From 6a330a6da5fb8ed01a45bed94de765ff48366ea2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Mal=C3=BD?= <michal.maly@ibt.cas.cz>
Date: Mon, 21 Mar 2022 07:28:00 +0100
Subject: [PATCH] ReDNATCO plugin stage 4
---
src/apps/rednatco/idents.ts | 2 +-
src/apps/rednatco/index.html | 2 +-
src/apps/rednatco/index.tsx | 380 +-
.../rednatco/reference-conformers-pdbs.ts | 3859 +++++++++++++++++
src/apps/rednatco/reference-conformers.ts | 190 +
src/apps/rednatco/step.ts | 71 +
src/apps/rednatco/superpose.ts | 30 +
src/apps/rednatco/util.ts | 13 +
8 files changed, 4524 insertions(+), 23 deletions(-)
create mode 100644 src/apps/rednatco/reference-conformers-pdbs.ts
create mode 100644 src/apps/rednatco/reference-conformers.ts
create mode 100644 src/apps/rednatco/step.ts
create mode 100644 src/apps/rednatco/superpose.ts
create mode 100644 src/apps/rednatco/util.ts
diff --git a/src/apps/rednatco/idents.ts b/src/apps/rednatco/idents.ts
index b83cb834a..6340bfb81 100644
--- a/src/apps/rednatco/idents.ts
+++ b/src/apps/rednatco/idents.ts
@@ -1,4 +1,4 @@
-export type ID ='data'|'trajectory'|'model'|'structure'|'visual'|'pyramids';
+export type ID ='data'|'trajectory'|'model'|'structure'|'visual'|'pyramids'|'superposition';
export type Substructure = 'nucleic'|'protein'|'water';
export function ID(id: ID, sub: Substructure|'', ref: string) {
diff --git a/src/apps/rednatco/index.html b/src/apps/rednatco/index.html
index 675cf4b28..a2633701a 100644
--- a/src/apps/rednatco/index.html
+++ b/src/apps/rednatco/index.html
@@ -4,7 +4,7 @@
<meta charset="utf-8" />
<link rel="stylesheet" type="text/css" href="molstar.css" />
</head>
- <body style="height: 100vh; display: flex; overflow: hidden;">
+ <body style="height: 95vh; display: flex; overflow: hidden;">
<div id="xxx-app" style="flex: 1"></div>
<script type="text/javascript" src="./molstar.js"></script>
<script>
diff --git a/src/apps/rednatco/index.tsx b/src/apps/rednatco/index.tsx
index 4085262b6..a86b75322 100644
--- a/src/apps/rednatco/index.tsx
+++ b/src/apps/rednatco/index.tsx
@@ -4,11 +4,17 @@ import { NtCColors } from './colors';
import { ColorPicker } from './color-picker';
import { PushButton, ToggleButton } from './controls';
import * as IDs from './idents';
+import * as RefCfmr from './reference-conformers';
+import { ReferenceConformersPdbs } from './reference-conformers-pdbs';
+import { Step } from './step';
+import { Superpose } from './superpose';
import { DnatcoConfalPyramids } from '../../extensions/dnatco';
import { ConfalPyramidsParams } from '../../extensions/dnatco/confal-pyramids/representation';
+import { OrderedSet } from '../../mol-data/int/ordered-set';
import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
import { Loci } from '../../mol-model/loci';
-import { Model, Structure, Trajectory } from '../../mol-model/structure';
+import { Model, Structure, StructureElement, StructureProperties, Trajectory } from '../../mol-model/structure';
+import { Location } from '../../mol-model/structure/structure/element/location';
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
import { PluginBehavior, PluginBehaviors } from '../../mol-plugin/behavior';
import { PluginCommands } from '../../mol-plugin/commands';
@@ -41,12 +47,22 @@ const Extensions = {
'ntc-balls-pyramids-prop': PluginSpec.Behavior(DnatcoConfalPyramids),
};
-const BaseRef = 'rdo';
const AnimationDurationMsec = 150;
+const BaseRef = 'rdo';
+const RCRef = 'rc';
+const NtCSupPrev = 'ntc-sup-prev';
+const NtCSupSel = 'ntc-sup-sel';
+const NtCSupNext = 'ntc-sup-next';
const SelectAllScript = Script('(sel.atom.atoms true)', 'mol-script');
const SphereBoundaryHelper = new BoundaryHelper('98');
+type StepInfo = {
+ name: string;
+ assignedNtC: string;
+ closestNtC: string; // Fallback for cases where assignedNtC is NANT
+}
+
function capitalize(s: string) {
if (s.length === 0)
return s;
@@ -54,6 +70,80 @@ function capitalize(s: string) {
}
+function dinucleotideBackbone(loci: StructureElement.Loci) {
+ const es = loci.elements[0];
+ const loc = Location.create(loci.structure, es.unit, es.unit.elements[OrderedSet.getAt(es.indices, 0)]);
+ const len = OrderedSet.size(es.indices);
+ const indices = [];
+
+ // Find split between first and second residue
+ const resNo1 = StructureProperties.residue.auth_seq_id(loc);
+ let secondIdx = -1;
+ for (let idx = 0; idx < len; idx++) {
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
+ const resNo = StructureProperties.residue.auth_seq_id(loc);
+ if (resNo !== resNo1) {
+ secondIdx = idx;
+ break;
+ }
+ }
+ if (secondIdx === -1)
+ return [];
+
+ // Gather ElementIndices for backbone atoms of the first residue
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, 0)];
+ const comp1 = StructureProperties.atom.label_comp_id(loc);
+ const ring1 = RefCfmr.CompoundRings[comp1 as keyof RefCfmr.CompoundRings];
+ if (!ring1)
+ return [];
+
+ const first = RefCfmr.BackboneAtoms.first.concat(RefCfmr.BackboneAtoms[ring1]);
+ for (const atom of first) {
+ let idx = 0;
+ for (; idx < secondIdx; idx++) {
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
+ const _atom = StructureProperties.atom.label_atom_id(loc);
+ if (atom === _atom) {
+ indices.push(loc.element);
+ break;
+ }
+ }
+ if (idx === secondIdx) {
+ console.error(`Cannot find backbone atom ${atom} in first residue of a step`);
+ return [];
+ }
+ }
+
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, secondIdx)];
+ const comp2 = StructureProperties.atom.label_comp_id(loc);
+ const ring2 = RefCfmr.CompoundRings[comp2 as keyof RefCfmr.CompoundRings];
+ if (!ring2)
+ return [];
+
+ const second = RefCfmr.BackboneAtoms.second.concat(RefCfmr.BackboneAtoms[ring2]);
+ for (const atom of second) {
+ let idx = secondIdx;
+ for (; idx < len; idx++) {
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
+ const _atom = StructureProperties.atom.label_atom_id(loc);
+ if (atom === _atom) {
+ indices.push(loc.element);
+ break;
+ }
+ }
+ if (idx === len) {
+ console.error(`Cannot find backbone atom ${atom} in second residue of a step`);
+ return [];
+ }
+ }
+
+ return indices;
+}
+
+function rcref(c: string, where: 'sel'|'prev'|'next'|'' = '') {
+ return `${RCRef}-${c}-${where}`;
+}
+
class ColorBox extends React.Component<{ caption: string, color: Color }> {
render() {
return (
@@ -127,20 +217,22 @@ const ReDNATCOLociLabelProvider = PluginBehavior.create({
const ReDNATCOLociSelectionBindings = {
clickFocus: Binding([Binding.Trigger(ButtonsType.Flag.Secondary)], 'Focus camera on selected loci using ${triggers}'),
- clickToggle: Binding([Binding.Trigger(ButtonsType.Flag.Primary)], 'Set selection to clicked element using ${triggers}.'),
+ clickSelectOnly: Binding([Binding.Trigger(ButtonsType.Flag.Primary)], 'Select the clicked element using ${triggers}.'),
clickDeselectAllOnEmpty: Binding([Binding.Trigger(ButtonsType.Flag.Primary)], 'Deselect all when clicking on nothing using ${triggers}.'),
};
const ReDNATCOLociSelectionParams = {
bindings: PD.Value(ReDNATCOLociSelectionBindings, { isHidden: true }),
+ onDeselected: PD.Value(() => {}, { isHidden: true }),
+ onSelected: PD.Value((loci: Representation.Loci) => {}, { isHidden: true }),
};
-type WatlasLociSelectionProps = PD.Values<typeof ReDNATCOLociSelectionParams>;
+type ReDNATCOLociSelectionProps = PD.Values<typeof ReDNATCOLociSelectionParams>;
const ReDNATCOLociSelectionProvider = PluginBehavior.create({
- name: 'watlas-loci-selection-provider',
+ name: 'rednatco-loci-selection-provider',
category: 'interaction',
- display: { name: 'Interactive loci selection' },
+ display: { name: 'Interactive step selection' },
params: () => ReDNATCOLociSelectionParams,
- ctor: class extends PluginBehavior.Handler<WatlasLociSelectionProps> {
+ ctor: class extends PluginBehavior.Handler<ReDNATCOLociSelectionProps> {
private spine: StateTreeSpine.Impl;
private lociMarkProvider = (reprLoci: Representation.Loci, action: MarkerAction) => {
if (!this.ctx.canvas3d) return;
@@ -178,12 +270,25 @@ const ReDNATCOLociSelectionProvider = PluginBehavior.create({
const actions: [keyof typeof ReDNATCOLociSelectionBindings, (current: Representation.Loci) => void, ((current: Representation.Loci) => boolean) | undefined][] = [
['clickFocus', current => this.focusOnLoci(current), lociIsNotEmpty],
- ['clickDeselectAllOnEmpty', () => this.ctx.managers.interactivity.lociSelects.deselectAll(), lociIsEmpty],
- ['clickToggle', current => {
- if (current.loci.kind === 'element-loci')
- this.ctx.managers.interactivity.lociSelects.toggle(current, true);
- },
- lociIsNotEmpty],
+ [
+ 'clickDeselectAllOnEmpty',
+ () => {
+ this.ctx.managers.interactivity.lociSelects.deselectAll();
+ this.params.onDeselected();
+ },
+ lociIsEmpty
+ ],
+ [
+ 'clickSelectOnly',
+ current => {
+ this.ctx.managers.interactivity.lociSelects.deselectAll();
+ if (current.loci.kind === 'element-loci') {
+ this.ctx.managers.interactivity.lociSelects.select(current);
+ this.params.onSelected(current);
+ }
+ },
+ lociIsNotEmpty
+ ],
];
// sort the action so that the ones with more modifiers trigger sooner.
