diff --git a/src/mol-script/transpilers/rasmol/*Backtrace* b/src/mol-script/transpilers/rasmol/*Backtrace*
new file mode 100644
index 0000000000000000000000000000000000000000..94aaf967745a35a07402f6d01b15564f9b474417
--- /dev/null
+++ b/src/mol-script/transpilers/rasmol/*Backtrace*
@@ -0,0 +1,6 @@
+Debugger entered--Lisp error: (void-variable *)
+ eval(* nil)
+ eval-last-sexp-1(nil)
+ eval-last-sexp(nil)
+ call-interactively(eval-last-sexp nil nil)
+ command-execute(eval-last-sexp)
diff --git a/src/mol-script/transpilers/rasmol/operators.ts b/src/mol-script/transpilers/rasmol/operators.ts
index 6f26deb9e51e7ccefa315b08ad8751bea509f9fc..582678e641b96e57f9731325be8fa66ac1a49296 100644
--- a/src/mol-script/transpilers/rasmol/operators.ts
+++ b/src/mol-script/transpilers/rasmol/operators.ts
@@ -46,7 +46,7 @@ export const operators: OperatorList = [
'@examples': ['within 5 of name FE'],
name: 'within',
type: h.prefix,
- rule: h.prefixOp(/WITHIN\s+([-+]?[0-9]*\.?[0-9]+)\s+OF/i, 1).map((x: any) => parseFloat(x)),
+ rule: h.prefixOp(/within\s+([-+]?[0-9]*\.?[0-9]+)\s+of/, 1).map((x: any) => parseFloat(x)),
map: (radius: number, selection: Expression) => {
return B.struct.modifier.includeSurroundings({ 0: selection, radius });
}
diff --git a/src/mol-script/transpilers/rasmol/parser.ts b/src/mol-script/transpilers/rasmol/parser.ts
index dfa12686e2419cda4140ac658f0fdf7f4913d3c0..133cf42a407264f96d098505377939a0dd9baa98 100644
--- a/src/mol-script/transpilers/rasmol/parser.ts
+++ b/src/mol-script/transpilers/rasmol/parser.ts
@@ -34,6 +34,8 @@ const colon = P.MonadicParser.string(':');
const star = P.MonadicParser.string('*');
const bra = P.MonadicParser.string('(');
const ket = P.MonadicParser.string(')');
+const commu = P.MonadicParser.string('[');
+const tator = P.MonadicParser.string(']');
/* is Parser -> MonadicParser substitution correct? */
@@ -63,6 +65,33 @@ function atomSelectionQuery2(x: any) {
return B.struct.generator.atomGroups(tests);
}
+function atomExpressionQuery(x: any[]) {
+ const resname = x[0];
+// 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 resProps = [];
+ 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);
+
+ const atomProps = [];
+ if (atomname) atomProps.push(B.core.rel.eq([B.ammp('auth_atom_id'), atomname]));
+ if (altloc) atomProps.push(B.core.rel.eq([B.ammp('label_alt_id'), altloc]));
+ if (atomProps.length) tests['atom-test'] = h.andExpr(atomProps);
+
+ return B.struct.generator.atomGroups(tests);
+*/
+ if (resname){
+ return B.struct.generator.atomGroups({'residue-test': B.core.rel.eq([B.ammp('label_comp_id'), resname])})
+ }
+
+}
+
const lang = P.MonadicParser.createLanguage({
@@ -71,7 +100,7 @@ const lang = P.MonadicParser.createLanguage({
r.Parens,
r.Operator,
r.Expression
- ).wrap(P.MonadicParser.string('['), P.MonadicParser.string(']'));
+ ).wrap(P.MonadicParser.string('{'), P.MonadicParser.string('}'));
},
Expression: function (r: any) {
@@ -80,7 +109,8 @@ const lang = P.MonadicParser.createLanguage({
r.Keywords,
r.NamedAtomProperties,
r.AtomSelectionMacro.map(atomSelectionQuery2),
- r.Object
+// r.AtomExpression.map(atomExpressionQuery),
+ r.Object
);
},
