diff --git a/src/mol-script/transpilers/pymol/properties.ts b/src/mol-script/transpilers/pymol/properties.ts
index 71cc81ab50af0d734170ef2bcfce6c2a83bccc16..7b29db7bf72abc619f242b2aa5b2ed921411945b 100644
--- a/src/mol-script/transpilers/pymol/properties.ts
+++ b/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)];
}
diff --git a/src/mol-script/transpilers/rasmol/parser.ts b/src/mol-script/transpilers/rasmol/parser.ts
index 818ccd8f39fa199a2f86d80f069312885566c59d..ba6c74bd9bac6f4443bdf826dc93323fab546667 100644
--- a/src/mol-script/transpilers/rasmol/parser.ts
+++ b/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
},