@@ -229,7 +334,7 @@ const ReDNATCOLociSelectionProvider = PluginBehavior.create({
}
unregister() {
}
- constructor(ctx: PluginContext, params: WatlasLociSelectionProps) {
+ constructor(ctx: PluginContext, params: ReDNATCOLociSelectionProps) {
super(ctx, params);
this.spine = new StateTreeSpine.Impl(ctx.state.data.cells);
}
@@ -237,7 +342,12 @@ const ReDNATCOLociSelectionProvider = PluginBehavior.create({
});
class ReDNATCOMspViewer {
- constructor(public plugin: PluginUIContext) {
+ private haveMultipleModels = false;
+ private steps: StepInfo[] = [];
+ private stepNames: Map<string, number> = new Map();
+
+ constructor(public plugin: PluginUIContext, interactionContext: { self?: ReDNATCOMspViewer }) {
+ interactionContext.self = this;
}
private getBuilder(id: IDs.ID, sub: IDs.Substructure|'' = '', ref = BaseRef) {
@@ -253,6 +363,13 @@ class ReDNATCOMspViewer {
return parent.obj?.type.name === 'Structure' ? parent.obj : undefined;
}
+ private ntcRef(id: number|undefined, where: 'sel'|'prev'|'next') {
+ if (id === undefined)
+ return undefined;
+ const info = this.steps[id];
+ return rcref(info.assignedNtC === 'NANT' ? info.closestNtC : info.assignedNtC, where);
+ }
+
private pyramidsParams(colors: NtCColors.Conformers, visible: Map<string, boolean>, transparent: boolean) {
const typeParams = {} as PD.Values<ConfalPyramidsParams>;
for (const k of Reflect.ownKeys(ConfalPyramidsParams) as (keyof ConfalPyramidsParams)[]) {
@@ -299,14 +416,32 @@ class ReDNATCOMspViewer {
PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: AnimationDurationMsec });
}
+ private superpose(reference: StructureElement.Loci, stru: StructureElement.Loci) {
+ const refElems = dinucleotideBackbone(reference);
+ const struElems = dinucleotideBackbone(stru);
+
+ return Superpose.superposition(
+ { elements: refElems, conformation: reference.elements[0].unit.conformation },
+ { elements: struElems, conformation: stru.elements[0].unit.conformation }
+ );
+ }
+
static async create(target: HTMLElement) {
+ const interactCtx: { self?: ReDNATCOMspViewer } = { self: undefined };
const defaultSpec = DefaultPluginUISpec();
const spec: PluginUISpec = {
...defaultSpec,
behaviors: [
PluginSpec.Behavior(ReDNATCOLociLabelProvider),
PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
- PluginSpec.Behavior(ReDNATCOLociSelectionProvider),
+ PluginSpec.Behavior(
+ ReDNATCOLociSelectionProvider,
+ {
+ bindings: ReDNATCOLociSelectionBindings,
+ onDeselected: () => interactCtx.self!.onDeselected(),
+ onSelected: (loci) => interactCtx.self!.onLociSelected(loci),
+ }
+ ),
...ObjectKeys(Extensions).map(k => Extensions[k]),
],
components: {
@@ -332,7 +467,7 @@ class ReDNATCOMspViewer {
plugin.managers.interactivity.setProps({ granularity: 'two-residues' });
plugin.selectionMode = true;
- return new ReDNATCOMspViewer(plugin);
+ return new ReDNATCOMspViewer(plugin, interactCtx);
}
async changeNtCColors(display: Partial<Display>) {
@@ -399,6 +534,61 @@ class ReDNATCOMspViewer {
await b.commit();
}
+ gatherNtCInfo(): { steps: StepInfo[], stepNames: Map<string, number> }|undefined {
+ const obj = this.plugin.state.data.cells.get(IDs.ID('model', '', BaseRef))?.obj;
+ if (!obj)
+ return void 0;
+ const model = (obj as StateObject<Model>);
+ const sourceData = model.data.sourceData;
+ if (!MmcifFormat.is(sourceData))
+ return void 0;
+
+ const tableSum = sourceData.data.frame.categories['ndb_struct_ntc_step_summary'];
+ const tableStep = sourceData.data.frame.categories['ndb_struct_ntc_step'];
+ if (!tableSum || !tableStep) {
+ console.warn('NtC information not present');
+ return void 0;
+ }
+
+ const _ids = tableStep.getField('id');
+ const _names = tableStep.getField('name');
+ const _stepIds = tableSum.getField('step_id');
+ const _assignedNtCs = tableSum.getField('assigned_NtC');
+ const _closestNtCs = tableSum.getField('closest_NtC');
+ if (!_ids || !_names || !_stepIds || !_assignedNtCs || !_closestNtCs) {
+ console.warn('Expected fields are not present in NtC categories');
+ return void 0;
+ }
+
+ const ids = _ids.toIntArray();
+ const names = _names.toStringArray();
+ const stepIds = _stepIds.toIntArray();
+ const assignedNtCs = _assignedNtCs.toStringArray();
+ const closestNtCs = _closestNtCs.toStringArray();
+ const len = ids.length;
+
+ const stepNames = new Map<string, number>();
+ const steps = new Array<StepInfo>(len);
+
+ for (let idx = 0; idx < len; idx++) {
+ const id = ids[idx];
+ const name = names[idx];
+ for (let jdx = 0; jdx < len; jdx++) {
+ if (stepIds[jdx] === id) {
+ const assignedNtC = assignedNtCs[jdx];
+ const closestNtC = closestNtCs[jdx];
+
+ // We're assuming that steps are ID'd with a contigious, monotonic sequence starting from 1
+ steps[id - 1] = { name, assignedNtC, closestNtC };
+ stepNames.set(name, id - 1);
+ break;
+ }
+ }
+ }
+
+ return { steps, stepNames };
+ }
+
getModelCount() {
const obj = this.plugin.state.data.cells.get(IDs.ID('trajectory', '', BaseRef))?.obj;
if (!obj)
@@ -460,7 +650,7 @@ class ReDNATCOMspViewer {
}
async loadStructure(data: string, type: 'pdb'|'cif', display: Partial<Display>) {
- await this.plugin.state.data.build().toRoot().commit();
+ // TODO: Remove the currently loaded structure
const b = (t => type === 'pdb'
? t.apply(StateTransforms.Model.TrajectoryFromPDB, {}, { ref: IDs.ID('trajectory', '', BaseRef) })
@@ -519,6 +709,53 @@ class ReDNATCOMspViewer {
}
await bb.commit();
+
+ this.haveMultipleModels = this.getModelCount() > 1;
+
+ const ntcInfo = this.gatherNtCInfo();
+ if (!ntcInfo) {
+ this.steps.length = 0;
+ this.stepNames.clear();
+ } else {
+ this.steps = ntcInfo.steps;
+ this.stepNames = ntcInfo.stepNames;
+ }
+ }
+
+ async loadReferenceConformers() {
+ const b = this.plugin.state.data.build().toRoot();
+
+ for (const c in ReferenceConformersPdbs) {
+ const cfmr = ReferenceConformersPdbs[c as keyof typeof ReferenceConformersPdbs];
+ const bRef = rcref(c);
+ const mRef = IDs.ID('model', '', bRef);
+ b.toRoot();
+ b.apply(RawData, { data: cfmr }, { ref: IDs.ID('data', '', bRef) })
+ .apply(StateTransforms.Model.TrajectoryFromPDB, {}, { ref: IDs.ID('trajectory', '', bRef) })
+ .apply(StateTransforms.Model.ModelFromTrajectory, {}, { ref: mRef })
+ .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'sel')) })
+ .to(mRef)
+ .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'prev')) })
+ .to(mRef)
+ .apply(StateTransforms.Model.StructureFromModel, {}, { ref: IDs.ID('structure', '', rcref(c, 'next')) });
+ }
+
+ await b.commit();
+ }
+
+ onDeselected() {
+ this.plugin.state.data.build()
+ .delete(IDs.ID('superposition', '', NtCSupSel))
+ .delete(IDs.ID('superposition', '', NtCSupPrev))
+ .delete(IDs.ID('superposition', '', NtCSupNext))
+ .commit();
+ }
+
+ onLociSelected(selected: Representation.Loci) {
+ const loci = Loci.normalize(selected.loci, 'two-residues');
+
+ if (loci.kind === 'element-loci')
+ this.superposeReferences(loci);
}
async switchModel(display: Partial<Display>) {
@@ -534,6 +771,105 @@ class ReDNATCOMspViewer {
await b.commit();
}
+ superposeReferences(selected: StructureElement.Loci) {
+ const step = Step.describe(selected);
+ if (!step)
+ return;
+
+ const stepName = Step.name(step, this.haveMultipleModels);
+ const stepId = this.stepNames.get(stepName);
+ if (stepId === undefined) {
+ console.error(`Unknown step name ${stepName}`);
+ return;
+ }
+
+ const stepIdPrev = stepId === 0 ? void 0 : stepId - 1;
+ const stepIdNext = stepId === this.steps.length - 1 ? void 0 : stepId + 1;
+
+ const ntcRefSel = this.ntcRef(stepId, 'sel');
+ const ntcRefPrev = this.ntcRef(stepIdPrev, 'prev');
+ const ntcRefNext = this.ntcRef(stepIdNext, 'next');
+
+ if (!ntcRefSel) {
+ console.error(`Seemingly invalid stepId ${stepId}`);
+ return;
+ }
+
+ const b = this.plugin.state.data.build()
+ .delete(IDs.ID('superposition', '', NtCSupSel))
+ .delete(IDs.ID('superposition', '', NtCSupPrev))
+ .delete(IDs.ID('superposition', '', NtCSupNext));
+
+ {
+ const stru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRefSel))!.obj!;
+ const loci = Script.toLoci(SelectAllScript, stru.data);
+
+ const { bTransform } = this.superpose(loci, selected);
+ if (isNaN(bTransform[0])) {
+ console.error(`Cannot superpose reference conformer ${ntcRefSel} onto selection`);
+ return;
+ }
+ b.to(IDs.ID('structure', '', ntcRefSel))
+ .apply(
+ StateTransforms.Model.TransformStructureConformation,
+ { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
+ { ref: IDs.ID('superposition', '', NtCSupSel) }
+ ).apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ { type: { name: 'ball-and-stick', params: { sizeFactor: 0.15 } } },
+ { ref: IDs.ID('visual', '', NtCSupSel) }
+ );
+ }
+
+ // TODO: These cannot be applied onto selection!!!
+ if (ntcRefPrev) {
+ const stru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRefPrev))!.obj!;
