diff --git a/CHANGELOG.md b/CHANGELOG.md
index 03a0ba8b8a9d01e71256b231df998e729ef3ac97..73d64332859fff29877d2c48885f3ff40b10ecd9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
- Add glTF (GLB) and STL support to ``geo-export`` extension.
+- Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
## [v2.0.5] - 2021-04-26
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 2f9110087b83b56a062cacd99d280b57ba6e5f91..f47df8d4336b940bb70989c44367eff716a56586 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -34,6 +34,7 @@ import { CustomStructureProperty } from '../../../mol-model-props/common/custom-
import { Trajectory } from '../trajectory';
import { RuntimeContext, Task } from '../../../mol-task';
import { computeStructureBoundary } from './util/boundary';
+import { PrincipalAxes } from '../../../mol-math/linear-algebra/matrix/principal-axes';
/** Internal structure state */
type State = {
@@ -1290,6 +1291,14 @@ namespace Structure {
export type Index = number;
export const Index = CustomStructureProperty.createSimple<Index>('index', 'root');
+
+ const PrincipalAxesProp = '__PrincipalAxes__';
+ export function getPrincipalAxes(structure: Structure): PrincipalAxes {
+ if (structure.currentPropertyData[PrincipalAxesProp]) return structure.currentPropertyData[PrincipalAxesProp];
+ const principalAxes = StructureElement.Loci.getPrincipalAxes(Structure.toStructureElementLoci(structure));
+ structure.currentPropertyData[PrincipalAxesProp] = principalAxes;
+ return principalAxes;
+ }
}
export { Structure };
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/common.ts b/src/mol-model/structure/structure/unit/bonds/common.ts
index 58331ef42f331a2a6404d30aeca9da5e501d51b4..01fa2d49213dde729063c1635290711602f3d49b 100644
--- a/src/mol-model/structure/structure/unit/bonds/common.ts
+++ b/src/mol-model/structure/structure/unit/bonds/common.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>
@@ -23,6 +23,10 @@ const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D
const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 2.0, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
/**
+ * Added O-S (316) as 1.8
+ * N-O-S bridge (e.g. LYS-CSO in 7B0L, 6ZWJ, 6ZWH)
+ * (https://www.nature.com/articles/s41586-021-03513-3?s=09)
+ *
* Increased N-N (112) threshold from 1.55 to 1.6 (e.g. for 0QH in 1BMA)
*
* More experimentally observed bond length here (https://cccbdb.nist.gov/expbondlengths1x.asp)
@@ -51,8 +55,8 @@ const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42,
* Added P-H (135) as 1.47
* P-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rPH)
* - Average 1.423 ((+/- 0.007)
- * - Min 0.912
- * - Max 1.033
+ * - Min 1.414
+ * - Max 1.435
*
* Added S-H (152) as 1.45
* S-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rSH)
@@ -63,7 +67,7 @@ const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42,
* Added Si-Si (420) as 2.37
* (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rSiSi)
*/
-const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.2, 35: 1.15, 44: 1.1, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.6, 113: 1.59, 114: 1.36, 129: 1.45, 135: 1.47, 144: 1.6, 152: 1.45, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 420: 2.37, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
+const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.2, 35: 1.15, 44: 1.1, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.6, 113: 1.59, 114: 1.36, 129: 1.45, 135: 1.47, 144: 1.6, 152: 1.45, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 316: 1.8, 420: 2.37, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
const __DefaultBondingRadius = 2.001;
diff --git a/src/mol-plugin-state/animation/built-in/spin-structure.ts b/src/mol-plugin-state/animation/built-in/spin-structure.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2fd9d64ba9c0021e142390835b39bcfaec046265
--- /dev/null
+++ b/src/mol-plugin-state/animation/built-in/spin-structure.ts
@@ -0,0 +1,73 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginCommands } from '../../../mol-plugin/commands';
+import { StateSelection } from '../../../mol-state';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginStateObject } from '../../objects';
+import { StateTransforms } from '../../transforms';
+import { PluginStateAnimation } from '../model';
+
+export const AnimateStructureSpin = PluginStateAnimation.create({
+ name: 'built-in.animate-structure-spin',
+ display: { name: 'Spin Structure' },
+ isExportable: true,
+ params: () => ({
+ durationInMs: PD.Numeric(3000, { min: 100, max: 10000, step: 100})
+ }),
