diff --git a/src/mol-script/transpilers/_spec/jmol.spec.ts b/src/mol-script/transpilers/_spec/jmol.spec.ts
index 27fefd5422f6751217338d0c073221a905c15ca0..c17470b9d954d5dc6e27538100648f9666f4883a 100644
--- a/src/mol-script/transpilers/_spec/jmol.spec.ts
+++ b/src/mol-script/transpilers/_spec/jmol.spec.ts
@@ -2,10 +2,11 @@
* Copyright (c) 2020-2021 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 * as u from './utils';
import { transpiler } from '../jmol/parser';
import { keywords } from '../jmol/keywords';
@@ -48,6 +49,35 @@ const general = {
' atomName = CA ',
'atomName = CA ',
' atomName = CA',
+
+ // value comparison
+ 'resno > 10',
+ // atom expression
+ '[LEU]100:A.CA',
+ '[LEU]100:A',
+ '[LEU]100.CA',
+ '[LEU]:A.CA',
+ '[LEU].CA',
+ // comma as OR
+ '100, 42, ALA',
+ // residue numbering
+ '(1-10,15,21-30)',
+ // within with parentheses
+ // '( within(5,[HEM]) ) and backbone',
+ // trimming
+ '[ALA] and [VAL] ',
+ ' [ALA] and [VAL] ',
+ ' [ALA] and [VAL]',
+ // within with whitespaces
+ // 'within ( 5 , [HEM] ) ',
+ // un-braketed residue name
+ 'LEU and ILE',
+ // un-parenthesized residue index range
+ '100-120,220',
+ // un-parenthesized residue index
+ '20',
+ // within in the head or the middle of sentence
+ // 'within ( 5 , [HEM] ) and backbone',
],
unsupported: [
// values outside of comparisons
diff --git a/src/mol-script/transpilers/helper.ts b/src/mol-script/transpilers/helper.ts
index fee41349bfe4eb5a401466638395c9847ecba923..b649116dd1b5e170d69b151563e78015f4e08d96 100644
--- a/src/mol-script/transpilers/helper.ts
+++ b/src/mol-script/transpilers/helper.ts
@@ -129,11 +129,11 @@ export function combineOperators(opList: any[], rule: P.MonadicParser<any>) {
}
export function infixOp(re: RegExp, group: number = 0) {
- return P.MonadicParser.whitespace.then(P.MonadicParser.regexp(re, group).skip(P.MonadicParser.whitespace));
+ return P.MonadicParser.optWhitespace.then(P.MonadicParser.regexp(re, group).skip(P.MonadicParser.optWhitespace));
}
export function prefixOp(re: RegExp, group: number = 0) {
- return P.MonadicParser.regexp(re, group).skip(P.MonadicParser.whitespace);
+ return P.MonadicParser.regexp(re, group).skip(P.MonadicParser.optWhitespace);
}
export function prefixOpNoWhiteSpace(re: RegExp, group: number = 0) {
@@ -141,7 +141,7 @@ export function prefixOpNoWhiteSpace(re: RegExp, group: number = 0) {
}
export function postfixOp(re: RegExp, group: number = 0) {
- return P.MonadicParser.whitespace.then(P.MonadicParser.regexp(re, group));
+ return P.MonadicParser.optWhitespace.then(P.MonadicParser.regexp(re, group));
}
export function ofOp(name: string, short?: string) {
diff --git a/src/mol-script/transpilers/jmol/operators.ts b/src/mol-script/transpilers/jmol/operators.ts
index 95bdec710797017c5f37d164ddb52644d5ff7f8e..b6d25ecb90256c55fc18f9daf07b51dcf1ec9238 100644
--- a/src/mol-script/transpilers/jmol/operators.ts
+++ b/src/mol-script/transpilers/jmol/operators.ts
@@ -1,17 +1,18 @@
-/*
+/**
* Copyright (c) 2017-2021 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 * 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';
-
export const operators: OperatorList = [
{
'@desc': 'Selects atoms that are not included in s1.',
@@ -34,7 +35,7 @@ export const operators: OperatorList = [
'@examples': ['ASP or GLU'],
name: 'or',
type: h.binaryLeft,
- rule: h.infixOp(/OR|\|/i),
+ rule: h.infixOp(/OR|\||,/i),
map: (op, s1, s2) => B.struct.combinator.merge([s1, s2])
}
];
diff --git a/src/mol-script/transpilers/jmol/parser.ts b/src/mol-script/transpilers/jmol/parser.ts
index dee1bd66fed31d7b6d0d8d8dfa2217543966a8bf..6553a0c826bf2a60df616608cbb3cce71714c6d5 100644
--- a/src/mol-script/transpilers/jmol/parser.ts
+++ b/src/mol-script/transpilers/jmol/parser.ts