+ const loci = Script.toLoci(SelectAllScript, stru.data);
+
+ const { bTransform } = this.superpose(loci, selected);
+ if (isNaN(bTransform[0])) {
+ console.error(`Cannot superpose reference conformer ${ntcRefPrev} onto selection`);
+ return;
+ }
+ b.to(IDs.ID('structure', '', ntcRefPrev))
+ .apply(
+ StateTransforms.Model.TransformStructureConformation,
+ { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
+ { ref: IDs.ID('superposition', '', NtCSupPrev) }
+ ).apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ { type: { name: 'ball-and-stick', params: { sizeFactor: 0.15 } } },
+ { ref: IDs.ID('visual', '', NtCSupPrev) }
+ );
+ }
+
+ // TODO: These cannot be applied onto selection!!!
+ if (ntcRefNext) {
+ const stru = this.plugin.state.data.cells.get(IDs.ID('structure', '', ntcRefNext))!.obj!;
+ const loci = Script.toLoci(SelectAllScript, stru.data);
+
+ const { bTransform } = this.superpose(loci, selected);
+ if (isNaN(bTransform[0])) {
+ console.error(`Cannot superpose reference conformer ${ntcRefNext} onto selection`);
+ return;
+ }
+ b.to(IDs.ID('structure', '', ntcRefNext))
+ .apply(
+ StateTransforms.Model.TransformStructureConformation,
+ { transform: { name: 'matrix', params: { data: bTransform, transpose: false } } },
+ { ref: IDs.ID('superposition', '', NtCSupNext) }
+ ).apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ { type: { name: 'ball-and-stick', params: { sizeFactor: 0.15 } } },
+ { ref: IDs.ID('visual', '', NtCSupNext) }
+ );
+ }
+
+ // TODO: Superpose previous and next step too!!!
+
+ b.commit();
+ }
+
async toggleSubstructure(sub: IDs.Substructure, display: Partial<Display>) {
const show = sub === 'nucleic' ? !!display.showNucleic :
sub === 'protein' ? !!display.showProtein : !!display.showWater;
@@ -619,10 +955,12 @@ class ReDNATCOMsp extends React.Component<ReDNATCOMsp.Props, State> {
const elem = document.getElementById(this.props.elemId + '-viewer');
ReDNATCOMspViewer.create(elem!).then(viewer => {
this.viewer = viewer;
- ReDNATCOMspApi.bind(this);
+ this.viewer.loadReferenceConformers().then(() => {
+ ReDNATCOMspApi.bind(this);
- if (this.props.onInited)
- this.props.onInited();
+ if (this.props.onInited)
+ this.props.onInited();
+ });
});
}
}
diff --git a/src/apps/rednatco/reference-conformers-pdbs.ts b/src/apps/rednatco/reference-conformers-pdbs.ts
new file mode 100644
index 000000000..356c8049f
--- /dev/null
+++ b/src/apps/rednatco/reference-conformers-pdbs.ts
@@ -0,0 +1,3859 @@
+/* eslint-disable @typescript-eslint/indent */
+export const ReferenceConformersPdbs = {
+AA00:
+`ATOM 1 C5' A A 1 0.747 -3.730 2.150 1.00 14.22 C
+ATOM 2 C4' A A 1 0.639 -3.734 0.647 1.00 13.01 C
+ATOM 3 O4' A A 1 -0.082 -4.906 0.203 1.00 13.16 O
+ATOM 4 C3' A A 1 -0.145 -2.603 -0.002 1.00 12.76 C
+ATOM 5 O3' A A 1 0.629 -1.463 -0.055 1.00 14.62 O
+ATOM 6 C2' A A 1 -0.399 -3.189 -1.373 1.00 11.36 C
+ATOM 7 O2' A A 1 0.764 -3.303 -2.092 1.00 14.58 O
+ATOM 8 C1' A A 1 -0.856 -4.582 -0.963 1.00 13.01 C
+ATOM 9 N9 A A 1 -2.262 -4.741 -0.607 1.00 12.11 N
+ATOM 10 C8 A A 1 -2.843 -4.858 0.637 1.00 12.46 C
+ATOM 11 N7 A A 1 -4.143 -5.000 0.604 1.00 13.37 N
+ATOM 12 C5 A A 1 -4.470 -4.979 -0.749 1.00 12.37 C
+ATOM 13 C6 A A 1 -5.703 -5.085 -1.451 1.00 12.48 C
+ATOM 14 N6 A A 1 -6.889 -5.238 -0.845 1.00 15.54 N
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+`,
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+ATOM 9 C8 DA A 1 -3.142 -5.168 -0.026 1.00 14.84 C
+ATOM 10 N7 DA A 1 -4.104 -5.888 -0.553 1.00 14.54 N
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+ATOM 14 N1 DA A 1 -4.272 -5.771 -4.258 1.00 11.49 N
+ATOM 15 C2 DA A 1 -3.237 -4.925 -4.351 1.00 13.66 C
+ATOM 16 N3 DA A 1 -2.490 -4.396 -3.382 1.00 14.48 N
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+ATOM 19 OP1 DA A 2 1.604 0.863 -0.198 1.00 16.29 O
+ATOM 20 OP2 DA A 2 -0.561 0.451 1.110 1.00 14.30 O
+ATOM 21 O5' DA A 2 -0.496 0.162 -1.351 1.00 13.91 O
+ATOM 22 C5' DA A 2 0.110 -0.148 -2.602 1.00 14.31 C
+ATOM 23 C4' DA A 2 -0.899 0.031 -3.708 1.00 13.34 C
+ATOM 24 O4' DA A 2 -1.893 -1.011 -3.636 1.00 14.50 O
+ATOM 25 C3' DA A 2 -1.657 1.358 -3.643 1.00 12.57 C
+ATOM 26 O3' DA A 2 -1.401 2.066 -4.850 1.00 13.22 O
+ATOM 27 C2' DA A 2 -3.118 0.966 -3.479 1.00 13.59 C
+ATOM 28 C1' DA A 2 -3.159 -0.474 -3.954 1.00 12.42 C
+ATOM 29 N9 DA A 2 -4.156 -1.307 -3.286 1.00 11.61 N
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+ATOM 32 C5 DA A 2 -5.783 -2.724 -2.858 1.00 10.11 C
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+ATOM 36 C2 DA A 2 -6.353 -3.062 -5.419 1.00 13.53 C
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+`,
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+ATOM 3 O4' DC A 1 -0.303 -4.608 0.246 1.00119.31 O
+ATOM 4 C3' DC A 1 -0.116 -2.363 1.056 1.00119.97 C
+ATOM 5 O3' DC A 1 0.691 -1.356 0.389 1.00120.57 O
+ATOM 6 C2' DC A 1 -1.495 -2.639 0.445 1.00119.39 C
+ATOM 7 C1' DC A 1 -1.178 -3.796 -0.499 1.00118.84 C
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+ATOM 14 C5 DC A 1 -4.371 -5.733 -0.488 1.00118.08 C
+ATOM 15 C6 DC A 1 -3.302 -5.032 -0.088 1.00118.21 C
+ATOM 16 P DC A 2 0.147 -0.099 -0.458 1.00120.75 P
+ATOM 17 OP1 DC A 2 1.298 0.813 -0.652 1.00120.75 O
+ATOM 18 OP2 DC A 2 -1.094 0.427 0.172 1.00120.58 O
+ATOM 19 O5' DC A 2 -0.217 -0.787 -1.864 1.00120.54 O
+ATOM 20 C5' DC A 2 0.252 -0.286 -3.116 1.00120.03 C
+ATOM 21 C4' DC A 2 -0.914 0.202 -3.960 1.00119.90 C
+ATOM 22 O4' DC A 2 -1.958 -0.806 -3.970 1.00119.45 O
+ATOM 23 C3' DC A 2 -1.570 1.495 -3.467 1.00120.04 C
+ATOM 24 O3' DC A 2 -1.847 2.376 -4.557 1.00120.31 O
+ATOM 25 C2' DC A 2 -2.862 1.013 -2.819 1.00119.62 C
+ATOM 26 C1' DC A 2 -3.196 -0.173 -3.718 1.00119.27 C
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+ATOM 28 C2 DC A 2 -4.995 -1.923 -3.978 1.00118.28 C
+ATOM 29 O2 DC A 2 -4.917 -1.803 -5.209 1.00117.53 O
+ATOM 30 N3 DC A 2 -5.868 -2.794 -3.412 1.00118.20 N
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+`,
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+ATOM 3 O4' DA A 1 -0.198 -4.445 -0.149 1.00 32.38 O
+ATOM 4 C3' DA A 1 0.147 -2.309 0.848 1.00 33.72 C
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+ATOM 6 C2' DA A 1 -1.293 -2.457 0.384 1.00 32.53 C
+ATOM 7 C1' DA A 1 -1.163 -3.550 -0.662 1.00 31.29 C
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+ATOM 13 N6 DA A 1 -5.797 -6.472 -3.197 1.00 26.40 N
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+ATOM 19 OP1 DC A 2 2.149 0.673 0.026 1.00 39.25 O
+ATOM 20 OP2 DC A 2 -0.159 0.461 1.144 1.00 37.48 O
+ATOM 21 O5' DC A 2 0.090 0.458 -1.362 1.00 36.17 O
+ATOM 22 C5' DC A 2 -0.745 -0.500 -1.985 1.00 35.50 C
+ATOM 23 C4' DC A 2 -1.035 -0.108 -3.412 1.00 34.44 C
+ATOM 24 O4' DC A 2 -1.997 -1.083 -3.883 1.00 34.09 O
+ATOM 25 C3' DC A 2 -1.713 1.254 -3.544 1.00 34.40 C
+ATOM 26 O3' DC A 2 -1.377 1.890 -4.790 1.00 35.87 O
+ATOM 27 C2' DC A 2 -3.188 0.920 -3.460 1.00 33.23 C
+ATOM 28 C1' DC A 2 -3.265 -0.472 -4.073 1.00 32.12 C
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+ATOM 32 N3 DC A 2 -6.093 -2.835 -3.748 1.00 26.65 N
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+`,
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+ATOM 25 C3' DG A 2 -1.966 1.623 -4.025 1.00 46.16 C
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+`,
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+`,
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+ATOM 14 N1 DA A 1 -4.787 -5.728 -3.933 1.00 15.37 N
+ATOM 15 C2 DA A 1 -3.542 -5.248 -4.045 1.00 20.58 C
+ATOM 16 N3 DA A 1 -2.704 -4.826 -3.091 1.00 17.07 N
+ATOM 17 C4 DA A 1 -3.269 -4.949 -1.881 1.00 15.56 C
+ATOM 18 P DC A 2 0.627 0.044 0.125 1.00 29.40 P
+ATOM 19 OP1 DC A 2 2.068 0.138 0.479 1.00 29.81 O
+ATOM 20 OP2 DC A 2 -0.410 0.511 1.082 1.00 25.11 O
+ATOM 21 O5' DC A 2 0.392 0.830 -1.234 1.00 30.78 O
+ATOM 22 C5' DC A 2 -0.924 0.970 -1.764 1.00 30.92 C
+ATOM 23 C4' DC A 2 -0.989 0.395 -3.157 1.00 28.76 C
+ATOM 24 O4' DC A 2 -1.618 -0.916 -3.062 1.00 27.46 O
+ATOM 25 C3' DC A 2 -1.857 1.234 -4.093 1.00 28.36 C
+ATOM 26 O3' DC A 2 -1.203 1.612 -5.291 1.00 28.32 O
+ATOM 27 C2' DC A 2 -3.058 0.369 -4.423 1.00 28.18 C
+ATOM 28 C1' DC A 2 -2.685 -1.043 -3.993 1.00 26.72 C
+ATOM 29 N1 DC A 2 -3.842 -1.603 -3.283 1.00 22.66 N
+ATOM 30 C2 DC A 2 -4.826 -2.257 -4.025 1.00 22.54 C
+ATOM 31 O2 DC A 2 -4.641 -2.438 -5.231 1.00 25.00 O
+ATOM 32 N3 DC A 2 -5.951 -2.674 -3.415 1.00 23.31 N
+ATOM 33 C4 DC A 2 -6.106 -2.478 -2.106 1.00 22.87 C
+ATOM 34 N4 DC A 2 -7.241 -2.904 -1.547 1.00 21.77 N
+ATOM 35 C5 DC A 2 -5.100 -1.842 -1.313 1.00 21.34 C
+ATOM 36 C6 DC A 2 -3.988 -1.438 -1.938 1.00 19.77 C
+`,
+BB07:
+`ATOM 1 C5' DC A 1 1.271 -4.153 1.259 1.00 66.91 C
+ATOM 2 C4' DC A 1 0.459 -3.462 0.193 1.00 66.91 C