+ initialState: () => ({ t: 0 }),
+ getDuration: p => ({ kind: 'fixed', durationMs: p.durationInMs }),
+ async setup(_, __, plugin) {
+ const state = plugin.state.data;
+ const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3D));
+
+ const update = state.build();
+ let changed = false;
+ for (const r of reprs) {
+ const spins = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.SpinStructureRepresentation3D, r.transform.ref));
+ if (spins.length > 0) continue;
+
+ changed = true;
+ update.to(r.transform.ref)
+ .apply(StateTransforms.Representation.SpinStructureRepresentation3D, { t: 0 }, { tags: 'animate-structure-spin' });
+ }
+
+ if (!changed) return;
+
+ return update.commit({ doNotUpdateCurrent: true });
+ },
+ teardown(_, __, plugin) {
+ const state = plugin.state.data;
+ const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3DState)
+ .withTag('animate-structure-spin'));
+ if (reprs.length === 0) return;
+
+ const update = state.build();
+ for (const r of reprs) update.delete(r.transform.ref);
+ return update.commit();
+ },
+ async apply(animState, t, ctx) {
+ const state = ctx.plugin.state.data;
+ const anims = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.SpinStructureRepresentation3D));
+
+ if (anims.length === 0) {
+ return { kind: 'finished' };
+ }
+
+ const update = state.build();
+
+ const d = (t.current - t.lastApplied) / ctx.params.durationInMs;
+ const newTime = (animState.t + d) % 1;
+
+ for (const m of anims) {
+ update.to(m).update({ ...m.params?.values, t: newTime });
+ }
+
+ await PluginCommands.State.Update(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+
+ return { kind: 'next', state: { t: newTime } };
+ }
+});
\ No newline at end of file
diff --git a/src/mol-plugin-state/animation/helpers.ts b/src/mol-plugin-state/animation/helpers.ts
index 700eef0f7cec7b3eb5b1eb464657ca98aec6893d..b3e554b1b26d8483452fbfa46befaa874c3d0ae9 100644
--- a/src/mol-plugin-state/animation/helpers.ts
+++ b/src/mol-plugin-state/animation/helpers.ts
@@ -1,9 +1,11 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 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>
*/
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { SymmetryOperator } from '../../mol-math/geometry';
import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
import { Structure } from '../../mol-model/structure';
@@ -32,4 +34,60 @@ export function explodeStructure(structure: Structure, unitTransforms: Structure
unitTransforms.setTransform(_transMat, u);
}
+}
+
+//
+
+export const SpinStructureParams = {
+ axis: PD.MappedStatic('custom', {
+ structure: PD.Group({
+ principalAxis: PD.Select('dirA', [['dirA', 'A'], ['dirB', 'B'], ['dirC', 'C']] as const)
+ }),
+ custom: PD.Group({
+ vector: PD.Vec3(Vec3.create(0, 0, 1))
+ })
+ }),
+ origin: PD.MappedStatic('structure', {
+ structure: PD.Group({}),
+ custom: PD.Group({
+ vector: PD.Vec3(Vec3.create(0, 0, 0))
+ })
+ }),
+};
+export type SpinStructureProps = PD.Values<typeof SpinStructureParams>
+
+export function getSpinStructureAxisAndOrigin(structure: Structure, props: SpinStructureProps) {
+ let axis: Vec3, origin: Vec3;
+
+ if (props.axis.name === 'custom') {
+ axis = props.axis.params.vector;
+ } else {
+ const pa = Structure.getPrincipalAxes(structure);
+ axis = pa.momentsAxes[props.axis.params.principalAxis];
+ }
+
+ if (props.origin.name === 'custom') {
+ origin = props.origin.params.vector;
+ } else {
+ const pa = Structure.getPrincipalAxes(structure);
+ origin = pa.momentsAxes.origin;
+ }
+
+ return { axis, origin };
+}
+
+const _rotMat = Mat4();
+const _transMat2 = Mat4();
+const _t = Mat4();
+export function spinStructure(structure: Structure, unitTransforms: StructureUnitTransforms, t: number, axis: Vec3, origin: Vec3) {
+ for (let i = 0, _i = structure.units.length; i < _i; i++) {
+ const u = structure.units[i];
+ Vec3.negate(_transVec, origin);
+ Mat4.fromTranslation(_transMat, _transVec);
+ Mat4.fromRotation(_rotMat, Math.PI * t * 2, axis);
+ Mat4.fromTranslation(_transMat2, origin);
+ Mat4.mul(_t, _rotMat, _transMat);
+ Mat4.mul(_t, _transMat2, _t);
+ unitTransforms.setTransform(_t, u);
+ }
}
\ No newline at end of file
diff --git a/src/mol-plugin-state/transforms/representation.ts b/src/mol-plugin-state/transforms/representation.ts
index 4e726697afacd3d3d788b1e6fd10f8195fde1c12..d4bb3e506bb40e988733dd96cfa111f1f4feb54e 100644
--- a/src/mol-plugin-state/transforms/representation.ts
+++ b/src/mol-plugin-state/transforms/representation.ts
@@ -20,7 +20,7 @@ import { PluginStateObject as SO, PluginStateTransform } from '../objects';
