lint PyMOL

src/mol-script/transpilers/pymol/properties.ts

@@ -16,61 +16,60 @@ function atomNameListMap(x: string) { return x.split('+').map(B.atomName); }
 function listMap(x: string) { return x.split('+').map(x => x.replace(/^["']|["']$/g, '')); }
 
 function listOrRangeMap(x: string) {
-    // cases 
+    // cases
     if (x.includes('-') && x.includes('+')) {
         const pSplit = x.split('+').map(x => x.replace(/^["']|["']$/g, ''));
         const res: number[] = [];
         pSplit.forEach(x => {
-	    if (x.includes('-') && !x.startsWith("-")) {
+	    if (x.includes('-') && !x.startsWith('-')) {
                 const [min, max] = x.split('-').map(x=>parseInt(x));
                 for (let i = min; i <= max; i++) {
 		    res.push(i);
                 }
-	    }else if (x.includes('-') && x.startsWith("-") && x.match(/[0-9]+-[-0-9]+/)) {
-		const min = -parseInt(x.split('-')[1]);
-		var max ;
-		if (x.includes('--')) {
-		    max = -parseInt(x.split('-')[3])
-		}else{
-		    max = parseInt(x.split('-')[2])
-		}
-		for (let i = min; i <= max; i++) {
+	    } else if (x.includes('-') && x.startsWith('-') && x.match(/[0-9]+-[-0-9]+/)) {
+                const min = -parseInt(x.split('-')[1]);
+                let max;
+                if (x.includes('--')) {
+		    max = -parseInt(x.split('-')[3]);
+                } else {
+		    max = parseInt(x.split('-')[2]);
+                }
+                for (let i = min; i <= max; i++) {
 		    res.push(i);
-                }		
-	    }else if (x.includes('-') && x.startsWith("-") && !x.match(/[0-9]+-[-0-9]+/)) {
-		res.push(parseInt(x));
-	    }else{
+                }
+	    } else if (x.includes('-') && x.startsWith('-') && !x.match(/[0-9]+-[-0-9]+/)) {
+                res.push(parseInt(x));
+	    } else {
                 res.push(parseInt(x));
 	    }
         });
         return res;
     } else if (x.includes('-') && !x.includes('+')) {
-	const res: number[] = [];
-	if (!x.startsWith("-")) {
+        const res: number[] = [];
+        if (!x.startsWith('-')) {
             const [min, max] = x.split('-').map(x=>parseInt(x));
             for (let i = min; i <= max; i++) {
-		res.push(i);
+                res.push(i);
             }
-	}else if (x.startsWith("-") && x.match(/[0-9]+-[-0-9]+/)) {	    
+        } else if (x.startsWith('-') && x.match(/[0-9]+-[-0-9]+/)) {
 	    const min = -parseInt(x.split('-')[1]);
-	    console.log(min)
-	    var max ;
+	    let max;
 	    if (x.includes('--')) {
-		max = -parseInt(x.split('-')[3])
-	    }else{
-		max = parseInt(x.split('-')[2])
+                max = -parseInt(x.split('-')[3]);
+	    } else {
+                max = parseInt(x.split('-')[2]);
 	    }
 	    for (let i = min; i <= max; i++) {
-		res.push(i);
-            }		
-	}else if (x.startsWith("-") && !x.match(/[0-9]+-[-0-9]+/)) {
+                res.push(i);
+            }
+        } else if (x.startsWith('-') && !x.match(/[0-9]+-[-0-9]+/)) {
 	    res.push(parseInt(x));
-	}else{
+        } else {
             res.push(parseInt(x));
-	}
-        return res;	
+        }
+        return res;
     } else if (!x.includes('-') && x.includes('+')) {
-	return listMap(x).map(x => parseInt(x));
+        return listMap(x).map(x => parseInt(x));
     } else {
         return [parseInt(x)];
     }

src/mol-script/transpilers/rasmol/parser.ts

@@ -20,29 +20,63 @@ import { Transpiler } from '../transpiler';
 function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/g, '')); }
 