+ATOM 3 O4' DC A 1 -0.366 -4.432 -0.491 1.00 66.91 O
+ATOM 4 C3' DC A 1 -0.503 -2.409 0.742 1.00 66.91 C
+ATOM 5 O3' DC A 1 -0.618 -1.364 -0.218 1.00 66.91 O
+ATOM 6 C2' DC A 1 -1.822 -3.160 0.805 1.00 66.91 C
+ATOM 7 C1' DC A 1 -1.711 -4.000 -0.456 1.00 66.91 C
+ATOM 8 N1 DC A 1 -2.584 -5.184 -0.556 1.00 70.06 N
+ATOM 9 C2 DC A 1 -2.986 -5.620 -1.834 1.00 70.06 C
+ATOM 10 O2 DC A 1 -2.570 -5.017 -2.836 1.00 70.06 O
+ATOM 11 N3 DC A 1 -3.809 -6.691 -1.939 1.00 70.06 N
+ATOM 12 C4 DC A 1 -4.220 -7.321 -0.837 1.00 70.06 C
+ATOM 13 N4 DC A 1 -5.040 -8.368 -0.987 1.00 70.06 N
+ATOM 14 C5 DC A 1 -3.814 -6.909 0.468 1.00 70.06 C
+ATOM 15 C6 DC A 1 -3.006 -5.846 0.562 1.00 70.06 C
+ATOM 16 P DG A 2 0.056 0.068 0.056 1.00 55.37 P
+ATOM 17 OP1 DG A 2 1.519 -0.145 0.220 1.00 60.57 O
+ATOM 18 OP2 DG A 2 -0.730 0.761 1.117 1.00 60.57 O
+ATOM 19 O5' DG A 2 -0.161 0.790 -1.343 1.00 55.37 O
+ATOM 20 C5' DG A 2 0.434 0.252 -2.522 1.00 55.37 C
+ATOM 21 C4' DG A 2 -0.554 0.254 -3.667 1.00 55.37 C
+ATOM 22 O4' DG A 2 -1.471 -0.871 -3.608 1.00 55.37 O
+ATOM 23 C3' DG A 2 -1.420 1.505 -3.776 1.00 55.37 C
+ATOM 24 O3' DG A 2 -1.622 1.760 -5.151 1.00 55.37 O
+ATOM 25 C2' DG A 2 -2.734 1.048 -3.177 1.00 55.37 C
+ATOM 26 C1' DG A 2 -2.804 -0.395 -3.662 1.00 55.37 C
+ATOM 27 N9 DG A 2 -3.632 -1.265 -2.830 1.00 60.57 N
+ATOM 28 C8 DG A 2 -3.752 -1.237 -1.459 1.00 60.57 C
+ATOM 29 N7 DG A 2 -4.587 -2.132 -0.998 1.00 60.57 N
+ATOM 30 C5 DG A 2 -5.043 -2.791 -2.132 1.00 60.57 C
+ATOM 31 C6 DG A 2 -5.975 -3.857 -2.270 1.00 60.57 C
+ATOM 32 O6 DG A 2 -6.582 -4.468 -1.390 1.00 60.57 O
+ATOM 33 N1 DG A 2 -6.165 -4.198 -3.600 1.00 60.57 N
+ATOM 34 C2 DG A 2 -5.537 -3.604 -4.666 1.00 60.57 C
+ATOM 35 N2 DG A 2 -5.876 -4.058 -5.879 1.00 60.57 N
+ATOM 36 N3 DG A 2 -4.652 -2.635 -4.553 1.00 60.57 N
+ATOM 37 C4 DG A 2 -4.460 -2.271 -3.270 1.00 60.57 C
+`,
+BB08:
+`ATOM 1 C5' DC A 1 1.295 -4.388 1.698 1.00 41.11 C
+ATOM 2 C4' DC A 1 0.594 -3.804 0.493 1.00 40.43 C
+ATOM 3 O4' DC A 1 -0.351 -4.762 -0.050 1.00 39.06 O
+ATOM 4 C3' DC A 1 -0.225 -2.539 0.781 1.00 40.50 C
+ATOM 5 O3' DC A 1 -0.110 -1.646 -0.318 1.00 43.00 O
+ATOM 6 C2' DC A 1 -1.652 -3.050 0.820 1.00 39.59 C
+ATOM 7 C1' DC A 1 -1.578 -4.081 -0.282 1.00 38.23 C
+ATOM 8 N1 DC A 1 -2.669 -5.068 -0.308 1.00 35.75 N
+ATOM 9 C2 DC A 1 -3.038 -5.619 -1.541 1.00 35.52 C
+ATOM 10 O2 DC A 1 -2.412 -5.276 -2.559 1.00 33.94 O
+ATOM 11 N3 DC A 1 -4.057 -6.510 -1.593 1.00 33.45 N
+ATOM 12 C4 DC A 1 -4.697 -6.851 -0.476 1.00 34.76 C
+ATOM 13 N4 DC A 1 -5.699 -7.730 -0.577 1.00 34.19 N
+ATOM 14 C5 DC A 1 -4.336 -6.313 0.795 1.00 35.42 C
+ATOM 15 C6 DC A 1 -3.326 -5.432 0.834 1.00 33.35 C
+ATOM 16 P DG A 2 0.656 -0.259 -0.129 1.00 43.17 P
+ATOM 17 OP1 DG A 2 2.100 -0.554 0.039 1.00 45.72 O
+ATOM 18 OP2 DG A 2 -0.074 0.509 0.909 1.00 42.11 O
+ATOM 19 O5' DG A 2 0.473 0.458 -1.529 1.00 41.36 O
+ATOM 20 C5' DG A 2 -0.814 0.842 -1.964 1.00 40.88 C
+ATOM 21 C4' DG A 2 -0.911 0.728 -3.461 1.00 38.25 C
+ATOM 22 O4' DG A 2 -1.498 -0.558 -3.758 1.00 37.21 O
+ATOM 23 C3' DG A 2 -1.862 1.757 -4.055 1.00 35.66 C
+ATOM 24 O3' DG A 2 -1.526 2.072 -5.400 1.00 35.33 O
+ATOM 25 C2' DG A 2 -3.207 1.071 -3.932 1.00 36.17 C
+ATOM 26 C1' DG A 2 -2.859 -0.399 -4.148 1.00 35.03 C
+ATOM 27 N9 DG A 2 -3.661 -1.315 -3.348 1.00 32.85 N
+ATOM 28 C8 DG A 2 -3.648 -1.448 -1.981 1.00 31.09 C
+ATOM 29 N7 DG A 2 -4.487 -2.347 -1.546 1.00 30.40 N
+ATOM 30 C5 DG A 2 -5.085 -2.839 -2.700 1.00 29.41 C
+ATOM 31 C6 DG A 2 -6.059 -3.851 -2.864 1.00 29.23 C
+ATOM 32 O6 DG A 2 -6.625 -4.515 -1.995 1.00 30.20 O
+ATOM 33 N1 DG A 2 -6.367 -4.059 -4.202 1.00 29.72 N
+ATOM 34 C2 DG A 2 -5.817 -3.381 -5.245 1.00 30.75 C
+ATOM 35 N2 DG A 2 -6.260 -3.728 -6.459 1.00 29.94 N
+ATOM 36 N3 DG A 2 -4.903 -2.431 -5.110 1.00 31.18 N
+ATOM 37 C4 DG A 2 -4.588 -2.215 -3.815 1.00 30.33 C
+`,
+BB10:
+`ATOM 1 C5' DG A 1 0.857 -4.193 2.010 1.00114.70 C
+ATOM 2 C4' DG A 1 0.501 -3.621 0.647 1.00115.86 C
+ATOM 3 O4' DG A 1 -0.327 -4.566 -0.086 1.00115.99 O
+ATOM 4 C3' DG A 1 -0.297 -2.316 0.686 1.00116.63 C
+ATOM 5 O3' DG A 1 0.238 -1.412 -0.292 1.00117.90 O
+ATOM 6 C2' DG A 1 -1.723 -2.770 0.361 1.00116.18 C
+ATOM 7 C1' DG A 1 -1.419 -3.867 -0.654 1.00115.69 C
+ATOM 8 N9 DG A 1 -2.521 -4.789 -0.947 1.00115.66 N
+ATOM 9 C8 DG A 1 -3.320 -5.441 -0.036 1.00115.36 C
+ATOM 10 N7 DG A 1 -4.225 -6.201 -0.587 1.00115.22 N
+ATOM 11 C5 DG A 1 -4.017 -6.052 -1.953 1.00115.38 C
+ATOM 12 C6 DG A 1 -4.697 -6.637 -3.057 1.00115.37 C
+ATOM 13 O6 DG A 1 -5.649 -7.422 -3.042 1.00115.58 O
+ATOM 14 N1 DG A 1 -4.189 -6.226 -4.285 1.00115.27 N
+ATOM 15 C2 DG A 1 -3.140 -5.353 -4.432 1.00115.29 C
+ATOM 16 N2 DG A 1 -2.792 -5.079 -5.695 1.00115.31 N
+ATOM 17 N3 DG A 1 -2.487 -4.796 -3.412 1.00115.48 N
+ATOM 18 C4 DG A 1 -2.972 -5.186 -2.196 1.00115.57 C
+ATOM 19 P DG A 2 -0.039 0.172 -0.237 1.00118.45 P
+ATOM 20 OP1 DG A 2 0.855 0.742 0.801 1.00118.04 O
+ATOM 21 OP2 DG A 2 -1.504 0.401 -0.146 1.00118.14 O
+ATOM 22 O5' DG A 2 0.453 0.683 -1.682 1.00117.75 O
+ATOM 23 C5' DG A 2 0.426 -0.141 -2.864 1.00116.51 C
+ATOM 24 C4' DG A 2 -0.789 0.129 -3.741 1.00115.44 C
+ATOM 25 O4' DG A 2 -1.698 -0.997 -3.626 1.00114.92 O
+ATOM 26 C3' DG A 2 -1.602 1.378 -3.389 1.00115.28 C
+ATOM 27 O3' DG A 2 -1.723 2.235 -4.548 1.00115.95 O
+ATOM 28 C2' DG A 2 -2.909 0.816 -2.823 1.00114.51 C
+ATOM 29 C1' DG A 2 -3.020 -0.505 -3.573 1.00113.52 C
+ATOM 30 N9 DG A 2 -3.933 -1.488 -2.981 1.00113.12 N
+ATOM 31 C8 DG A 2 -4.117 -1.769 -1.643 1.00112.82 C
+ATOM 32 N7 DG A 2 -5.008 -2.693 -1.415 1.00112.69 N
+ATOM 33 C5 DG A 2 -5.460 -3.044 -2.686 1.00112.86 C
+ATOM 34 C6 DG A 2 -6.440 -4.000 -3.082 1.00113.05 C
+ATOM 35 O6 DG A 2 -7.123 -4.751 -2.366 1.00112.80 O
+ATOM 36 N1 DG A 2 -6.590 -4.048 -4.470 1.00112.86 N
+ATOM 37 C2 DG A 2 -5.887 -3.269 -5.361 1.00112.55 C
+ATOM 38 N2 DG A 2 -6.181 -3.457 -6.651 1.00112.73 N
+ATOM 39 N3 DG A 2 -4.971 -2.371 -5.011 1.00112.13 N
+ATOM 40 C4 DG A 2 -4.807 -2.312 -3.661 1.00112.64 C
+`,
+BB12:
+`ATOM 1 C5' DG A 1 0.814 -4.601 1.487 1.00 39.19 C
+ATOM 2 C4' DG A 1 0.649 -3.711 0.280 1.00 37.22 C
+ATOM 3 O4' DG A 1 -0.308 -4.287 -0.635 1.00 36.46 O
+ATOM 4 C3' DG A 1 0.155 -2.294 0.557 1.00 33.32 C
+ATOM 5 O3' DG A 1 0.816 -1.438 -0.369 1.00 32.03 O
+ATOM 6 C2' DG A 1 -1.334 -2.375 0.254 1.00 31.06 C
+ATOM 7 C1' DG A 1 -1.364 -3.369 -0.891 1.00 32.96 C
+ATOM 8 N9 DG A 1 -2.580 -4.163 -1.013 1.00 31.80 N
+ATOM 9 C8 DG A 1 -3.408 -4.585 -0.001 1.00 32.18 C
+ATOM 10 N7 DG A 1 -4.361 -5.372 -0.417 1.00 32.12 N
+ATOM 11 C5 DG A 1 -4.160 -5.460 -1.787 1.00 30.44 C
+ATOM 12 C6 DG A 1 -4.861 -6.202 -2.778 1.00 32.25 C
+ATOM 13 O6 DG A 1 -5.819 -6.972 -2.634 1.00 34.50 O
+ATOM 14 N1 DG A 1 -4.333 -5.983 -4.046 1.00 32.97 N
+ATOM 15 C2 DG A 1 -3.260 -5.170 -4.324 1.00 32.73 C
+ATOM 16 N2 DG A 1 -2.922 -5.058 -5.614 1.00 33.93 N
+ATOM 17 N3 DG A 1 -2.578 -4.505 -3.407 1.00 29.50 N
+ATOM 18 C4 DG A 1 -3.082 -4.691 -2.172 1.00 30.54 C
+ATOM 19 P DA A 2 0.807 0.141 -0.136 1.00 31.07 P
+ATOM 20 OP1 DA A 2 1.788 0.695 -1.104 1.00 31.80 O
+ATOM 21 OP2 DA A 2 0.984 0.405 1.315 1.00 29.58 O
+ATOM 22 O5' DA A 2 -0.677 0.564 -0.547 1.00 30.10 O
+ATOM 23 C5' DA A 2 -0.938 1.245 -1.772 1.00 28.67 C
+ATOM 24 C4' DA A 2 -0.997 0.253 -2.906 1.00 27.06 C
+ATOM 25 O4' DA A 2 -1.967 -0.776 -2.602 1.00 26.29 O
+ATOM 26 C3' DA A 2 -1.412 0.825 -4.259 1.00 28.93 C
+ATOM 27 O3' DA A 2 -0.654 0.164 -5.282 1.00 30.94 O
+ATOM 28 C2' DA A 2 -2.881 0.438 -4.366 1.00 26.51 C
+ATOM 29 C1' DA A 2 -2.844 -0.924 -3.708 1.00 27.78 C
+ATOM 30 N9 DA A 2 -4.105 -1.487 -3.221 1.00 26.09 N
+ATOM 31 C8 DA A 2 -4.616 -1.446 -1.943 1.00 26.86 C
+ATOM 32 N7 DA A 2 -5.698 -2.168 -1.781 1.00 26.81 N
+ATOM 33 C5 DA A 2 -5.929 -2.702 -3.040 1.00 28.36 C
+ATOM 34 C6 DA A 2 -6.907 -3.583 -3.528 1.00 28.94 C
+ATOM 35 N6 DA A 2 -7.854 -4.131 -2.767 1.00 29.68 N
+ATOM 36 N1 DA A 2 -6.872 -3.896 -4.842 1.00 31.55 N
+ATOM 37 C2 DA A 2 -5.905 -3.360 -5.605 1.00 30.92 C
+ATOM 38 N3 DA A 2 -4.922 -2.536 -5.259 1.00 28.59 N
+ATOM 39 C4 DA A 2 -4.985 -2.248 -3.947 1.00 26.74 C
+`,
+BB13:
+`ATOM 1 C5' DA A 1 0.879 -4.537 2.052 1.00113.54 C
+ATOM 2 C4' DA A 1 0.725 -3.931 0.676 1.00115.56 C
+ATOM 3 O4' DA A 1 -0.272 -4.651 -0.092 1.00115.56 O
+ATOM 4 C3' DA A 1 0.280 -2.467 0.679 1.00117.40 C
+ATOM 5 O3' DA A 1 0.993 -1.743 -0.326 1.00119.21 O
+ATOM 6 C2' DA A 1 -1.193 -2.548 0.316 1.00116.82 C
+ATOM 7 C1' DA A 1 -1.194 -3.722 -0.640 1.00116.23 C
+ATOM 8 N9 DA A 1 -2.485 -4.390 -0.805 1.00115.90 N
+ATOM 9 C8 DA A 1 -3.427 -4.680 0.152 1.00115.65 C
+ATOM 10 N7 DA A 1 -4.497 -5.274 -0.323 1.00115.74 N
+ATOM 11 C5 DA A 1 -4.240 -5.388 -1.684 1.00115.74 C
+ATOM 12 C6 DA A 1 -4.988 -5.932 -2.755 1.00115.29 C
+ATOM 13 N6 DA A 1 -6.195 -6.484 -2.614 1.00114.84 N
+ATOM 14 N1 DA A 1 -4.441 -5.885 -3.990 1.00114.89 N
+ATOM 15 C2 DA A 1 -3.231 -5.330 -4.134 1.00115.24 C
