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operators.ts 12.90 KiB
/**
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
*
* Adapted from MolQL project
*/
import * as P from '../../../mol-util/monadic-parser';
import * as h from '../helper';
import { MolScriptBuilder } from '../../../mol-script/language/builder';
const B = MolScriptBuilder;
import { OperatorList } from '../types';
import { Expression } from '../../language/expression';
export const operators: OperatorList = [
{
'@desc': 'Selects atoms that are not included in s1.',
'@examples': [
'NOT resn ALA',
'not (resi 42 or chain A)',
'!resi 42 or chain A',
],
name: 'not',
type: h.prefix,
rule: P.MonadicParser.alt(
P.MonadicParser.regexp(/NOT/i).skip(P.MonadicParser.whitespace),
P.MonadicParser.string('!').skip(P.MonadicParser.optWhitespace)
),
map: (op, selection) => h.invertExpr(selection),
},
{
'@desc': 'Selects atoms included in both s1 and s2.',
'@examples': ['chain A AND name CA'],
name: 'and',
type: h.binaryLeft,
rule: h.infixOp(/AND|&/i),
map: (op, selection, by) =>
B.struct.modifier.intersectBy({ 0: selection, by }),
},
{
'@desc': 'Selects atoms included in either s1 or s2.',
'@examples': ['chain A OR chain B'],
name: 'or',
type: h.binaryLeft,
rule: h.infixOp(/OR|\|/i),
map: (op: string, s1: Expression, s2: Expression) => B.struct.combinator.merge([s1, s2]),
},
{
'@desc':
'Selects atoms in s1 whose identifiers name, resi, resn, chain and segi all match atoms in s2.',
'@examples': ['chain A IN chain B'],
name: 'in',
type: h.binaryLeft,
rule: h.infixOp(/IN/i),
map: (op: string, selection: Expression, source: Expression) => {
return B.struct.filter.withSameAtomProperties({
0: selection,
source,
property: B.core.type.compositeKey([
B.ammp('label_atom_id'),
B.ammp('label_seq_id'),
B.ammp('label_comp_id'),
B.ammp('auth_asym_id'),
B.ammp('label_asym_id'),
]),
});
},
}, {
'@desc':
'Selects atoms in s1 whose identifiers name and resi match atoms in s2.',
'@examples': ['chain A LIKE chain B'],
name: 'like',
type: h.binaryLeft,
rule: h.infixOp(/LIKE|l\./i),
map: (op: string, selection: Expression, source: Expression) => {
return B.struct.filter.withSameAtomProperties({
0: selection,
source,
property: B.core.type.compositeKey([
B.ammp('label_atom_id'),
B.ammp('label_seq_id'),
]),
});
},
},
{
'@desc':
'Selects all atoms whose van der Waals radii are separated from the van der Waals radii of s1 by a minimum of X Angstroms.',
'@examples': ['solvent GAP 2'],
name: 'gap',
type: h.postfix,
rule: h
.postfixOp(/GAP\s+([-+]?[0-9]*\.?[0-9]+)/i, 1)
.map((x: any) => parseFloat(x)),
map: (distance: number, target: Expression) => {
return B.struct.filter.within({
'0': B.struct.generator.all(),
target,
'atom-radius': B.acp('vdw'),
'max-radius': distance,
invert: true,
});
},
},
{
'@desc':
'Selects atoms with centers within X Angstroms of the center of any atom in s1.',
'@examples': ['resname LIG AROUND 1'],
name: 'around',
abbr: ['a.'],
type: h.postfix,
rule: h
.postfixOp(/(AROUND|a\.)\s+([-+]?[0-9]*\.?[0-9]+)/i, 2)
.map((x: any) => parseFloat(x)),
map: (radius: number, target: Expression) => {
