From 92a41b5c46d44b7321800d3933558ec6bb56922f Mon Sep 17 00:00:00 2001
From: yakomaxa <47655565+yakomaxa@users.noreply.github.com>
Date: Sun, 21 Aug 2022 16:48:41 +0900
Subject: [PATCH] Unparenthesized residue range enabled in RasMol, which should
be ported to Jmol
---
src/mol-script/transpilers/rasmol/parser.ts | 64 ++++++++++++++++++---
1 file changed, 57 insertions(+), 7 deletions(-)
diff --git a/src/mol-script/transpilers/rasmol/parser.ts b/src/mol-script/transpilers/rasmol/parser.ts
index ef685d673..c62790188 100644
--- a/src/mol-script/transpilers/rasmol/parser.ts
+++ b/src/mol-script/transpilers/rasmol/parser.ts
@@ -17,6 +17,41 @@ import { AtomGroupArgs } from '../types';
import { Transpiler } from '../transpiler';
+function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/g, '')); }
+function rangeMap(x: string) {
+ const [min, max] = x.split('-').map(x => parseInt(x));
+ return { min, max };
+}
+function listOrRangeMap(x: string) {
+ if (x.includes('-') && x.includes(',')) {
+ const pSplit = x.split(',').map(x => x.replace(/^["']|["']$/g, ''));
+ const res: number[] = [];
+ pSplit.forEach(x => {
+ if (x.includes('-')) {
+ const [min, max] = x.split('-').map(x=>parseInt(x));
+ for (let i = min; i <= max; i++) {
+ res.push(i);
+ }
+ } else {
+ res.push(parseInt(x));
+ }
+ });
+ return res;
+ } else if (x.includes('-') && !x.includes(',')) {
+ const res: number[] = [];
+ const [min, max] = x.split('-').map(x=>parseInt(x));
+ for (let i = min; i <= max; i++) {
+ res.push(i);
+ }
+ return res;
+ } else if (!x.includes('-') && x.includes(',')) {
+ return listMap(x).map(x => parseInt(x));
+ } else {
+ return [parseInt(x)];
+ }
+}
+
+
const propertiesDict = h.getPropertyRules(macroproperties);
const dot = P.MonadicParser.string('.');
@@ -53,7 +88,7 @@ function atomSelectionQuery2(x: any) {
}
function atomExpressionQuery(x: any[]) {
- const [resno, inscode, chainname, atomname, altloc] = x[1];
+ const [resnorange, resno, inscode, chainname, atomname, altloc] = x[1];
const tests: AtomGroupArgs = {};
if (chainname) {
@@ -61,8 +96,21 @@ function atomExpressionQuery(x: any[]) {
tests['chain-test'] = B.core.rel.eq([B.ammp('auth_asym_id'), chainname]);
}
- const resProps = [];
- if (resno) resProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), resno]));
+ const resnoRangeProps:any = [];
+ console.log(resnorange)
+ if (resnorange){
+ resnorange.forEach((x:number) =>{
+ resnoRangeProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), x]));
+ })
+ console.log(resnoRangeProps);
+ };
+ if (resnoRangeProps.length) tests['residue-test'] = h.orExpr(resnoRangeProps);
+
+ const resProps:any = [];
+ if (resno){
+ console.log(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);
@@ -93,9 +141,6 @@ const lang = P.MonadicParser.createLanguage({
r.Keywords,
r.NamedAtomProperties,
r.AtomSelectionMacro.map(atomSelectionQuery2),
- 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),
r.Element.map((x: string) => B.struct.generator.atomGroups({
'atom-test': B.core.rel.eq([B.acp('elementSymbol'), B.struct.type.elementSymbol(x)])
@@ -252,6 +297,7 @@ const lang = P.MonadicParser.createLanguage({
return P.MonadicParser.seq(
P.MonadicParser.lookahead(r.AtomPrefix),
P.MonadicParser.seq(
+ r.ResnoRange.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)),
@@ -273,7 +319,11 @@ const lang = P.MonadicParser.createLanguage({
Inscode: () => P.MonadicParser.regexp(/\^([a-zA-Z0-9])/, 1).desc('inscode'),
-
+ ResnoRange: function (r:any) {
+ return P.MonadicParser.regex(/[0-9,-]+/).map( listOrRangeMap ).desc('resnorange')
+ // // 123-200
+ // // -12--3
+ },
Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)),
--
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