+ATOM 16 N3 DA A 1 -2.434 -4.788 -3.211 1.00115.58 N
+ATOM 17 C4 DA A 1 -3.004 -4.849 -1.994 1.00115.81 C
+ATOM 18 P DC A 2 0.821 -0.153 -0.428 1.00120.47 P
+ATOM 19 OP1 DC A 2 1.686 0.323 -1.541 1.00119.68 O
+ATOM 20 OP2 DC A 2 1.006 0.399 0.941 1.00119.69 O
+ATOM 21 O5' DC A 2 -0.705 0.031 -0.850 1.00121.31 O
+ATOM 22 C5' DC A 2 -1.097 1.044 -1.772 1.00123.07 C
+ATOM 23 C4' DC A 2 -1.048 0.508 -3.184 1.00124.03 C
+ATOM 24 O4' DC A 2 -1.779 -0.740 -3.239 1.00123.85 O
+ATOM 25 C3' DC A 2 -1.693 1.416 -4.232 1.00124.45 C
+ATOM 26 O3' DC A 2 -1.129 1.209 -5.534 1.00124.38 O
+ATOM 27 C2' DC A 2 -3.121 0.903 -4.277 1.00124.32 C
+ATOM 28 C1' DC A 2 -2.938 -0.595 -4.048 1.00124.02 C
+ATOM 29 N1 DC A 2 -4.061 -1.225 -3.335 1.00123.59 N
+ATOM 30 C2 DC A 2 -4.965 -2.003 -4.060 1.00123.27 C
+ATOM 31 O2 DC A 2 -4.780 -2.160 -5.279 1.00122.61 O
+ATOM 32 N3 DC A 2 -6.012 -2.569 -3.416 1.00123.02 N
+ATOM 33 C4 DC A 2 -6.168 -2.384 -2.103 1.00122.81 C
+ATOM 34 N4 DC A 2 -7.217 -2.961 -1.512 1.00122.08 N
+ATOM 35 C5 DC A 2 -5.255 -1.602 -1.339 1.00122.90 C
+ATOM 36 C6 DC A 2 -4.224 -1.046 -1.989 1.00123.16 C
+`,
+BB14:
+`ATOM 1 C5' DC A 1 1.389 -4.319 1.576 1.00114.35 C
+ATOM 2 C4' DC A 1 0.573 -3.537 0.549 1.00115.62 C
+ATOM 3 O4' DC A 1 -0.348 -4.455 -0.090 1.00115.49 O
+ATOM 4 C3' DC A 1 -0.285 -2.361 1.047 1.00116.60 C
+ATOM 5 O3' DC A 1 0.343 -1.077 0.748 1.00118.34 O
+ATOM 6 C2' DC A 1 -1.676 -2.590 0.441 1.00116.09 C
+ATOM 7 C1' DC A 1 -1.457 -3.718 -0.566 1.00115.59 C
+ATOM 8 N1 DC A 1 -2.640 -4.642 -0.773 1.00115.16 N
+ATOM 9 C2 DC A 1 -2.890 -5.205 -2.043 1.00114.76 C
+ATOM 10 O2 DC A 1 -2.146 -4.956 -2.996 1.00114.62 O
+ATOM 11 N3 DC A 1 -3.957 -6.029 -2.206 1.00114.46 N
+ATOM 12 C4 DC A 1 -4.756 -6.298 -1.173 1.00114.47 C
+ATOM 13 N4 DC A 1 -5.787 -7.114 -1.392 1.00114.17 N
+ATOM 14 C5 DC A 1 -4.531 -5.742 0.125 1.00114.68 C
+ATOM 15 C6 DC A 1 -3.476 -4.929 0.277 1.00114.97 C
+ATOM 16 P DA A 2 -0.132 0.017 -0.336 1.00119.72 P
+ATOM 17 OP1 DA A 2 0.899 1.078 -0.342 1.00120.16 O
+ATOM 18 OP2 DA A 2 -1.533 0.405 -0.056 1.00119.43 O
+ATOM 19 O5' DA A 2 -0.066 -0.780 -1.729 1.00120.74 O
+ATOM 20 C5' DA A 2 0.397 -0.162 -2.938 1.00122.32 C
+ATOM 21 C4' DA A 2 -0.754 0.215 -3.863 1.00123.48 C
+ATOM 22 O4' DA A 2 -1.742 -0.854 -3.885 1.00123.91 O
+ATOM 23 C3' DA A 2 -1.513 1.494 -3.496 1.00124.19 C
+ATOM 24 O3' DA A 2 -1.788 2.275 -4.678 1.00124.76 O
+ATOM 25 C2' DA A 2 -2.791 0.956 -2.849 1.00124.17 C
+ATOM 26 C1' DA A 2 -3.027 -0.286 -3.698 1.00124.21 C
+ATOM 27 N9 DA A 2 -3.974 -1.255 -3.129 1.00124.20 N
+ATOM 28 C8 DA A 2 -4.277 -1.456 -1.807 1.00124.14 C
+ATOM 29 N7 DA A 2 -5.173 -2.392 -1.601 1.00124.10 N
+ATOM 30 C5 DA A 2 -5.485 -2.835 -2.875 1.00124.05 C
+ATOM 31 C6 DA A 2 -6.374 -3.823 -3.350 1.00123.94 C
+ATOM 32 N6 DA A 2 -7.138 -4.563 -2.543 1.00123.67 N
+ATOM 33 N1 DA A 2 -6.452 -4.022 -4.686 1.00124.03 N
+ATOM 34 C2 DA A 2 -5.686 -3.277 -5.498 1.00124.18 C
+ATOM 35 N3 DA A 2 -4.814 -2.320 -5.168 1.00124.14 N
+ATOM 36 C4 DA A 2 -4.759 -2.145 -3.832 1.00124.13 C
+`,
+BB15:
+`ATOM 1 C5' DG A 1 0.568 -4.502 2.011 1.00 12.88 C
+ATOM 2 C4' DG A 1 0.678 -3.715 0.724 1.00 11.66 C
+ATOM 3 O4' DG A 1 -0.092 -4.382 -0.308 1.00 12.33 O
+ATOM 4 C3' DG A 1 0.097 -2.301 0.799 1.00 11.88 C
+ATOM 5 O3' DG A 1 0.842 -1.429 -0.060 1.00 14.55 O
+ATOM 6 C2' DG A 1 -1.344 -2.487 0.347 1.00 13.76 C
+ATOM 7 C1' DG A 1 -1.226 -3.592 -0.692 1.00 12.27 C
+ATOM 8 N9 DG A 1 -2.390 -4.470 -0.795 1.00 11.11 N
+ATOM 9 C8 DG A 1 -3.124 -4.961 0.263 1.00 10.93 C
+ATOM 10 N7 DG A 1 -4.098 -5.747 -0.109 1.00 9.10 N
+ATOM 11 C5 DG A 1 -4.008 -5.779 -1.498 1.00 11.36 C
+ATOM 12 C6 DG A 1 -4.803 -6.477 -2.449 1.00 12.29 C
+ATOM 13 O6 DG A 1 -5.746 -7.239 -2.240 1.00 11.98 O
+ATOM 14 N1 DG A 1 -4.390 -6.221 -3.760 1.00 11.30 N
+ATOM 15 C2 DG A 1 -3.337 -5.409 -4.108 1.00 11.98 C
+ATOM 16 N2 DG A 1 -3.093 -5.293 -5.438 1.00 14.44 N
+ATOM 17 N3 DG A 1 -2.578 -4.758 -3.227 1.00 11.94 N
+ATOM 18 C4 DG A 1 -2.970 -4.989 -1.944 1.00 11.58 C
+ATOM 19 P DC A 2 0.574 0.155 -0.031 1.00 15.74 P
+ATOM 20 OP1 DC A 2 1.879 0.846 -0.209 1.00 16.81 O
+ATOM 21 OP2 DC A 2 -0.291 0.507 1.125 1.00 16.86 O
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+ATOM 27 O3' DC A 2 -1.444 2.087 -4.763 1.00 22.95 O
+ATOM 28 C2' DC A 2 -3.052 0.963 -3.236 1.00 18.20 C
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+`,
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+ATOM 26 C2' DT A 2 -2.738 -0.473 -2.806 1.00 7.80 C
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+`,
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+ATOM 26 C2' C A 2 -2.681 1.672 -3.108 1.00 47.54 C
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+`,
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+ATOM 27 O2' U A 2 -3.306 2.887 -3.730 1.00 39.84 O
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+`,
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+`,
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+`,
+IC05:
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+ATOM 4 C3' DC A 1 -0.601 -2.703 0.969 1.00 10.95 C
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+`,
+IC06:
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+ATOM 19 O5' DG A 2 -0.086 0.131 -1.718 1.00 20.80 O
+ATOM 20 C5' DG A 2 0.179 -0.221 -3.065 1.00 19.83 C
+ATOM 21 C4' DG A 2 -0.962 0.258 -3.927 1.00 19.64 C
+ATOM 22 O4' DG A 2 -2.128 -0.554 -3.692 1.00 18.33 O
+ATOM 23 C3' DG A 2 -1.397 1.703 -3.649 1.00 19.68 C
+ATOM 24 O3' DG A 2 -1.771 2.193 -4.924 1.00 22.21 O
+ATOM 25 C2' DG A 2 -2.698 1.530 -2.894 1.00 18.74 C
+ATOM 26 C1' DG A 2 -3.241 0.305 -3.588 1.00 17.66 C
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+ATOM 20 O5' A A 2 -0.526 0.243 -1.358 1.00 61.00 O
+ATOM 21 C5' A A 2 0.138 0.289 -2.628 1.00 63.30 C
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+ATOM 23 O4' A A 2 -1.546 -1.046 -3.794 1.00 65.83 O
+ATOM 24 C3' A A 2 -1.932 1.278 -3.785 1.00 65.82 C
+ATOM 25 O3' A A 2 -1.459 2.465 -4.423 1.00 69.10 O
+ATOM 26 C2' A A 2 -3.069 0.613 -4.563 1.00 66.80 C
+ATOM 27 O2' A A 2 -3.024 0.792 -5.965 1.00 69.48 O
+ATOM 28 C1' A A 2 -2.883 -0.860 -4.222 1.00 66.57 C
+ATOM 29 N9 A A 2 -3.837 -1.264 -3.188 1.00 64.64 N
+ATOM 30 C8 A A 2 -3.615 -1.394 -1.845 1.00 62.24 C
+ATOM 31 N7 A A 2 -4.677 -1.768 -1.174 1.00 61.77 N
+ATOM 32 C5 A A 2 -5.670 -1.886 -2.138 1.00 64.06 C
+ATOM 33 C6 A A 2 -7.040 -2.249 -2.080 1.00 64.98 C
+ATOM 34 N6 A A 2 -7.681 -2.578 -0.948 1.00 64.06 N
+ATOM 35 N1 A A 2 -7.742 -2.257 -3.238 1.00 67.20 N
+ATOM 36 C2 A A 2 -7.114 -1.930 -4.377 1.00 68.52 C
+ATOM 37 N3 A A 2 -5.839 -1.575 -4.554 1.00 67.84 N
+ATOM 38 C4 A A 2 -5.165 -1.574 -3.388 1.00 65.50 C
+`,
+AB1S:
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+ATOM 2 C4' DA A 1 0.476 -3.717 0.747 1.00 18.05 C
+ATOM 3 O4' DA A 1 -0.144 -4.926 0.337 1.00 17.89 O
+ATOM 4 C3' DA A 1 -0.326 -2.614 0.085 1.00 19.08 C
+ATOM 5 O3' DA A 1 0.539 -1.489 -0.104 1.00 20.31 O
+ATOM 6 C2' DA A 1 -0.719 -3.253 -1.240 1.00 17.61 C
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+ATOM 8 N9 DA A 1 -2.265 -5.167 -0.766 1.00 17.56 N
+ATOM 9 C8 DA A 1 -3.266 -4.694 0.042 1.00 17.76 C
+ATOM 10 N7 DA A 1 -4.424 -5.267 -0.147 1.00 18.10 N
+ATOM 11 C5 DA A 1 -4.167 -6.192 -1.157 1.00 17.68 C
+ATOM 12 C6 DA A 1 -4.978 -7.128 -1.833 1.00 16.54 C
+ATOM 13 N6 DA A 1 -6.292 -7.277 -1.623 1.00 15.04 N
+ATOM 14 N1 DA A 1 -4.381 -7.879 -2.769 1.00 16.27 N
+ATOM 15 C2 DA A 1 -3.095 -7.721 -3.024 1.00 15.07 C
+ATOM 16 N3 DA A 1 -2.242 -6.888 -2.473 1.00 16.55 N
+ATOM 17 C4 DA A 1 -2.852 -6.139 -1.532 1.00 16.93 C
+ATOM 18 P DG A 2 0.028 0.043 -0.034 1.00 22.87 P
+ATOM 19 OP1 DG A 2 1.225 0.910 0.024 1.00 24.01 O
+ATOM 20 OP2 DG A 2 -1.027 0.162 1.003 1.00 24.01 O
+ATOM 21 O5' DG A 2 -0.666 0.239 -1.453 1.00 22.34 O
+ATOM 22 C5' DG A 2 0.099 0.127 -2.647 1.00 22.54 C
+ATOM 23 C4' DG A 2 -0.756 0.339 -3.880 1.00 24.34 C
+ATOM 24 O4' DG A 2 -1.736 -0.695 -4.021 1.00 24.05 O
+ATOM 25 C3' DG A 2 -1.526 1.656 -3.781 1.00 25.36 C
+ATOM 26 O3' DG A 2 -1.552 2.259 -5.067 1.00 29.44 O
+ATOM 27 C2' DG A 2 -2.920 1.185 -3.384 1.00 23.82 C
+ATOM 28 C1' DG A 2 -3.013 -0.092 -4.210 1.00 23.33 C
+ATOM 29 N9 DG A 2 -4.102 -0.975 -3.744 1.00 22.00 N
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+ATOM 31 N7 DG A 2 -5.911 -2.304 -3.801 1.00 20.70 N
+ATOM 32 C5 DG A 2 -5.490 -2.131 -2.488 1.00 21.84 C
+ATOM 33 C6 DG A 2 -6.036 -2.650 -1.281 1.00 21.66 C
+ATOM 34 O6 DG A 2 -7.023 -3.374 -1.144 1.00 22.23 O
+ATOM 35 N1 DG A 2 -5.315 -2.232 -0.169 1.00 20.96 N
+ATOM 36 C2 DG A 2 -4.204 -1.414 -0.206 1.00 21.00 C
+ATOM 37 N2 DG A 2 -3.632 -1.114 0.961 1.00 21.67 N
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+`,
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+ATOM 3 O4' G A 1 -0.294 -4.873 0.213 1.00 42.25 O