return B.struct.modifier.exceptBy({
'0': B.struct.filter.within({
'0': B.struct.generator.all(),
target,
'max-radius': radius,
}),
by: target,
});
},
},
{
'@desc':
'Expands s1 by all atoms within X Angstroms of the center of any atom in s1.',
'@examples': ['chain A EXPAND 3'],
name: 'expand',
abbr: ['x.'],
type: h.postfix,
rule: h
.postfixOp(/(EXPAND|x\.)\s+([-+]?[0-9]*\.?[0-9]+)/i, 2)
.map((x: any) => parseFloat(x)),
map: (radius: number, selection: Expression) => {
return B.struct.modifier.includeSurroundings({ 0: selection, radius }); },
},
{
'@desc':
'Selects atoms in s1 that are within X Angstroms of any atom in s2.',
'@examples': ['chain A WITHIN 3 OF chain B'],
name: 'within',
abbr: ['w.'],
type: h.binaryLeft,
rule: h.ofOp('WITHIN', 'w.'),
map: (radius: number, selection: Expression, target: Expression) => {
return B.struct.filter.within({
0: selection,
target,
'max-radius': radius,
});
},
},
{
'@desc':
'Same as within, but excludes s2 from the selection (and thus is identical to s1 and s2 around X).',
'@examples': ['chain A NEAR_TO 3 OF chain B'],
name: 'near_to',
abbr: ['nto.'],
type: h.binaryLeft,
rule: h.ofOp('NEAR_TO', 'nto.'),
map: (radius: number, selection: Expression, target: Expression) => {
return B.struct.modifier.exceptBy({
'0': B.struct.filter.within({
'0': selection,
target,
'max-radius': radius,
}),
by: target,
});
},
},
{
'@desc': 'Selects atoms in s1 that are at least X Anstroms away from s2.',
'@examples': ['solvent BEYOND 2 OF chain A'],
name: 'beyond',
abbr: ['be.'],
type: h.binaryLeft,
rule: h.ofOp('BEYOND', 'be.'),
map: (radius: number, selection: Expression, target: Expression) => {
return B.struct.modifier.exceptBy({
'0': B.struct.filter.within({
'0': selection,
target,
'max-radius': radius,
invert: true,
}),
by: target,
});
},
},
{
'@desc': 'Expands selection to complete residues.',
'@examples': ['BYRESIDUE name N'],
name: 'byresidue',
abbr: ['byresi', 'byres', 'br.'],
type: h.prefix,
rule: h.prefixOp(/BYRESIDUE|byresi|byres|br\./i),
map: (op: string, selection: Expression) => {
return h.asAtoms(
B.struct.modifier.expandProperty({
'0': B.struct.modifier.union({ 0: selection }),
property: B.ammp('residueKey'),
})
); },
},
{
'@desc':
'Completely selects all alpha carbons in all residues covered by a selection.',
'@examples': ['BYCALPHA chain A'],
name: 'bycalpha',
abbr: ['bca.'],
type: h.prefix,
rule: h.prefixOp(/BYCALPHA|bca\./i),
map: (op: string, selection: Expression) => {
return B.struct.generator.queryInSelection({
'0': B.struct.modifier.expandProperty({
'0': B.struct.modifier.union({ 0: selection }),
property: B.ammp('residueKey'),
}),
query: B.struct.generator.atomGroups({
'atom-test': B.core.rel.eq([
B.atomName('CA'),
B.ammp('label_atom_id'),
]),
}),
});
},
},
{
'@desc': 'Expands selection to complete molecules.',
'@examples': ['BYMOLECULE resi 20-30'],
name: 'bymolecule',
isUnsupported: true, // structure-query.atom-property.topology.connected-component-key' is not implemented
abbr: ['bymol', 'bm.'],
type: h.prefix,
rule: h.prefixOp(/BYMOLECULE|bymol|bm\./i),
map: (op: string, selection: Expression) => {
return h.asAtoms(