@@ -133,38 +163,40 @@ const lang = P.MonadicParser.createLanguage({
)
)),
// lys:a.ca lys:a lys lys.ca
- P.MonadicParser.alt(
- P.MonadicParser.alt(
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(colon),
- orNull(propertiesDict.chain).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { resn: x[0], chain: x[1], name: x[2] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(star),
- orNull(propertiesDict.chain).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { resn: x[0], chain: x[1], name: x[2] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(colon),
- orNull(propertiesDict.chain),
- ).map(x => { return { resn: x[0], chain: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(star),
- orNull(propertiesDict.chain),
- ).map(x => { return { resn: x[0], chain: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(dot),
- orNull(propertiesDict.name),
- ).map(x => { return { resn: x[0], name: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn),
- ).map(x => { return { resn: x[0] }; }),
+ // [lys]:a.ca [lys]:a [lys] [lys].ca
+ commu.then(P.MonadicParser.alt(
+ P.MonadicParser.alt(
+ P.MonadicParser.alt(
+ P.MonadicParser.seq(
+ orNull(propertiesDict.resn).skip(tator).skip(colon),
+ orNull(propertiesDict.chain).skip(dot),
+ orNull(propertiesDict.name)
+ ).map(x => { return { resn: x[0], chain: x[1], name: x[2] }; }),
+ P.MonadicParser.seq(
+ orNull(propertiesDict.resn).skip(tator).skip(star),
+ orNull(propertiesDict.chain).skip(dot),
+ orNull(propertiesDict.name)
+ ).map(x => { return { resn: x[0], chain: x[1], name: x[2] }; }),
+ P.MonadicParser.seq(
+ orNull(propertiesDict.resn).skip(tator).skip(colon),
+ orNull(propertiesDict.chain),
+ ).map(x => { return { resn: x[0], chain: x[1] }; }),
+ P.MonadicParser.seq(
+ orNull(propertiesDict.resn).skip(tator).skip(star),
+ orNull(propertiesDict.chain),
+ ).map(x => { return { resn: x[0], chain: x[1] }; }),
+ P.MonadicParser.seq(
+ orNull(propertiesDict.resn).skip(tator).skip(dot),
+ orNull(propertiesDict.name),
+ ).map(x => { return { resn: x[0], name: x[1] }; }),
+ P.MonadicParser.seq(
+ orNull(propertiesDict.resn).skip(tator),
+ ).map(x => { return { resn: x[0]}; })
+ )
)
)
-
- );
-
+ )
+ )
},
ObjectProperty: () => {
@@ -184,6 +216,14 @@ const lang = P.MonadicParser.createLanguage({
.map((x: any) => { throw new Error(`property 'object' not supported, value '${x}'`); });
},
+ AtomExpression: function (r: any) {
+ return P.MonadicParser.seq(r.Resname.or(P.MonadicParser.of(null)));
+ },
+
+
+// Resname: () => P.MonadicParser.regexp(s/[a-zA-Z0-9]{1,4}/).desc('resname'),
+ Resname: () => P.MonadicParser.regexp(/\[[A-Z0-9]{1,4}\]/).desc('resname'),
+
NamedAtomProperties: function () {
return P.MonadicParser.alt(...h.getNamedPropertyRules(properties));
},
diff --git a/src/mol-script/transpilers/rasmol/special_properties.ts b/src/mol-script/transpilers/rasmol/special_properties.ts
index 247374e3529c29ba5fdb71dea2420fc831be92c0..5b3f975033c93ab0cb22371a8959db03baa5ee9c 100644
--- a/src/mol-script/transpilers/rasmol/special_properties.ts
+++ b/src/mol-script/transpilers/rasmol/special_properties.ts
@@ -1,4 +1,4 @@
-/**
+\[/**
* Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>