diff --git a/src/mol-script/transpilers/_spec/jmol.spec.ts b/src/mol-script/transpilers/_spec/jmol.spec.ts
index c17470b9d954d5dc6e27538100648f9666f4883a..62a134bb70cd06f38c25ea08847f9d46864fb077 100644
--- a/src/mol-script/transpilers/_spec/jmol.spec.ts
+++ b/src/mol-script/transpilers/_spec/jmol.spec.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Koya Sakuma <koya.sakuma.work@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -62,14 +62,17 @@ const general = {
'100, 42, ALA',
// residue numbering
'(1-10,15,21-30)',
+ // within
+ 'within(5,[HEM])',
// within with parentheses
- // '( within(5,[HEM]) ) and backbone',
+ '(within(5,[HEM])) and backbone',
+ '( within(5,[HEM]) ) and backbone',
// trimming
'[ALA] and [VAL] ',
' [ALA] and [VAL] ',
' [ALA] and [VAL]',
// within with whitespaces
- // 'within ( 5 , [HEM] ) ',
+ 'within ( 5 , [HEM] ) ',
// un-braketed residue name
'LEU and ILE',
// un-parenthesized residue index range
@@ -77,7 +80,7 @@ const general = {
// un-parenthesized residue index
'20',
// within in the head or the middle of sentence
- // 'within ( 5 , [HEM] ) and backbone',
+ 'within ( 5 , [HEM] ) and backbone',
],
unsupported: [
// values outside of comparisons
diff --git a/src/mol-script/transpilers/jmol/keywords.ts b/src/mol-script/transpilers/jmol/keywords.ts
index 0654de13ac04d271fc4815e6f13eab3de7eae15a..b1ea906094da754a11d5913a1814d3e7c7fbecb0 100644
--- a/src/mol-script/transpilers/jmol/keywords.ts
+++ b/src/mol-script/transpilers/jmol/keywords.ts
@@ -1,8 +1,11 @@
/**
- * 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 Koya Sakuma <koya.sakuma.work@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ *
* Adapted from MolQL project
-**/
+ */
import { MolScriptBuilder } from '../../../mol-script/language/builder';
@@ -10,12 +13,34 @@ const B = MolScriptBuilder;
import * as h from '../helper';
import { KeywordDict } from '../types';
+const ResDict = {
+ acidic: ['ASP', 'GLU'],
+ aliphatic: ['ALA', 'GLY', 'ILE', 'LEU', 'VAL'],
+ amino: ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'ASX', 'GLX', 'UNK'],
+ aromatic: ['HIS', 'PHE', 'TRP', 'TYR'],
+ basic: ['ARG', 'HIS', 'LYS'],
+ buried: ['ALA', 'CYS', 'ILE', 'LEU', 'MET', 'PHE', 'TRP', 'VAL'],
+ cg: ['CYT', 'C', 'GUA', 'G'],
+ cyclic: ['HIS', 'PHE', 'PRO', 'TRP', 'TYR'],
+ hydrophobic: ['ALA', 'GLY', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'TYR', 'VAL'],
+ large: ['ARG', 'GLU', 'GLN', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'TRP', 'TYR'],
+ medium: ['ASN', 'ASP', 'CYS', 'PRO', 'THR', 'VAL'],
+ small: ['ALA', 'GLY', 'SER'],
+
+ nucleic: ['G', 'C', 'A', 'T', 'U', 'I', 'DG', 'DC', 'DA', 'DT', 'DU', 'DI', '+G', '+C', '+A', '+T', '+U', '+I']
+};
+
+const Backbone = {
+ nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*',
+ "C2'", "C1'", "O4'", "O2'"],
+ protein: ['C', 'N', 'CA']
+};
function nucleicExpr() {
return B.struct.combinator.merge([
B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
- B.set(...['G', 'C', 'A', 'T', 'U', 'I', 'DG', 'DC', 'DA', 'DT', 'DU', 'DI', '+G', '+C', '+A', '+T', '+U', '+I']),
+ B.set(...ResDict.nucleic),
B.ammp('label_comp_id')
])
}),
@@ -46,20 +71,49 @@ function nucleicExpr() {
]);
}
-const ResDict = {
- acidic: ['ASP', 'GLU'],
- aliphatic: ['ALA', 'GLY', 'ILE', 'LEU', 'VAL'],
- amino: ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'ASX', 'GLX', 'UNK'],
- aromatic: ['HIS', 'PHE', 'TRP', 'TYR'],
- basic: ['ARG', 'HIS', 'LYS'],
- buried: ['ALA', 'CYS', 'ILE', 'LEU', 'MET', 'PHE', 'TRP', 'VAL'],
- cg: ['CYT', 'C', 'GUA', 'G'],
- cyclic: ['HIS', 'PHE', 'PRO', 'TRP', 'TYR'],
- hydrophobic: ['ALA', 'GLY', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'TYR', 'VAL'],
- large: ['ARG', 'GLU', 'GLN', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'TRP', 'TYR'],
- medium: ['ASN', 'ASP', 'CYS', 'PRO', 'THR', 'VAL'],
- small: ['ALA', 'GLY', 'SER'],
-};
+// TODO: improve, see keywords.protein['@desc'] below
+function proteinExpr() {
+ return B.struct.generator.atomGroups({
+ 'residue-test': B.core.set.has([
+ B.set(...ResDict.amino),
+ B.ammp('label_comp_id')
+ ])
+ });
+}
+
+// TODO: improve, see keywords.backbone['@desc'] below