B.struct.modifier.expandProperty({
'0': B.struct.modifier.union({ 0: selection }),
property: B.atp('connectedComponentKey'),
})
);
},
},
{
'@desc': 'Expands selection to complete fragments.',
'@examples': ['BYFRAGMENT resi 10'],
name: 'byfragment',
abbr: ['byfrag', 'bf.'],
isUnsupported: true,
type: h.prefix,
rule: h.prefixOp(/BYFRAGMENT|byfrag|bf\./i),
map: (op: string, selection: Expression) => [op, selection],
},
{
'@desc': 'Expands selection to complete segments.',
'@examples': ['BYSEGMENT resn CYS'],
name: 'bysegment',
abbr: ['bysegi', 'byseg', 'bs.'],
type: h.prefix,
rule: h.prefixOp(/BYSEGMENT|bysegi|byseg|bs\./i),
map: (op: string, selection: Expression) => {
return h.asAtoms(
B.struct.modifier.expandProperty({
'0': B.struct.modifier.union({ 0: selection }),
property: B.ammp('chainKey'),
})
);
},
},
{
'@desc': 'Expands selection to complete objects.', '@examples': ['BYOBJECT chain A'],
name: 'byobject',
abbr: ['byobj', 'bo.'],
isUnsupported: true,
type: h.prefix,
rule: h.prefixOp(/BYOBJECT|byobj|bo\./i),
map: (op: string, selection: Expression) => [op, selection],
},
{
'@desc': 'Expands selection to unit cell.',
'@examples': ['BYCELL chain A'],
name: 'bycell',
isUnsupported: true,
type: h.prefix,
rule: h.prefixOp(/BYCELL/i),
map: (op: string, selection: Expression) => [op, selection],
},
{
'@desc': 'All rings of size ≤ 7 which have at least one atom in s1.',
'@examples': ['BYRING resn HEM'],
name: 'byring',
// isUnsupported: true, // structure-query.atom-set.atom-count' is not implemented.
type: h.prefix,
rule: h.prefixOp(/BYRING/i),
map: (op: string, selection: Expression) => {
return h.asAtoms(
B.struct.modifier.intersectBy({
'0': B.struct.filter.pick({
'0': B.struct.generator.rings(),
test: B.core.logic.and([
B.core.rel.lte([B.struct.atomSet.atomCount(), 7]),
B.core.rel.gr([B.struct.atomSet.countQuery([selection]), 1]),
]),
}),
by: selection,
})
);
},
},
{
'@desc': 'Selects atoms directly bonded to s1, excludes s1.',
'@examples': ['NEIGHBOR resn CYS'],
name: 'neighbor',
type: h.prefix,
abbr: ['nbr.'],
rule: h.prefixOp(/NEIGHBOR|nbr\./i),
map: (op: string, selection: Expression) => {
return B.struct.modifier.exceptBy({
'0': h.asAtoms(
B.struct.modifier.includeConnected({
'0': B.struct.modifier.union({ 0: selection }),
'bond-test': true,
})
),
by: selection,
});
},
},
{
'@desc': 'Selects atoms directly bonded to s1, may include s1.',
'@examples': ['BOUND_TO name CA'],
name: 'bound_to',
abbr: ['bto.'],
type: h.prefix,
rule: h.prefixOp(/BOUND_TO|bto\./i),
map: (op: string, selection: Expression) => {
return h.asAtoms(
B.struct.modifier.includeConnected({
'0': B.struct.modifier.union({ 0: selection }),
}) );
},
},
{
'@desc': 'Extends s1 by X bonds connected to atoms in s1.',
'@examples': ['resname LIG EXTEND 3'],
name: 'extend',
abbr: ['xt.'],
type: h.postfix,
rule: h.postfixOp(/(EXTEND|xt\.)\s+([0-9]+)/i, 2).map((x: any) => parseInt(x)),
map: (count: number, selection: Expression) => {
return h.asAtoms(
B.struct.modifier.includeConnected({
'0': B.struct.modifier.union({ 0: selection }),
'bond-test': true,
'layer-count': count,
})
);
},
},
];