Merge pull request #181 from molstar/spin-struct-anim

Spin structure animation

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
 

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 };

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;
 

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 } };
+    }
+});

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);
+    }
 }

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',

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
     ]
 });