+function backboneExpr() {
+ return B.struct.combinator.merge([
+ B.struct.modifier.intersectBy({
+ 0: B.struct.generator.atomGroups({
+ 'residue-test': B.core.set.has([
+ B.core.type.set(ResDict.amino),
+ B.ammp('label_comp_id')
+ ])
+ }),
+ by: B.struct.generator.atomGroups({
+ 'atom-test': B.core.set.has([
+ B.core.type.set(Backbone.protein),
+ B.ammp('label_atom_id')
+ ])
+ })
+ }),
+ B.struct.modifier.intersectBy({
+ 0: B.struct.generator.atomGroups({
+ 'residue-test': B.core.set.has([
+ B.core.type.set(ResDict.nucleic),
+ B.ammp('label_comp_id')
+ ])
+ }),
+ by: B.struct.generator.atomGroups({
+ 'atom-test': B.core.set.has([
+ B.core.type.set(Backbone.nucleic),
+ B.ammp('label_atom_id')
+ ])
+ })
+ }),
+ ]);
+}
export const keywords: KeywordDict = {
// general terms
@@ -336,7 +390,8 @@ export const keywords: KeywordDict = {
})
},
protein: {
- '@desc': 'defined as a group that (a) has one of the following group names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, or UNK; or (b) contains PDB atom designations [C, O, CA, and N] bonded correctly; or (c) does not contain "O" but contains [C, CA, and N] bonded correctly; or (d) has only one atom, which has name CA and does not have the group name CA (indicating a calcium atom).'
+ '@desc': 'defined as a group that (a) has one of the following group names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, or UNK; or (b) contains PDB atom designations [C, O, CA, and N] bonded correctly; or (c) does not contain "O" but contains [C, CA, and N] bonded correctly; or (d) has only one atom, which has name CA and does not have the group name CA (indicating a calcium atom).',
+ map: () => proteinExpr()
},
acidic: {
'@desc': 'ASP GLU',
@@ -496,7 +551,8 @@ export const keywords: KeywordDict = {
},
backbone: {
'@desc': '(*.C, *.CA, *.N, and all nucleic other than the bases themselves)',
- abbr: ['mainchain']
+ abbr: ['mainchain'],
+ map: () => backboneExpr()
},
sidechain: {
'@desc': '((protein or nucleic) and not backbone)'
diff --git a/src/mol-script/transpilers/jmol/parser.ts b/src/mol-script/transpilers/jmol/parser.ts
index 6553a0c826bf2a60df616608cbb3cce71714c6d5..bc814ed933191eef7370e3f99b5452596c03ee09 100644
--- a/src/mol-script/transpilers/jmol/parser.ts
+++ b/src/mol-script/transpilers/jmol/parser.ts
@@ -1,5 +1,5 @@
/**
- * 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 Koya Sakuma < koya.sakuma.work@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -18,6 +18,7 @@ import { keywords } from './keywords';
import { AtomGroupArgs } from '../types';
import { Transpiler } from '../transpiler';
import { OperatorList } from '../types';
+import { Expression } from '../../language/expression';
// <, <=, =, >=, >, !=, and LIKE
const valueOperators: OperatorList = [
@@ -116,7 +117,7 @@ const lang = P.MonadicParser.createLanguage({
r.Parens,
r.Operator,
r.Expression
- ).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
+ ).wrap(P.MonadicParser.regexp(/\(\s*/), P.MonadicParser.regexp(/\s*\)/));
},
Expression: function (r: any) {
@@ -129,11 +130,12 @@ const lang = P.MonadicParser.createLanguage({
B.core.rel.lte([B.ammp('auth_seq_id'), x[1]])
])
})),
- r.Resno.lookahead(P.MonadicParser.regexp(/\s*(?!(LIKE|>=|<=|!=|[\[:^%/.=><]))/i)).map((x: any) => B.struct.generator.atomGroups({
+ r.Resno.lookahead(P.MonadicParser.regexp(/\s*(?!(LIKE|>=|<=|!=|[\[:^%/.=><]))/i)).map((x: number) => B.struct.generator.atomGroups({
'residue-test': B.core.rel.eq([B.ammp('auth_seq_id'), x])
})),
r.AtomExpression.map(atomExpressionQuery),
+ r.Within.map((x: [number, Expression]) => B.struct.modifier.includeSurroundings({ 0: x[1], radius: x[0] })),
r.ValueQuery,
r.Element.map((x: string) => B.struct.generator.atomGroups({
@@ -186,6 +188,15 @@ const lang = P.MonadicParser.createLanguage({
r.Integer
).desc('resno-range');
},
+ Within: (r: any) => {
+ return P.MonadicParser.regexp(/within/i)
+ .skip(P.MonadicParser.regexp(/\s*\(\s*/))
+ .then(P.MonadicParser.seq(
+ r.Integer.skip(P.MonadicParser.regexp(/\s*,\s*/)),
+ r.Query
+ ))
+ .skip(P.MonadicParser.regexp(/\)/));
+ },
Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)).desc('keyword'),