import { ColorNames } from '../../mol-util/color/names';
import { ShapeRepresentation } from '../../mol-repr/shape/representation';
import { StructureUnitTransforms } from '../../mol-model/structure/structure/util/unit-transforms';
-import { unwindStructureAssembly, explodeStructure } from '../animation/helpers';
+import { unwindStructureAssembly, explodeStructure, spinStructure, SpinStructureParams, getSpinStructureAxisAndOrigin } from '../animation/helpers';
import { Color } from '../../mol-util/color';
import { Overpaint } from '../../mol-theme/overpaint';
import { Transparency } from '../../mol-theme/transparency';
@@ -43,6 +43,7 @@ import { Box3D } from '../../mol-math/geometry';
export { StructureRepresentation3D };
export { ExplodeStructureRepresentation3D };
+export { SpinStructureRepresentation3D };
export { UnwindStructureAssemblyRepresentation3D };
export { OverpaintStructureRepresentation3DFromScript };
export { OverpaintStructureRepresentation3DFromBundle };
@@ -222,7 +223,6 @@ const UnwindStructureAssemblyRepresentation3D = PluginStateTransform.BuiltIn({
}
});
-
type ExplodeStructureRepresentation3D = typeof ExplodeStructureRepresentation3D
const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
name: 'explode-structure-representation-3d',
@@ -259,6 +259,49 @@ const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
}
});
+type SpinStructureRepresentation3D = typeof SpinStructureRepresentation3D
+const SpinStructureRepresentation3D = PluginStateTransform.BuiltIn({
+ name: 'spin-structure-representation-3d',
+ display: 'Spin 3D Representation',
+ from: SO.Molecule.Structure.Representation3D,
+ to: SO.Molecule.Structure.Representation3DState,
+ params: {
+ t: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }),
+ ...SpinStructureParams
+ }
+})({
+ canAutoUpdate() {
+ return true;
+ },
+ apply({ a, params }) {
+ const structure = a.data.sourceData;
+ const unitTransforms = new StructureUnitTransforms(structure.root);
+
+ const { axis, origin } = getSpinStructureAxisAndOrigin(structure.root, params);
+ spinStructure(structure, unitTransforms, params.t, axis, origin);
+ return new SO.Molecule.Structure.Representation3DState({
+ state: { unitTransforms },
+ initialState: { unitTransforms: new StructureUnitTransforms(structure.root) },
+ info: structure.root,
+ repr: a.data.repr
+ }, { label: `Spin T = ${params.t.toFixed(2)}` });
+ },
+ update({ a, b, newParams, oldParams }) {
+ const structure = a.data.sourceData;
+ if (b.data.info !== structure.root) return StateTransformer.UpdateResult.Recreate;
+ if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
+
+ if (oldParams.t === newParams.t && oldParams.axis === newParams.axis && oldParams.origin === newParams.origin) return StateTransformer.UpdateResult.Unchanged;
+
+ const unitTransforms = b.data.state.unitTransforms!;
+ const { axis, origin } = getSpinStructureAxisAndOrigin(structure.root, newParams);
+ spinStructure(structure.root, unitTransforms, newParams.t, axis, origin);
+ b.label = `Spin T = ${newParams.t.toFixed(2)}`;
+ b.data.repr = a.data.repr;
+ return StateTransformer.UpdateResult.Updated;
+ }
+});
+
type OverpaintStructureRepresentation3DFromScript = typeof OverpaintStructureRepresentation3DFromScript
const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn({
name: 'overpaint-structure-representation-3d-from-script',
diff --git a/src/mol-plugin/spec.ts b/src/mol-plugin/spec.ts
index d9cca1117df7f8a1fd57aed01baa160820db42de..1438a1cfc6bdfe21bb4be97575d208d6301894c4 100644
--- a/src/mol-plugin/spec.ts
+++ b/src/mol-plugin/spec.ts
@@ -22,6 +22,7 @@ import { AssignColorVolume } from '../mol-plugin-state/actions/volume';
import { StateTransforms } from '../mol-plugin-state/transforms';
import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
import { AnimateStateInterpolation } from '../mol-plugin-state/animation/built-in/state-interpolation';
+import { AnimateStructureSpin } from '../mol-plugin-state/animation/built-in/spin-structure';
export { PluginSpec };
@@ -96,6 +97,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
PluginSpec.Action(StateTransforms.Representation.ModelUnitcell3D),
PluginSpec.Action(StateTransforms.Representation.StructureBoundingBox3D),
PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
+ PluginSpec.Action(StateTransforms.Representation.SpinStructureRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
@@ -128,6 +130,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
AnimateCameraSpin,
AnimateStateSnapshots,
AnimateAssemblyUnwind,
+ AnimateStructureSpin,
AnimateStateInterpolation
]
});
\ No newline at end of file