/**
* Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2017-2022 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>
*/
import { SecondaryStructureType } from '../types';
import { ResidueIndex } from '../indexing';
import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
/** Secondary structure "indexed" by residues. */
interface SecondaryStructure {
......@@ -37,7 +39,7 @@ namespace SecondaryStructure {
export interface Helix {
kind: 'helix',
flags: SecondaryStructureType,
type_id: string, // TODO: use aliased type?
type_id: mmCIF_Schema['struct_conf']['conf_type_id']['T'],
helix_class: string,
details?: string
}
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src/mol-model/structure/model/types.ts
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......@@ -501,48 +501,50 @@ export namespace SecondaryStructureType {
NA = 0x20000000, // 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 SecondaryStructureMmcif: { [value in mmCIF_Schema['struct_conf']['conf_type_id']['T']]: 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 (rhcleic 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)
bend: Flag.Bend, // region with high backbone curvature without specific hydrogen bonding, a bend at residue i occurs when the angle between C$\_alpha(i)-C_\alpha(i-2) and C_\alpha(i+2) - C_\alpha(i)$ is greater than 70 degrees (protein)
other: Flag.None, // secondary structure type that does not conform to an accepted category, random coil (protein)
};
export const SecondaryStructurePdb: { [value: string]: number } = {
......
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