+ATOM 4 C3' G A 1 -0.259 -2.542 -0.081 1.00 42.29 C
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+ATOM 6 C2' G A 1 -0.557 -3.177 -1.439 1.00 44.50 C
+ATOM 7 O2' G A 1 0.605 -3.170 -2.254 1.00 46.78 O
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+ATOM 9 N9 G A 1 -2.297 -4.978 -1.013 1.00 31.46 N
+ATOM 10 C8 G A 1 -3.087 -5.062 0.103 1.00 32.08 C
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+ATOM 12 C5 G A 1 -4.335 -5.637 -1.534 1.00 30.37 C
+ATOM 13 C6 G A 1 -5.389 -6.048 -2.399 1.00 34.37 C
+ATOM 14 O6 G A 1 -6.567 -6.327 -2.130 1.00 44.21 O
+ATOM 15 N1 G A 1 -4.963 -6.119 -3.718 1.00 31.11 N
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+ATOM 17 N2 G A 1 -3.486 -5.950 -5.476 1.00 22.02 N
+ATOM 18 N3 G A 1 -2.719 -5.428 -3.360 1.00 23.88 N
+ATOM 19 C4 G A 1 -3.099 -5.357 -2.071 1.00 23.74 C
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+ATOM 21 OP1 G A 2 1.279 0.953 0.169 1.00 46.60 O
+ATOM 22 OP2 G A 2 -1.018 0.137 1.065 1.00 34.69 O
+ATOM 23 O5' G A 2 -0.537 0.485 -1.356 1.00 31.48 O
+ATOM 24 C5' G A 2 0.185 0.223 -2.549 1.00 27.64 C
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+ATOM 26 O4' G A 2 -1.592 -0.883 -3.759 1.00 28.35 O
+ATOM 27 C3' G A 2 -1.636 1.516 -3.817 1.00 24.64 C
+ATOM 28 O3' G A 2 -1.742 1.957 -5.165 1.00 30.75 O
+ATOM 29 C2' G A 2 -2.985 0.947 -3.387 1.00 25.38 C
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+ATOM 31 C1' G A 2 -2.913 -0.450 -3.980 1.00 27.99 C
+ATOM 32 N9 G A 2 -3.904 -1.366 -3.423 1.00 24.66 N
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+ATOM 34 N7 G A 2 -5.629 -2.788 -3.489 1.00 28.40 N
+ATOM 35 C5 G A 2 -5.322 -2.464 -2.174 1.00 23.84 C
+ATOM 36 C6 G A 2 -5.925 -2.920 -0.980 1.00 32.86 C
+ATOM 37 O6 G A 2 -6.863 -3.722 -0.857 1.00 39.55 O
+ATOM 38 N1 G A 2 -5.309 -2.370 0.143 1.00 34.31 N
+ATOM 39 C2 G A 2 -4.259 -1.481 0.112 1.00 40.51 C
+ATOM 40 N2 G A 2 -3.827 -1.063 1.311 1.00 42.36 N
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+`,
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+ATOM 3 O4' DG A 1 -0.065 -4.702 0.342 1.00 28.94 O
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+ATOM 7 C1' DG A 1 -1.110 -3.895 -0.148 1.00 26.75 C
+ATOM 8 N9 DG A 1 -2.263 -4.774 -0.306 1.00 24.54 N
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+ATOM 10 N7 DG A 1 -3.877 -6.224 0.242 1.00 24.10 N
+ATOM 11 C5 DG A 1 -3.866 -6.002 -1.115 1.00 24.64 C
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+ATOM 13 O6 DG A 1 -5.607 -7.350 -1.886 1.00 25.76 O
+ATOM 14 N1 DG A 1 -4.407 -6.080 -3.400 1.00 24.17 N
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+ATOM 17 N3 DG A 1 -2.570 -4.676 -2.738 1.00 24.21 N
+ATOM 18 C4 DG A 1 -2.888 -5.119 -1.488 1.00 24.13 C
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+ATOM 21 OP2 DG A 2 0.741 0.524 0.755 1.00 39.22 O
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+ATOM 23 C5' DG A 2 -1.235 -0.721 -2.225 1.00 32.27 C
+ATOM 24 C4' DG A 2 -1.237 0.117 -3.483 1.00 27.77 C
+ATOM 25 O4' DG A 2 -2.002 -0.605 -4.467 1.00 26.36 O
+ATOM 26 C3' DG A 2 -1.904 1.487 -3.407 1.00 28.01 C
+ATOM 27 O3' DG A 2 -1.253 2.310 -4.359 1.00 29.67 O
+ATOM 28 C2' DG A 2 -3.341 1.225 -3.838 1.00 26.43 C
+ATOM 29 C1' DG A 2 -3.101 0.151 -4.885 1.00 24.75 C
+ATOM 30 N9 DG A 2 -4.178 -0.807 -5.017 1.00 23.00 N
+ATOM 31 C8 DG A 2 -4.819 -1.139 -6.184 1.00 23.29 C
+ATOM 32 N7 DG A 2 -5.765 -2.024 -6.018 1.00 23.42 N
+ATOM 33 C5 DG A 2 -5.754 -2.312 -4.656 1.00 23.49 C
+ATOM 34 C6 DG A 2 -6.543 -3.213 -3.885 1.00 23.38 C
+ATOM 35 O6 DG A 2 -7.471 -4.002 -4.193 1.00 20.86 O
+ATOM 36 N1 DG A 2 -6.192 -3.196 -2.557 1.00 23.69 N
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+`,
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+ATOM 4 C3' DG A 1 0.137 -2.465 0.927 1.00 36.24 C
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+ATOM 7 C1' DG A 1 -1.261 -3.882 -0.320 1.00 34.87 C
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+ATOM 9 C8 DG A 1 -3.220 -5.208 0.605 1.00 34.34 C
+ATOM 10 N7 DG A 1 -4.207 -5.961 0.200 1.00 32.09 N
+ATOM 11 C5 DG A 1 -4.092 -5.968 -1.184 1.00 33.37 C
+ATOM 12 C6 DG A 1 -4.884 -6.616 -2.170 1.00 33.40 C
+ATOM 13 O6 DG A 1 -5.884 -7.335 -2.010 1.00 33.36 O
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+ATOM 26 C3' DG A 2 -1.887 1.486 -3.552 1.00 37.40 C
+ATOM 27 O3' DG A 2 -1.377 2.322 -4.599 1.00 38.40 O
+ATOM 28 C2' DG A 2 -3.312 1.038 -3.828 1.00 36.01 C
+ATOM 29 C1' DG A 2 -3.099 -0.161 -4.738 1.00 35.12 C
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+ATOM 31 C8 DG A 2 -4.760 -1.750 -5.792 1.00 32.68 C
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+ATOM 33 C5 DG A 2 -5.585 -2.720 -4.082 1.00 32.76 C
+ATOM 34 C6 DG A 2 -6.310 -3.536 -3.169 1.00 33.81 C
+ATOM 35 O6 DG A 2 -7.147 -4.402 -3.421 1.00 32.68 O
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+`,
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+ATOM 4 C3' DG A 1 -0.252 -2.301 0.574 1.00 55.57 C
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+ATOM 6 C2' DG A 1 -1.434 -2.518 -0.354 1.00 53.40 C
+ATOM 7 C1' DG A 1 -0.951 -3.675 -1.213 1.00 52.89 C
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+ATOM 9 C8 DG A 1 -2.116 -4.916 -3.088 1.00 50.60 C
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+ATOM 11 C5 DG A 1 -3.751 -5.818 -2.062 1.00 50.17 C
+ATOM 12 C6 DG A 1 -4.914 -6.542 -1.678 1.00 50.09 C
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+ATOM 21 OP2 DG A 2 -0.241 0.512 1.140 1.00 57.14 O
+ATOM 22 O5' DG A 2 -0.238 0.419 -1.362 1.00 55.60 O
+ATOM 23 C5' DG A 2 0.288 0.054 -2.637 1.00 54.95 C
+ATOM 24 C4' DG A 2 -0.795 0.100 -3.691 1.00 56.73 C
+ATOM 25 O4' DG A 2 -1.755 -0.976 -3.483 1.00 55.78 O
+ATOM 26 C3' DG A 2 -1.613 1.401 -3.749 1.00 56.77 C
+ATOM 27 O3' DG A 2 -1.748 1.838 -5.114 1.00 58.87 O
+ATOM 28 C2' DG A 2 -2.962 0.997 -3.172 1.00 54.87 C
+ATOM 29 C1' DG A 2 -3.062 -0.445 -3.632 1.00 54.94 C
+ATOM 30 N9 DG A 2 -4.013 -1.282 -2.900 1.00 52.63 N
+ATOM 31 C8 DG A 2 -4.437 -1.129 -1.598 1.00 51.99 C
+ATOM 32 N7 DG A 2 -5.378 -1.973 -1.262 1.00 49.99 N
+ATOM 33 C5 DG A 2 -5.573 -2.745 -2.400 1.00 50.31 C
+ATOM 34 C6 DG A 2 -6.487 -3.812 -2.651 1.00 49.15 C
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+ATOM 36 N1 DG A 2 -6.339 -4.319 -3.941 1.00 48.50 N
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+`,
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+ATOM 3 O4' U A 1 -1.106 -4.128 1.128 1.00 40.24 O
+ATOM 4 C3' U A 1 0.020 -2.937 -0.545 1.00 38.75 C
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+ATOM 6 C2' U A 1 -0.136 -4.372 -1.032 1.00 38.85 C
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+ATOM 8 C1' U A 1 -1.174 -4.917 -0.050 1.00 39.16 C
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+ATOM 15 C5 U A 1 -4.611 -3.700 -0.816 1.00 39.80 C
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+ATOM 21 C5' C A 2 0.395 0.674 -3.075 1.00 39.03 C
+ATOM 22 C4' C A 2 -1.009 1.134 -3.392 1.00 39.36 C
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+ATOM 25 O3' C A 2 -2.864 2.343 -2.459 1.00 38.86 O
+ATOM 26 C2' C A 2 -2.640 -0.026 -2.119 1.00 40.04 C
+ATOM 27 O2' C A 2 -3.877 0.055 -1.442 1.00 40.98 O
+ATOM 28 C1' C A 2 -2.838 -0.309 -3.610 1.00 40.17 C
+ATOM 29 N1 C A 2 -3.049 -1.725 -3.972 1.00 38.55 N
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+ATOM 31 O2 C A 2 -5.288 -1.337 -4.215 1.00 39.35 O
+ATOM 32 N3 C A 2 -4.552 -3.448 -4.631 1.00 38.76 N
+ATOM 33 C4 C A 2 -3.523 -4.295 -4.679 1.00 38.28 C
+ATOM 34 N4 C A 2 -3.772 -5.554 -5.042 1.00 37.80 N
+ATOM 35 C5 C A 2 -2.194 -3.889 -4.360 1.00 37.45 C
+ATOM 36 C6 C A 2 -2.003 -2.609 -4.017 1.00 39.12 C
+`,
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+ATOM 2 C4' A A 1 -0.845 -3.222 -1.176 1.00 41.26 C
+ATOM 3 O4' A A 1 -1.746 -4.194 -0.587 1.00 41.46 O
+ATOM 4 C3' A A 1 0.094 -2.779 -0.071 1.00 41.01 C
+ATOM 5 O3' A A 1 -0.376 -1.569 0.481 1.00 41.92 O
+ATOM 6 C2' A A 1 -0.043 -3.875 0.969 1.00 40.73 C
+ATOM 7 O2' A A 1 0.185 -3.458 2.300 1.00 40.94 O
+ATOM 8 C1' A A 1 -1.483 -4.310 0.785 1.00 41.40 C
+ATOM 9 N9 A A 1 -1.644 -5.687 1.216 1.00 40.97 N
+ATOM 10 C8 A A 1 -0.859 -6.738 0.823 1.00 39.98 C
+ATOM 11 N7 A A 1 -1.156 -7.861 1.423 1.00 39.78 N
+ATOM 12 C5 A A 1 -2.175 -7.513 2.305 1.00 40.69 C
+ATOM 13 C6 A A 1 -2.919 -8.260 3.241 1.00 41.00 C
+ATOM 14 N6 A A 1 -2.743 -9.558 3.471 1.00 40.41 N
+ATOM 15 N1 A A 1 -3.872 -7.599 3.947 1.00 41.99 N
+ATOM 16 C2 A A 1 -4.046 -6.278 3.738 1.00 42.62 C
+ATOM 17 N3 A A 1 -3.402 -5.471 2.896 1.00 42.41 N
+ATOM 18 C4 A A 1 -2.478 -6.159 2.197 1.00 41.43 C
+ATOM 19 P C A 2 0.279 -0.201 -0.015 1.00 40.71 P
+ATOM 20 OP1 C A 2 1.732 -0.440 -0.221 1.00 39.69 O
+ATOM 21 OP2 C A 2 -0.222 0.826 0.930 1.00 41.63 O
