Rasmol parser WIP 5

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

@@ -32,7 +32,7 @@ function listOrRangeMap(x: string) {
                 res.push(parseInt(x));
             }
         });
-        console.log(res)
+//        console.log(res)
         return res;
     }else if(x.includes('-') && !x.includes('+')){
         return rangeMap(x)

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

@@ -12,15 +12,15 @@ import { PropertyDict } from '../types';
 const reFloat = /[-+]?[0-9]*\.?[0-9]+/;
 // const rePosInt = /[0-9]+/;
 
-function atomNameListMap(x: string) { return x.split('+').map(B.atomName); }
-function listMap(x: string) { return x.split('+').map(x => x.replace(/^["']|["']$/g, '')); }
+function atomNameListMap(x: string) { return x.split(',').map(B.atomName); }
+function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/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(/^["']|["']$/g, ''));
+    if (x.includes('-') && x.includes(',')){
+	const pSplit = x.split(',').map(x => x.replace(/^["']|["']$/g, ''));
 	const res : number[] =[];
 	pSplit.forEach( x => {
 	    if (x.includes('-')){
@@ -32,11 +32,11 @@ function listOrRangeMap(x: string) {
 		res.push(parseInt(x));
 	    }
 	});
-	console.log(res)
+//	console.log(res)
 	return res;		    	
-    }else if(x.includes('-') && !x.includes('+')){
+    }else if(x.includes('-') && !x.includes(',')){
 	return rangeMap(x)
-    }else if(!x.includes('-') && x.includes('+')){
+    }else if(!x.includes('-') && x.includes(',')){
 	return listMap(x)
     }
 }
@@ -61,112 +61,38 @@ export const special_properties: PropertyDict = {
     symbol: {
         '@desc': 'chemical-symbol-list: list of 1- or 2-letter chemical symbols from the periodic table',
         '@examples': ['symbol O+N'],
-        abbr: ['e.'], regex: /[a-zA-Z'"+]+/, map: elementListMap,
+        abbr: ['e.'], regex: /[a-zA-Z'",]+/, map: elementListMap,
         level: 'atom-test', property: B.acp('elementSymbol')
     },
     name: {
         '@desc': 'atom-name-list: list of up to 4-letter codes for atoms in proteins or nucleic acids',
         '@examples': ['name CA+CB+CG+CD'],
-        abbr: ['n.'], regex: /[a-zA-Z0-9'"+]+/, map: atomNameListMap,
+        abbr: ['n.'], regex: /[a-zA-Z0-9'",]+/, map: atomNameListMap,
         level: 'atom-test', property: B.ammp('label_atom_id')
     },
     resn: {
         '@desc': 'residue-name-list: list of 3-letter codes for amino acids or list of up to 2-letter codes for nucleic acids',
         '@examples': ['resn ASP+GLU+ASN+GLN', 'resn A+G'],
-        abbr: ['resname', 'r.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        abbr: ['resname', 'r.'], regex: /[a-zA-Z0-9'",]+/, map: listMap,
         level: 'residue-test', property: B.ammp('label_comp_id')
     },
     resi: {
         '@desc': 'residue-identifier-list list of up to 4-digit residue numbers or residue-identifier-range',
         '@examples': ['resi 1+10+100+1000', 'resi 1-10'],
-        abbr: ['resident', 'residue', 'resid', 'i.'], regex: /[0-9+-]+/, map: listOrRangeMap,
+        abbr: ['resident', 'residue', 'resid', 'i.'], regex: /[0-9,-]+/, map: listOrRangeMap,
         level: 'residue-test', property: B.ammp('auth_seq_id')
     },
     alt: {
         '@desc': 'alternate-conformation-identifier-list list of single letters',
         '@examples': ['alt A+B', 'alt ""', 'alt ""+A'],
-        abbr: [], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        abbr: [], regex: /[a-zA-Z0-9'",]+/, map: listMap,
         level: 'atom-test', property: B.ammp('label_alt_id')
     },
     chain: {
         '@desc': 'chain-identifier-list list of single letters or sometimes numbers',
         '@examples': ['chain A'],
-        abbr: ['c.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        abbr: ['c.'], regex: /[a-zA-Z0-9'",]+/, map: listMap,
         level: 'chain-test', property: B.ammp('auth_asym_id')
     },
-    segi: {
-        '@desc': 'segment-identifier-list list of up to 4 letter identifiers',
-        '@examples': ['segi lig'],
-        abbr: ['segid', 's.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
-        level: 'chain-test', property: B.ammp('label_asym_id')
-    },
-    flag: {
-        '@desc': 'flag-number a single integer from 0 to 31',
-        '@examples': ['flag 0'],
-        isUnsupported: true,
-        abbr: ['f.'], regex: /[0-9]+/, map: x => parseInt(x),
-        level: 'atom-test'
-    },
-    numeric_type: {
-        '@desc': 'type-number a single integer',
-        '@examples': ['nt. 5'],
-        isUnsupported: true,
-        abbr: ['nt.'], regex: /[0-9]+/, map: x => parseInt(x),
-        level: 'atom-test'
-    },
-    text_type: {
-        '@desc': 'type-string a list of up to 4 letter codes',
-        '@examples': ['text_type HA+HC'],
-        isUnsupported: true,
-        abbr: ['tt.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
-        level: 'atom-test'
-    },
-    id: {
-        '@desc': 'external-index-number a single integer',
-        '@examples': ['id 23'],
-        regex: /[0-9+-]+/, map: listOrRangeMap,
-        level: 'atom-test', property: B.ammp('id')
-    },
-    index: {
-        '@desc': 'internal-index-number a single integer',
-        '@examples': ['index 11'],
-        regex: /[0-9+-]+/, map: listOrRangeMap,
-        level: 'atom-test', property: B.ammp('id')
-    },
-    ss: {
-        '@desc': 'secondary-structure-type list of single letters. Helical regions should be assigned H and sheet regions S. Loop regions can either be assigned L or be blank.',
-        '@examples': ['ss H+S+L', 'ss S+""'],
-        abbr: [], regex: /[a-zA-Z'"+]+/, map: sstrucListMap,
-        level: 'residue-test', property: B.ammp('secondaryStructureFlags')
-    },
 
-    b: {
-        '@desc': 'comparison-operator b-factor-value a real number',
-        '@examples': ['b > 10'],
-        isNumeric: true,
-        abbr: [], regex: reFloat, map: x => parseFloat(x),
-        level: 'atom-test', property: B.ammp('B_iso_or_equiv')
-    },
-    q: {
-        '@desc': 'comparison-operator occupancy-value a real number',
-        '@examples': ['q <0.50'],
-        isNumeric: true,
-        abbr: [], regex: reFloat, map: x => parseFloat(x),
-        level: 'atom-test', property: B.ammp('occupancy')
-    },
-    formal_charge: {
-        '@desc': 'comparison-operator formal charge-value an integer',
-        '@examples': ['fc. = -1'],
-        isNumeric: true,
-        abbr: ['fc.'], regex: reFloat, map: x => parseFloat(x),
-        level: 'atom-test', property: B.ammp('pdbx_formal_charge')
-    },
-    partial_charge: {
-        '@desc': 'comparison-operator partial charge-value a real number',
-        '@examples': ['pc. > 1'],
-        isUnsupported: true,
-        isNumeric: true,
-        abbr: ['pc.'], regex: reFloat, map: x => parseFloat(x),
-        level: 'atom-test'
-    }
 };