@@ -1,6 +1,9 @@
/**
* Copyright (c) 2017-2021 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
**/
@@ -83,15 +86,16 @@ const valueOperators: OperatorList = [
];
function atomExpressionQuery(x: any[]) {
- const [resno, inscode, chainname, atomname, altloc] = x[1];
+ const [resname, resno, inscode, chainname, atomname, altloc] = x[1];
const tests: AtomGroupArgs = {};
if (chainname) {
- // should be configurable, there is an option in Jmol to use auth or label
+ // TODO: should be configurable, there is an option in Jmol to use auth or label
tests['chain-test'] = B.core.rel.eq([B.ammp('auth_asym_id'), chainname]);
}
const resProps = [];
+ if (resname) resProps.push(B.core.rel.eq([B.ammp('label_comp_id'), resname]));
if (resno) resProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), resno]));
if (inscode) resProps.push(B.core.rel.eq([B.ammp('pdbx_PDB_ins_code'), inscode]));
if (resProps.length) tests['residue-test'] = h.andExpr(resProps);
@@ -119,7 +123,13 @@ const lang = P.MonadicParser.createLanguage({
return P.MonadicParser.alt(
r.Keywords,
- r.Resno.lookahead(P.MonadicParser.regexp(/\s*(?!(LIKE|>=|<=|!=|[:^%/.=><]))/i)).map((x: any) => B.struct.generator.atomGroups({
+ r.ResnoRange.map((x: [number, number]) => B.struct.generator.atomGroups({
+ 'residue-test': B.core.logic.and([
+ B.core.rel.gre([B.ammp('auth_seq_id'), x[0]]),
+ 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({
'residue-test': B.core.rel.eq([B.ammp('auth_seq_id'), x])
})),
r.AtomExpression.map(atomExpressionQuery),
@@ -143,6 +153,7 @@ const lang = P.MonadicParser.createLanguage({
return P.MonadicParser.seq(
P.MonadicParser.lookahead(r.AtomPrefix),
P.MonadicParser.seq(
+ r.BracketedResname.or(P.MonadicParser.of(null)),
r.Resno.or(P.MonadicParser.of(null)),
r.Inscode.or(P.MonadicParser.of(null)),
r.Chainname.or(P.MonadicParser.of(null)),
@@ -150,10 +161,10 @@ const lang = P.MonadicParser.createLanguage({
r.Altloc.or(P.MonadicParser.of(null)),
r.Model.or(P.MonadicParser.of(null))
)
- );
+ ).desc('expression');
},
- AtomPrefix: () => P.MonadicParser.regexp(/[0-9:^%/.]/).desc('atom-prefix'),
+ AtomPrefix: () => P.MonadicParser.regexp(/[\[0-9:^%/.]/).desc('atom-prefix'),
Chainname: () => P.MonadicParser.regexp(/:([A-Za-z]{1,3})/, 1).desc('chainname'),
Model: () => P.MonadicParser.regexp(/\/([0-9]+)/, 1).map(Number).desc('model'),
@@ -164,22 +175,19 @@ const lang = P.MonadicParser.createLanguage({
Altloc: () => P.MonadicParser.regexp(/%([a-zA-Z0-9])/, 1).desc('altloc'),
Inscode: () => P.MonadicParser.regexp(/\^([a-zA-Z0-9])/, 1).desc('inscode'),
+ BracketedResname: () => P.MonadicParser.regexp(/\[([a-zA-Z0-9]{1,4})\]/, 1).desc('bracketed-resname'),
+ ResnoRange: (r: any) => {
+ return P.MonadicParser.seq(
+ r.Integer.skip(P.MonadicParser.seq(
+ P.MonadicParser.optWhitespace,
+ P.MonadicParser.string('-'),
+ P.MonadicParser.optWhitespace
+ )),
+ r.Integer
+ ).desc('resno-range');
+ },
- // TODO: Support bracketed resname and resno range.
- // BracketedResname: function (r) {
- // return P.regex(/\.([a-zA-Z0-9]{1,4})/, 1)
- // .desc('bracketed-resname')
- // // [0SD]
- // },
-
- // ResnoRange: function (r) {
- // return P.regex(/\.([\s]){1,3}/, 1)
- // .desc('resno-range')
- // // 123-200
- // // -12--3
- // },
-
- Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)),
+ Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)).desc('keyword'),
Query: function (r: any) {
return P.MonadicParser.alt(
@@ -202,7 +210,7 @@ const lang = P.MonadicParser.createLanguage({
P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i')),
P.MonadicParser.regexp(/'((?:[^"\\]|\\.)*)'/, 1),
P.MonadicParser.regexp(/"((?:[^"\\]|\\.)*)"/, 1).map(x => B.core.type.regex([`^${x}$`, 'i']))
- );
+ ).desc('string');
},
Value: function (r: any) {