+ATOM 22 O5' C A 2 -0.451 0.094 -1.410 1.00 41.09 O
+ATOM 23 C5' C A 2 0.267 0.589 -2.528 1.00 40.75 C
+ATOM 24 C4' C A 2 -0.648 0.794 -3.709 1.00 41.28 C
+ATOM 25 O4' C A 2 -1.137 -0.487 -4.174 1.00 40.93 O
+ATOM 26 C3' C A 2 -1.892 1.607 -3.437 1.00 42.48 C
+ATOM 27 O3' C A 2 -1.615 2.993 -3.564 1.00 42.96 O
+ATOM 28 C2' C A 2 -2.889 1.075 -4.468 1.00 42.75 C
+ATOM 29 O2' C A 2 -2.681 1.724 -5.712 1.00 42.81 O
+ATOM 30 C1' C A 2 -2.455 -0.383 -4.632 1.00 41.77 C
+ATOM 31 N1 C A 2 -3.209 -1.362 -3.839 1.00 41.90 N
+ATOM 32 C2 C A 2 -3.164 -2.695 -4.305 1.00 41.23 C
+ATOM 33 O2 C A 2 -2.586 -2.986 -5.362 1.00 40.63 O
+ATOM 34 N3 C A 2 -3.777 -3.665 -3.590 1.00 41.27 N
+ATOM 35 C4 C A 2 -4.409 -3.338 -2.451 1.00 41.94 C
+ATOM 36 N4 C A 2 -5.005 -4.322 -1.777 1.00 41.98 N
+ATOM 37 C5 C A 2 -4.439 -2.009 -1.952 1.00 42.61 C
+ATOM 38 C6 C A 2 -3.815 -1.059 -2.659 1.00 42.55 C
+`,
+ZZ1S:
+`ATOM 1 C5' DC A 1 0.148 -3.897 -2.393 1.00 6.84 C
+ATOM 2 C4' DC A 1 -0.605 -3.110 -1.317 1.00 6.76 C
+ATOM 3 O4' DC A 1 -1.778 -3.828 -0.924 1.00 6.82 O
+ATOM 4 C3' DC A 1 0.185 -2.845 -0.034 1.00 7.23 C
+ATOM 5 O3' DC A 1 -0.178 -1.596 0.501 1.00 8.29 O
+ATOM 6 C2' DC A 1 -0.289 -3.895 0.923 1.00 7.01 C
+ATOM 7 C1' DC A 1 -1.750 -3.976 0.498 1.00 6.65 C
+ATOM 8 N1 DC A 1 -2.392 -5.270 0.809 1.00 6.27 N
+ATOM 9 C2 DC A 1 -2.992 -5.406 2.080 1.00 6.39 C
+ATOM 10 O2 DC A 1 -2.983 -4.464 2.857 1.00 6.84 O
+ATOM 11 N3 DC A 1 -3.587 -6.619 2.366 1.00 6.05 N
+ATOM 12 C4 DC A 1 -3.564 -7.603 1.486 1.00 6.43 C
+ATOM 13 N4 DC A 1 -4.160 -8.755 1.842 1.00 7.42 N
+ATOM 14 C5 DC A 1 -2.926 -7.466 0.201 1.00 7.12 C
+ATOM 15 C6 DC A 1 -2.368 -6.280 -0.066 1.00 6.73 C
+ATOM 16 P DG A 2 0.683 -0.250 0.246 1.00 9.27 P
+ATOM 17 OP1 DG A 2 2.156 -0.590 0.315 1.00 12.46 O
+ATOM 18 OP2 DG A 2 0.056 0.778 1.136 1.00 14.73 O
+ATOM 19 O5' DG A 2 0.389 0.120 -1.268 1.00 7.56 O
+ATOM 20 C5' DG A 2 -0.889 0.612 -1.666 1.00 6.32 C
+ATOM 21 C4' DG A 2 -0.982 0.715 -3.162 1.00 5.92 C
+ATOM 22 O4' DG A 2 -0.788 -0.594 -3.724 1.00 5.78 O
+ATOM 23 C3' DG A 2 -2.339 1.201 -3.698 1.00 5.01 C
+ATOM 24 O3' DG A 2 -2.250 2.627 -3.807 1.00 5.69 O
+ATOM 25 C2' DG A 2 -2.522 0.474 -5.004 1.00 6.12 C
+ATOM 26 C1' DG A 2 -1.673 -0.771 -4.913 1.00 5.64 C
+ATOM 27 N9 DG A 2 -2.321 -2.055 -4.706 1.00 5.85 N
+ATOM 28 C8 DG A 2 -2.227 -3.141 -5.561 1.00 7.25 C
+ATOM 29 N7 DG A 2 -2.889 -4.187 -5.172 1.00 7.01 N
+ATOM 30 C5 DG A 2 -3.464 -3.769 -3.948 1.00 5.60 C
+ATOM 31 C6 DG A 2 -4.302 -4.487 -3.045 1.00 5.58 C
+ATOM 32 O6 DG A 2 -4.691 -5.665 -3.178 1.00 6.97 O
+ATOM 33 N1 DG A 2 -4.666 -3.716 -1.951 1.00 5.26 N
+ATOM 34 C2 DG A 2 -4.275 -2.437 -1.743 1.00 4.93 C
+ATOM 35 N2 DG A 2 -4.732 -1.865 -0.607 1.00 5.47 N
+ATOM 36 N3 DG A 2 -3.492 -1.734 -2.586 1.00 5.01 N
+ATOM 37 C4 DG A 2 -3.139 -2.477 -3.656 1.00 5.12 C
+`,
+ZZ2S:
+`ATOM 1 C5' DC A 1 0.081 -3.608 -2.478 1.00 13.43 C
+ATOM 2 C4' DC A 1 -0.672 -3.088 -1.263 1.00 11.81 C
+ATOM 3 O4' DC A 1 -1.749 -3.949 -0.886 1.00 10.18 O
+ATOM 4 C3' DC A 1 0.177 -2.878 -0.051 1.00 11.02 C
+ATOM 5 O3' DC A 1 -0.321 -1.702 0.534 1.00 12.08 O
+ATOM 6 C2' DC A 1 -0.188 -4.075 0.811 1.00 10.99 C
+ATOM 7 C1' DC A 1 -1.654 -4.285 0.516 1.00 11.09 C
+ATOM 8 N1 DC A 1 -2.137 -5.665 0.774 1.00 7.55 N
+ATOM 9 C2 DC A 1 -2.705 -5.957 2.010 1.00 6.30 C
+ATOM 10 O2 DC A 1 -2.820 -5.165 2.932 1.00 7.29 O
+ATOM 11 N3 DC A 1 -3.179 -7.204 2.217 1.00 7.19 N
+ATOM 12 C4 DC A 1 -3.102 -8.145 1.266 1.00 4.28 C
+ATOM 13 N4 DC A 1 -3.602 -9.357 1.547 1.00 6.30 N
+ATOM 14 C5 DC A 1 -2.507 -7.865 -0.010 1.00 4.61 C
+ATOM 15 C6 DC A 1 -2.031 -6.620 -0.204 1.00 3.96 C
+ATOM 16 P DG A 2 0.427 -0.273 0.368 1.00 11.66 P
+ATOM 17 OP1 DG A 2 1.859 -0.496 0.554 1.00 12.48 O
+ATOM 18 OP2 DG A 2 -0.372 0.628 1.223 1.00 12.55 O
+ATOM 19 O5' DG A 2 0.216 0.125 -1.170 1.00 11.03 O
+ATOM 20 C5' DG A 2 -1.026 0.670 -1.599 1.00 7.72 C
+ATOM 21 C4' DG A 2 -0.887 0.864 -3.113 1.00 8.19 C
+ATOM 22 O4' DG A 2 -0.889 -0.381 -3.823 1.00 6.38 O
+ATOM 23 C3' DG A 2 -2.066 1.657 -3.669 1.00 7.89 C
+ATOM 24 O3' DG A 2 -1.575 2.500 -4.734 1.00 9.52 O
+ATOM 25 C2' DG A 2 -3.002 0.585 -4.253 1.00 7.56 C
+ATOM 26 C1' DG A 2 -2.048 -0.518 -4.656 1.00 6.94 C
+ATOM 27 N9 DG A 2 -2.565 -1.879 -4.487 1.00 7.44 N
+ATOM 28 C8 DG A 2 -2.360 -2.909 -5.373 1.00 7.27 C
+ATOM 29 N7 DG A 2 -2.870 -4.027 -4.998 1.00 7.63 N
+ATOM 30 C5 DG A 2 -3.446 -3.744 -3.742 1.00 8.84 C
+ATOM 31 C6 DG A 2 -4.087 -4.616 -2.836 1.00 8.30 C
+ATOM 32 O6 DG A 2 -4.229 -5.812 -2.979 1.00 7.96 O
+ATOM 33 N1 DG A 2 -4.520 -3.975 -1.667 1.00 8.78 N
+ATOM 34 C2 DG A 2 -4.310 -2.635 -1.383 1.00 8.22 C
+ATOM 35 N2 DG A 2 -4.724 -2.165 -0.197 1.00 5.43 N
+ATOM 36 N3 DG A 2 -3.699 -1.819 -2.256 1.00 8.07 N
+ATOM 37 C4 DG A 2 -3.279 -2.432 -3.406 1.00 7.63 C
+`,
+ZZS1:
+`ATOM 1 C5' DG A 1 -0.848 -2.629 2.035 1.00 5.87 C
+ATOM 2 C4' DG A 1 -0.013 -3.461 1.050 1.00 5.61 C
+ATOM 3 O4' DG A 1 -0.486 -4.814 1.039 1.00 6.39 O
+ATOM 4 C3' DG A 1 -0.073 -2.933 -0.379 1.00 6.20 C
+ATOM 5 O3' DG A 1 1.027 -2.077 -0.676 1.00 6.92 O
+ATOM 6 C2' DG A 1 -0.062 -4.209 -1.221 1.00 6.66 C
+ATOM 7 C1' DG A 1 -0.521 -5.324 -0.320 1.00 6.44 C
+ATOM 8 N9 DG A 1 -1.892 -5.815 -0.512 1.00 5.88 N
+ATOM 9 C8 DG A 1 -2.241 -7.132 -0.701 1.00 6.66 C
+ATOM 10 N7 DG A 1 -3.534 -7.317 -0.838 1.00 6.84 N
+ATOM 11 C5 DG A 1 -4.074 -6.035 -0.736 1.00 5.83 C
+ATOM 12 C6 DG A 1 -5.417 -5.625 -0.823 1.00 5.83 C
+ATOM 13 O6 DG A 1 -6.448 -6.310 -0.999 1.00 7.03 O
+ATOM 14 N1 DG A 1 -5.519 -4.214 -0.677 1.00 5.52 N
+ATOM 15 C2 DG A 1 -4.473 -3.360 -0.471 1.00 5.22 C
+ATOM 16 N2 DG A 1 -4.774 -2.077 -0.347 1.00 5.90 N
+ATOM 17 N3 DG A 1 -3.205 -3.765 -0.398 1.00 5.73 N
+ATOM 18 C4 DG A 1 -3.073 -5.096 -0.538 1.00 5.44 C
+ATOM 19 P DC A 2 0.864 -0.524 -0.960 1.00 7.01 P
+ATOM 20 OP1 DC A 2 2.241 0.003 -1.141 1.00 8.31 O
+ATOM 21 OP2 DC A 2 -0.027 0.074 0.084 1.00 10.11 O
+ATOM 22 O5' DC A 2 0.155 -0.574 -2.372 1.00 8.26 O
+ATOM 23 C5' DC A 2 0.385 0.407 -3.387 1.00 6.44 C
+ATOM 24 C4' DC A 2 -0.925 1.015 -3.832 1.00 6.19 C
+ATOM 25 O4' DC A 2 -1.709 0.004 -4.505 1.00 6.22 O
+ATOM 26 C3' DC A 2 -1.854 1.571 -2.735 1.00 6.74 C
+ATOM 27 O3' DC A 2 -2.479 2.784 -3.127 1.00 7.06 O
+ATOM 28 C2' DC A 2 -2.895 0.508 -2.553 1.00 7.26 C
+ATOM 29 C1' DC A 2 -3.018 -0.065 -3.936 1.00 6.21 C
+ATOM 30 N1 DC A 2 -3.422 -1.481 -3.983 1.00 5.66 N
+ATOM 31 C2 DC A 2 -4.790 -1.786 -3.996 1.00 5.46 C
+ATOM 32 O2 DC A 2 -5.612 -0.837 -3.991 1.00 6.74 O
+ATOM 33 N3 DC A 2 -5.203 -3.071 -4.034 1.00 5.33 N
+ATOM 34 C4 DC A 2 -4.277 -4.050 -4.031 1.00 5.54 C
+ATOM 35 N4 DC A 2 -4.727 -5.318 -4.082 1.00 6.29 N
+ATOM 36 C5 DC A 2 -2.872 -3.782 -4.000 1.00 6.28 C
+ATOM 37 C6 DC A 2 -2.511 -2.500 -3.971 1.00 5.99 C
+`,
+ZZS2:
+`ATOM 1 C5' DG A 1 -1.122 -2.312 1.847 1.00 5.26 C
+ATOM 2 C4' DG A 1 -0.239 -3.240 1.061 1.00 4.67 C
+ATOM 3 O4' DG A 1 -0.749 -4.546 1.104 1.00 5.75 O
+ATOM 4 C3' DG A 1 -0.116 -2.925 -0.423 1.00 4.31 C
+ATOM 5 O3' DG A 1 1.045 -2.050 -0.591 1.00 4.76 O
+ATOM 6 C2' DG A 1 0.139 -4.278 -1.125 1.00 4.83 C
+ATOM 7 C1' DG A 1 -0.570 -5.235 -0.198 1.00 4.31 C
+ATOM 8 N9 DG A 1 -1.806 -5.756 -0.553 1.00 3.92 N
+ATOM 9 C8 DG A 1 -2.090 -7.068 -0.634 1.00 5.63 C
+ATOM 10 N7 DG A 1 -3.388 -7.320 -0.915 1.00 6.26 N
+ATOM 11 C5 DG A 1 -3.974 -6.064 -0.982 1.00 3.62 C
+ATOM 12 C6 DG A 1 -5.290 -5.693 -1.130 1.00 3.88 C
+ATOM 13 O6 DG A 1 -6.295 -6.435 -1.286 1.00 5.93 O
+ATOM 14 N1 DG A 1 -5.536 -4.355 -1.036 1.00 3.98 N
+ATOM 15 C2 DG A 1 -4.550 -3.474 -0.766 1.00 6.12 C
+ATOM 16 N2 DG A 1 -4.874 -2.177 -0.627 1.00 5.87 N
+ATOM 17 N3 DG A 1 -3.296 -3.746 -0.603 1.00 4.22 N
+ATOM 18 C4 DG A 1 -3.073 -5.118 -0.669 1.00 3.36 C
+ATOM 19 P DC A 2 1.475 -1.399 -1.956 1.00 6.03 P
+ATOM 20 OP1 DC A 2 1.616 -2.327 -3.093 1.00 9.10 O
+ATOM 21 OP2 DC A 2 2.673 -0.546 -1.614 1.00 9.06 O
+ATOM 22 O5' DC A 2 0.248 -0.368 -2.244 1.00 4.54 O
+ATOM 23 C5' DC A 2 0.426 0.555 -3.319 1.00 4.36 C
+ATOM 24 C4' DC A 2 -1.030 1.120 -3.673 1.00 4.59 C
+ATOM 25 O4' DC A 2 -1.691 0.106 -4.384 1.00 4.74 O
+ATOM 26 C3' DC A 2 -1.935 1.426 -2.464 1.00 4.78 C
+ATOM 27 O3' DC A 2 -2.698 2.611 -2.778 1.00 6.46 O
+ATOM 28 C2' DC A 2 -2.848 0.265 -2.278 1.00 3.96 C
+ATOM 29 C1' DC A 2 -2.980 -0.079 -3.814 1.00 5.68 C
+ATOM 30 N1 DC A 2 -3.269 -1.620 -3.953 1.00 4.51 N
+ATOM 31 C2 DC A 2 -4.590 -1.966 -4.127 1.00 3.36 C
+ATOM 32 O2 DC A 2 -5.519 -1.151 -4.157 1.00 5.57 O
+ATOM 33 N3 DC A 2 -4.869 -3.311 -4.251 1.00 3.73 N
+ATOM 34 C4 DC A 2 -3.886 -4.223 -4.218 1.00 4.01 C
+ATOM 35 N4 DC A 2 -4.198 -5.546 -4.308 1.00 4.19 N
+ATOM 36 C5 DC A 2 -2.532 -3.865 -4.018 1.00 3.43 C
+ATOM 37 C6 DC A 2 -2.268 -2.574 -3.973 1.00 4.95 C
+`,
+};
diff --git a/src/apps/rednatco/reference-conformers.ts b/src/apps/rednatco/reference-conformers.ts
new file mode 100644
index 000000000..043b143e2
--- /dev/null
