diff --git a/src/mol-script/transpilers/pymol/keywords.ts b/src/mol-script/transpilers/pymol/keywords.ts index 04471609f55ad67b91dc5be3605061f854e057d7..1e3c95107e26a6dadfe340d0b97560b257907e3c 100644 --- a/src/mol-script/transpilers/pymol/keywords.ts +++ b/src/mol-script/transpilers/pymol/keywords.ts @@ -1,8 +1,10 @@ /** - * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info. + * 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 { MolScriptBuilder } from '../../../mol-script/language/builder'; @@ -34,7 +36,8 @@ function backboneExpr() { by: B.struct.generator.atomGroups({ 'atom-test': B.core.set.has([ B.core.type.set(Backbone.protein), - B.ammp('label_atom_id')]) + B.ammp('label_atom_id') + ]) }) }), B.struct.modifier.intersectBy({ @@ -47,14 +50,13 @@ function backboneExpr() { by: B.struct.generator.atomGroups({ 'atom-test': B.core.set.has([ B.core.type.set(Backbone.nucleic), - B.ammp('label_atom_id')]) + B.ammp('label_atom_id') + ]) }) }), ]); - } - export const keywords: KeywordDict = { all: { '@desc': 'All atoms currently loaded into PyMOL', @@ -104,7 +106,8 @@ export const keywords: KeywordDict = { '0': B.struct.generator.atomGroups({ 'residue-test': B.core.set.has([ B.core.type.set(ResDict.nucleic.concat(ResDict.protein)), - B.ammp('label_comp_id')]) + B.ammp('label_comp_id') + ]) }), by: backboneExpr() }); @@ -231,7 +234,7 @@ export const keywords: KeywordDict = { }), B.struct.generator.atomGroups({ 'atom-test': B.core.set.has([ - h.atomNameSet(['C4*', 'C4']), + h.atomNameSet(['C4*', 'C4\'']), B.ammp('label_atom_id') ]), 'residue-test': B.core.set.has([ @@ -245,12 +248,12 @@ export const keywords: KeywordDict = { '@desc': 'All metal atoms (new in PyMOL 1.6.1)' }, backbone: { - '@desc': 'the C, N, CA, and O atoms of a protein and the equivalent atoms in a nucleic acid.', + '@desc': 'Polymer backbone atoms (new in PyMOL 1.6.1)', abbr: ['bb.'], map: () => backboneExpr() }, - 'bFCLHMz55tjm16c9': { - '@desc': 'protein', + 'polymer.protein': { + '@desc': 'Protein (New in PyMOL 2.1)', abbr: ['polymer.protein'], map: () => B.struct.generator.atomGroups({ 'residue-test': B.core.set.has([ @@ -259,8 +262,8 @@ export const keywords: KeywordDict = { ]) }) }, - 'bFCLHMz55tjm16c0': { - '@desc': 'nucleic acid', + 'polymer.nucleic': { + '@desc': 'Nucleic Acid (New in PyMOL 2.1)', abbr: ['polymer.nucleic'], map: () => B.struct.generator.atomGroups({ 'residue-test': B.core.set.has([