molstar
Version:
A comprehensive macromolecular library.
90 lines (89 loc) • 3.7 kB
JavaScript
/**
* Copyright (c) 2018-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { FormatPropertyProvider } from '../../../mol-model-formats/structure/common/property';
export { ModelCrossLinkRestraint };
var ModelCrossLinkRestraint;
(function (ModelCrossLinkRestraint) {
ModelCrossLinkRestraint.Descriptor = {
name: 'ihm_cross_link_restraint',
// TODO cifExport
};
ModelCrossLinkRestraint.Provider = FormatPropertyProvider.create(ModelCrossLinkRestraint.Descriptor);
function fromTable(table, model) {
var p1 = {
entity_id: table.entity_id_1,
asym_id: table.asym_id_1,
seq_id: table.seq_id_1,
atom_id: table.atom_id_1,
};
var p2 = {
entity_id: table.entity_id_2,
asym_id: table.asym_id_2,
seq_id: table.seq_id_2,
atom_id: table.atom_id_2,
};
function _add(map, element, row) {
var indices = map.get(element);
if (indices)
indices.push(row);
else
map.set(element, [row]);
}
function add(row, ps) {
var entityId = ps.entity_id.value(row);
var asymId = ps.asym_id.value(row);
var seqId = ps.seq_id.value(row);
if (table.model_granularity.value(row) === 'by-atom') {
var atomicElement = model.atomicHierarchy.index.findAtom({
auth_seq_id: seqId,
label_asym_id: asymId,
label_atom_id: ps.atom_id.value(row),
label_entity_id: entityId,
});
if (atomicElement >= 0)
_add(atomicElementMap, atomicElement, row);
}
else if (model.coarseHierarchy.isDefined) {
var sphereElement = model.coarseHierarchy.spheres.findSequenceKey(entityId, asymId, seqId);
if (sphereElement >= 0) {
_add(sphereElementMap, sphereElement, row);
}
else {
var gaussianElement = model.coarseHierarchy.gaussians.findSequenceKey(entityId, asymId, seqId);
if (gaussianElement >= 0)
_add(gaussianElementMap, gaussianElement, row);
}
}
}
function getMapByKind(kind) {
switch (kind) {
case 0 /* Unit.Kind.Atomic */: return atomicElementMap;
case 1 /* Unit.Kind.Spheres */: return sphereElementMap;
case 2 /* Unit.Kind.Gaussians */: return gaussianElementMap;
}
}
/** map from atomic element to cross link indices */
var atomicElementMap = new Map();
/** map from sphere element to cross link indices */
var sphereElementMap = new Map();
/** map from gaussian element to cross link indices */
var gaussianElementMap = new Map();
var emptyIndexArray = [];
for (var i = 0; i < table._rowCount; ++i) {
add(i, p1);
add(i, p2);
}
return {
getIndicesByElement: function (element, kind) {
var map = getMapByKind(kind);
var idx = map.get(element);
return idx !== undefined ? idx : emptyIndexArray;
},
data: table
};
}
ModelCrossLinkRestraint.fromTable = fromTable;
})(ModelCrossLinkRestraint || (ModelCrossLinkRestraint = {}));