+++ b/src/apps/rednatco/reference-conformers.ts
@@ -0,0 +1,190 @@
+export type Ring = 'purine'|'pyrimidine';
+
+/* eslint-disable array-bracket-spacing, no-multi-spaces */
+export const ReferenceCompounds: Record<string, [string, string]> = {
+ AA00: [ 'A', 'G'],
+ AA01: ['DC', 'DG'],
+ AA02: ['DA', 'DA'],
+ AA03: [ 'U', 'C'],
+ AA04: [ 'A', 'G'],
+ AA05: [ 'A', 'G'],
+ AA06: [ 'U', 'G'],
+ AA07: [ 'U', 'A'],
+ AA08: [ 'G', 'C'],
+ AA09: [ 'A', 'A'],
+ AA10: [ 'A', 'G'],
+ AA11: [ 'A', 'A'],
+ AA12: [ 'U', 'G'],
+ AA13: [ 'G', 'U'],
+ AB01: ['DC', 'DG'],
+ AB02: ['DG', 'DG'],
+ AB03: ['DC', 'DA'],
+ AB04: ['DT', 'DA'],
+ AB05: [ 'G', 'U'],
+ BA01: ['DA', 'DT'],
+ BA05: ['DA', 'DC'],
+ BA09: ['DG', 'DG'],
+ BA08: ['DC', 'DG'],
+ BA10: ['DA', 'DG'],
+ BA13: ['DG', 'DA'],
+ BA16: [ 'U', 'U'],
+ BA17: ['DC', 'DT'],
+ BB00: ['DG', 'DA'],
+ BB01: ['DA', 'DA'],
+ BB17: ['DC', 'DC'],
+ BB02: ['DA', 'DC'],
+ BB03: ['DA', 'DG'],
+ BB11: ['DT', 'DT'],
+ BB16: ['DC', 'DG'],
+ BB04: ['DC', 'DG'],
+ BB05: ['DA', 'DC'],
+ BB07: ['DC', 'DG'],
+ BB08: ['DC', 'DG'],
+ BB10: ['DG', 'DG'],
+ BB12: ['DG', 'DA'],
+ BB13: ['DA', 'DC'],
+ BB14: ['DC', 'DA'],
+ BB15: ['DG', 'DC'],
+ BB20: ['DT', 'DT'],
+ IC01: [ 'C', 'C'],
+ IC02: [ 'U', 'U'],
+ IC03: [ 'G', 'A'],
+ IC04: ['DC', 'DG'],
+ IC05: ['DC', 'DG'],
+ IC06: ['DC', 'DG'],
+ IC07: [ 'G', 'U'],
+ OP01: [ 'C', 'A'],
+ OP02: [ 'G', 'U'],
+ OP03: [ 'G', 'A'],
+ OP04: [ 'G', 'A'],
+ OP05: [ 'G', 'U'],
+ OP06: [ 'U', 'U'],
+ OP07: [ 'G', 'C'],
+ OP08: [ 'G', 'A'],
+ OP09: [ 'U', 'U'],
+ OP10: [ 'G', 'A'],
+ OP11: [ 'A', 'G'],
+ OP12: [ 'U', 'C'],
+ OP13: [ 'U', 'G'],
+ OP14: [ 'A', 'G'],
+ OP15: [ 'G', 'U'],
+ OP16: [ 'G', 'G'],
+ OP17: [ 'G', 'U'],
+ OP18: [ 'U', 'U'],
+ OP19: ['DG', 'DT'],
+ OP20: ['DA', 'DC'],
+ OP21: [ 'U', 'U'],
+ OP22: ['DU', 'DU'],
+ OP23: [ 'A', 'G'],
+ OP24: [ 'A', 'A'],
+ OP25: [ 'A', 'U'],
+ OP26: [ 'U', 'C'],
+ OP27: [ 'C', 'G'],
+ OP28: [ 'G', 'U'],
+ OP29: [ 'A', 'U'],
+ OP30: [ 'C', 'G'],
+ OP31: [ 'A', 'G'],
+ OPS1: [ 'U', 'C'],
+ OP1S: ['DT', 'DG'],
+ AAS1: [ 'C', 'A'],
+ AB1S: ['DA', 'DG'],
+ AB2S: [ 'G', 'G'],
+ BB1S: ['DG', 'DG'],
+ BB2S: ['DG', 'DG'],
+ BBS1: ['DG', 'DG'],
+ ZZ01: [ 'U', 'C'],
+ ZZ02: [ 'A', 'C'],
+ ZZ1S: ['DC', 'DG'],
+ ZZ2S: ['DC', 'DG'],
+ ZZS1: ['DG', 'DC'],
+ ZZS2: ['DG', 'DC'],
+};
+export type ReferenceCompounds = typeof ReferenceCompounds;
+
+/* eslint-disable no-multi-spaces */
+export const CompoundRings: Record<string, Ring> = {
+ A: 'purine',
+ G: 'purine',
+ DA: 'purine',
+ DG: 'purine',
+ DDG: 'purine',
+ EDA: 'purine',
+ GNE: 'purine',
+ N2G: 'purine',
+ N5I: 'purine',
+ '2DA': 'purine',
+ '7DA': 'purine',
+ PRN: 'purine',
+ AD2: 'purine',
+ A3P: 'purine',
+ A5L: 'purine',
+ FMG: 'purine',
+ MA7: 'purine',
+ MG1: 'purine',
+ O2G: 'purine',
+ PPW: 'purine',
+ '1AP': 'purine',
+ '2FI': 'purine',
+ '2PR': 'purine',
+ '6MA': 'purine',
+ '6OG': 'purine',
+ '7GU': 'purine',
+ '8OG': 'purine',
+ TGP: 'purine',
+ GFL: 'purine',
+ A2M: 'purine',
+ OMG: 'purine',
+ GTP: 'purine',
+ GDP: 'purine',
+ '2MG': 'purine',
+ G7M: 'purine',
+ IGU: 'purine',
+ '6NW': 'purine',
+ T: 'pyrimidine',
+ C: 'pyrimidine',
+ U: 'pyrimidine',
+ DT: 'pyrimidine',
+ '2DT': 'pyrimidine',
+ '5NC': 'pyrimidine',
+ DC: 'pyrimidine',
+ DU: 'pyrimidine',
+ BRU: 'pyrimidine',
+ CBR: 'pyrimidine',
+ C38: 'pyrimidine',
+ DOC: 'pyrimidine',
+ ME6: 'pyrimidine',
+ OMC: 'pyrimidine',
+ UMP: 'pyrimidine',
+ Z: 'pyrimidine',
+ '5CM': 'pyrimidine',
+ '5IU': 'pyrimidine',
+ '5PY': 'pyrimidine',
+ PST: 'pyrimidine',
+ SPT: 'pyrimidine',
+ TPC: 'pyrimidine',
+ TSP: 'pyrimidine',
+ UPS: 'pyrimidine',
+ US1: 'pyrimidine',
+ '4PC': 'pyrimidine',
+ '5HU': 'pyrimidine',
+ '5FC': 'pyrimidine',
+ UFT: 'pyrimidine',
+ CFL: 'pyrimidine',
+ TAF: 'pyrimidine',
+ '5HC': 'pyrimidine',
+ CCC: 'pyrimidine',
+ IMC: 'pyrimidine',
+ '5BU': 'pyrimidine',
+ '6OO': 'pyrimidine',
+ F2T: 'pyrimidine',
+ XFC: 'pyrimidine'
+};
+export type CompoundRings = typeof CompoundRings;
+
+export const BackboneAtoms = {
+ first: ["C5'", "C4'", "O4'", "C3'", "O3'", "C1'"],
+ /* eslint-disable @typescript-eslint/quotes */
+ second: ["P", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C1'"],
+ purine: ['N9', 'C4'],
+ pyrimidine: ['N1', 'C2'],
+};
diff --git a/src/apps/rednatco/step.ts b/src/apps/rednatco/step.ts
new file mode 100644
index 000000000..c35bdc271
--- /dev/null
+++ b/src/apps/rednatco/step.ts
@@ -0,0 +1,71 @@
+import { OrderedSet } from '../../mol-data/int/ordered-set';
+import { StructureElement, StructureProperties } from '../../mol-model/structure';
+import { Location } from '../../mol-model/structure/structure/element/location';
+
+export namespace Step {
+ export type Description = {
+ model: number;
+ entryId: string;
+ chain: string;
+ resNo1: number;
+ comp1: string;
+ altId1?: string;
+ insCode1?: string;
+ resNo2: number;
+ comp2: string;
+ altId2?: string;
+ insCode2?: string;
+ };
+
+ function nameResidue(seqId: number, compId: string, altId?: string, insCode?: string) {
+ return `${compId}${altId ? `.${altId}` : ''}_${seqId}${insCode ? `.${insCode}` : '' }`;
+ }
+
+ export function describe(loci: StructureElement.Loci) {
+ const es = loci.elements[0]; // Ignore multiple selections
+
+ const loc = Location.create(loci.structure, es.unit);
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, 0)]; // We're assuming a non-empty set
+
+ const description: Description = {
+ model: es.unit.model.modelNum,
+ entryId: loci.structure.model.entryId.toLowerCase(),
+ chain: StructureProperties.chain.auth_asym_id(loc),
+ resNo1: StructureProperties.residue.auth_seq_id(loc),
+ comp1: StructureProperties.atom.auth_comp_id(loc),
+ altId1: StructureProperties.atom.label_alt_id(loc),
+ insCode1: StructureProperties.residue.pdbx_PDB_ins_code(loc),
+ resNo2: -1,
+ comp2: '',
+ altId2: void 0,
+ insCode2: void 0,
+ };
+
+ let found = false;
+ const len = OrderedSet.size(es.indices);
+ for (let idx = 1; idx < len; idx++) {
+ loc.element = es.unit.elements[OrderedSet.getAt(es.indices, idx)];
+ if (StructureProperties.residue.auth_seq_id(loc) !== description.resNo1) {
+ found = true;
+ break;
+ }
+ }
+
+ if (!found)
+ return void 0;
+
+ description.resNo2 = StructureProperties.residue.auth_seq_id(loc);
+ description.comp2 = StructureProperties.atom.auth_comp_id(loc);
+ description.altId2 = StructureProperties.atom.label_alt_id(loc);
+ description.insCode2 = StructureProperties.residue.pdbx_PDB_ins_code(loc);
+
+ return description;
+ }
+
+ export function name(description: Description, multipleModels: boolean) {
+ const res1 = nameResidue(description.resNo1, description.comp1, description.altId1, description.insCode1);
+ const res2 = nameResidue(description.resNo2, description.comp2, description.altId2, description.insCode2);
+
+ return `${description.entryId}${multipleModels ? `-m${description.model}` : ''}_${description.chain}_${res1}_${res2}`;
+ }
+}
diff --git a/src/apps/rednatco/superpose.ts b/src/apps/rednatco/superpose.ts
new file mode 100644
index 000000000..b0197f974
--- /dev/null
+++ b/src/apps/rednatco/superpose.ts
@@ -0,0 +1,30 @@
+import { SymmetryOperator } from '../../mol-math/geometry/symmetry-operator';
+import { MinimizeRmsd } from '../../mol-math/linear-algebra/3d/minimize-rmsd';
+import { ElementIndex } from '../../mol-model/structure';
+
+export namespace Superpose {
+ export type Input = {
+ elements: ElementIndex[],
+ conformation: SymmetryOperator.ArrayMapping<ElementIndex>,
+ }
+
+ export function positions(points: ElementIndex[], conformation: SymmetryOperator.ArrayMapping<ElementIndex>) {
+ const positions = MinimizeRmsd.Positions.empty(points.length);
+
+ const { x, y, z } = conformation;
+ points.forEach((v, idx) => {
+ positions.x[idx] = x(v);
+ positions.y[idx] = y(v);
+ positions.z[idx] = z(v);
+ });
+
+ return positions;
+ }
+
+ export function superposition(ofWhat: Input, onto: Input) {
+ const a = Superpose.positions(onto.elements, onto.conformation);
+ const b = Superpose.positions(ofWhat.elements, ofWhat.conformation);
+
+ return MinimizeRmsd.compute({ a, b });
+ }
+}
diff --git a/src/apps/rednatco/util.ts b/src/apps/rednatco/util.ts
new file mode 100644
index 000000000..ee4f8f7bb
--- /dev/null
+++ b/src/apps/rednatco/util.ts
@@ -0,0 +1,13 @@
+import { OrderedSet } from '../../mol-data/int/ordered-set';
+import { ElementIndex, StructureElement, Unit } from '../../mol-model/structure';
+
+export function lociElements(loci: StructureElement.Loci) {
+ const es = loci.elements[0]; // Ignore anything but the first chuck
+
+ if (!Unit.isAtomic(es.unit))
+ return [];
+
+ const elems = new Array<ElementIndex>();
+ OrderedSet.forEach(es.indices, uI => elems.push(es.unit.elements[uI]));
+ return elems;
+}
--
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