 function listOrRangeMap(x: string) {
+    // cases 
+    // case1: 1-100,200
+    console.log(x)
     if (x.includes('-') && x.includes(',')) {
         const pSplit = x.split(',').map(x => x.replace(/^["']|["']$/g, ''));
         const res: number[] = [];
         pSplit.forEach(x => {
-	    if (x.includes('-')) {
+	    if (x.includes('-') && !x.startsWith("-")) {
                 const [min, max] = x.split('-').map(x=>parseInt(x));
                 for (let i = min; i <= max; i++) {
 		    res.push(i);
                 }
-	    } else {
+	    }else if (x.includes('-') && x.startsWith("-") && x.match(/[0-9]+-[-0-9]+/)) {
+		const min = -parseInt(x.split('-')[1]);
+		var max ;
+		if (x.includes('--')) {
+		    max = -parseInt(x.split('-')[3])
+		}else{
+		    max = parseInt(x.split('-')[2])
+		}
+		for (let i = min; i <= max; i++) {
+		    res.push(i);
+                }		
+	    }else if (x.includes('-') && x.startsWith("-") && !x.match(/[0-9]+-[-0-9]+/)) {
+		res.push(parseInt(x));
+	    }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;
+	const res: number[] = [];
+	if (!x.startsWith("-")) {
+            const [min, max] = x.split('-').map(x=>parseInt(x));
+            for (let i = min; i <= max; i++) {
+		res.push(i);
+            }
+	}else if (x.startsWith("-") && x.match(/[0-9]+-[-0-9]+/)) {	    
+	    const min = -parseInt(x.split('-')[1]);
+	    console.log(min)
+	    var max ;
+	    if (x.includes('--')) {
+		max = -parseInt(x.split('-')[3])
+	    }else{
+		max = parseInt(x.split('-')[2])
+	    }
+	    for (let i = min; i <= max; i++) {
+		res.push(i);
+            }		
+	}else if (x.startsWith("-") && !x.match(/[0-9]+-[-0-9]+/)) {
+	    res.push(parseInt(x));
+	}else{
+            res.push(parseInt(x));
+	}
+        return res;	
     } else if (!x.includes('-') && x.includes(',')) {
-        return listMap(x).map(x => parseInt(x));
+	return listMap(x).map(x => parseInt(x));
     } else {
         return [parseInt(x)];
     }
@@ -84,6 +118,7 @@ function atomSelectionQuery2(x: any) {
 
 function atomExpressionQuery(x: any[]) {
     const [resnorange, resno, inscode, chainname, atomname, altloc] = x[1];
+    //const [resnorange,  inscode, chainname, atomname, altloc] = x[1];
     const tests: AtomGroupArgs = {};
 
     if (chainname) {
@@ -101,7 +136,7 @@ function atomExpressionQuery(x: any[]) {
 
     const resProps: any = [];
     if (resno) {
-        console.log(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]));
@@ -115,6 +150,28 @@ function atomExpressionQuery(x: any[]) {
     return B.struct.generator.atomGroups(tests);
 }
 
+function resnorangeExpressionQuery(x: any[]) {
+    const [resnorange, chainname] = x;
+    //const [resnorange,  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
+        tests['chain-test'] = B.core.rel.eq([B.ammp('auth_asym_id'), chainname]);
+    }
+    
+
+    const resnoRangeProps: any = [];
+    if (resnorange) {
+        resnorange.forEach((x: number) =>{
+            resnoRangeProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), x]));
+        });
+    };
+    if (resnoRangeProps.length) tests['residue-test'] = h.orExpr(resnoRangeProps);
+    
+    return B.struct.generator.atomGroups(tests);
+}
+
 
 const lang = P.MonadicParser.createLanguage({
 
@@ -134,7 +191,21 @@ const lang = P.MonadicParser.createLanguage({
 	    r.Keywords,
 	    r.NamedAtomProperties,
 	    r.AtomSelectionMacro.map(atomSelectionQuery2),
+/*	    r.ResnoRange.map((x:string) => {
+		const resnorange=listOrRangeMap(x);
+		const resnoRangeProps: any = [];
+		const tests: AtomGroupArgs = {};
+		console.log(resnorange)
+		resnorange.forEach((a: number) =>{
+		    resnoRangeProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), a]));
+		});
+		console.log(resnoRangeProps)
+		tests['residue-test'] = h.orExpr(resnoRangeProps);
+		return B.struct.generator.atomGroups(tests);
+	    }),
+*/
 	    r.AtomExpression.map(atomExpressionQuery),
+	    r.ResnoRangeExpression.map(resnorangeExpressionQuery),
 	    r.Element.map((x: string) => B.struct.generator.atomGroups({
                 'atom-test': B.core.rel.eq([B.acp('elementSymbol'), B.struct.type.elementSymbol(x)])
             })),
@@ -272,7 +343,7 @@ const lang = P.MonadicParser.createLanguage({
     },
 
     Operator: function (r: any) {
-        return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression, r.Operator));
+        return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression,r.Operator));
     },
 
     AtomExpression: function (r: any) {
@@ -280,7 +351,7 @@ const lang = P.MonadicParser.createLanguage({
             P.MonadicParser.lookahead(r.AtomPrefix),
             P.MonadicParser.seq(
                 r.ResnoRange.or(P.MonadicParser.of(null)),
-                r.Resno.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)),
                 r.Atomname.or(P.MonadicParser.of(null)),
@@ -290,6 +361,13 @@ const lang = P.MonadicParser.createLanguage({
         );
     },
 
+    ResnoRangeExpression: function (r: any) {
+        return P.MonadicParser.seq(
+            r.ResnoRange.or(P.MonadicParser.of(null)),
+	    r.Chainname.or(P.MonadicParser.of(null)),
+        )
+    },
+
     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'),
@@ -300,9 +378,15 @@ 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'),
 
+    Number: function () {
+        return P.MonadicParser.regexp(/-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/)
+            .map(Number)
+            .desc('number');
+    },
+
 
     ResnoRange: function (r: any) {
-        return P.MonadicParser.regex(/[0-9,-]+/).map(listOrRangeMap).desc('resnorange');
+        return P.MonadicParser.regex(/-?[0-9,-]+/).map(listOrRangeMap).desc('resnorange');
         //   // 123-200
     //   // -12--3
     },