From da6a153985710cf82cad7f8c238fbc0747d84413 Mon Sep 17 00:00:00 2001
From: yakomaxa <47655565+yakomaxa@users.noreply.github.com>
Date: Sun, 14 Aug 2022 04:03:48 +0900
Subject: [PATCH] Construction of rasmol selection command has nearly finished
---
src/mol-script/transpilers/rasmol/parser.ts | 230 ++----------------
.../transpilers/rasmol/special_properties.ts | 26 +-
2 files changed, 35 insertions(+), 221 deletions(-)
diff --git a/src/mol-script/transpilers/rasmol/parser.ts b/src/mol-script/transpilers/rasmol/parser.ts
index f28e713df..6401a4e53 100644
--- a/src/mol-script/transpilers/rasmol/parser.ts
+++ b/src/mol-script/transpilers/rasmol/parser.ts
@@ -34,7 +34,7 @@ const comma = P.MonadicParser.string(',');
const star = P.MonadicParser.string('*');
const bra = P.MonadicParser.string('(');
const ket = P.MonadicParser.string(')');
-const numbers = P.MonadicParser.regexp(/[0-9]/);
+
/* is Parser -> MonadicParser substitution correct? */
function orNull(rule: P.MonadicParser<any>) {
@@ -64,96 +64,6 @@ function atomSelectionQuery2(x: any) {
}
-
-// <, <=, =, >=, >, !=, and LIKE
-const valueOperators: OperatorList = [
- {
- '@desc': 'value comparisons',
- '@examples': [],
- name: '=',
- abbr: ['=='],
- type: h.binaryLeft,
- rule: P.MonadicParser.regexp(/\s*(LIKE|>=|<=|=|!=|>|<)\s*/i, 1),
- map: (op, e1, e2) => {
- // console.log(op, e1, e2)
- let expr;
- if (e1 === 'structure') {
- expr = B.core.flags.hasAny([B.ammp('secondaryStructureFlags'), structureMap(e2)]);
- } else if (e2 === 'structure') {
- expr = B.core.flags.hasAny([B.ammp('secondaryStructureFlags'), structureMap(e1)]);
- } else if (e1.head !== undefined) {
- if (e1.head.name === 'core.type.regex') {
- expr = B.core.str.match([e1, B.core.type.str([e2])]);
- }
- } else if (e2.head !== undefined) {
- if (e2.head.name === 'core.type.regex') {
- expr = B.core.str.match([e2, B.core.type.str([e1])]);
- }
- } else if (op.toUpperCase() === 'LIKE') {
- if (e1.head) {
- expr = B.core.str.match([
- B.core.type.regex([`^${e2}$`, 'i']),
- B.core.type.str([e1])
- ]);
- } else {
- expr = B.core.str.match([
- B.core.type.regex([`^${e1}$`, 'i']),
- B.core.type.str([e2])
- ]);
- }
- }
- if (!expr) {
- if (e1.head) e2 = h.wrapValue(e1, e2);
- if (e2.head) e1 = h.wrapValue(e2, e1);
- switch (op) {
- case '=':
- expr = B.core.rel.eq([e1, e2]);
- break;
- case '!=':
- expr = B.core.rel.neq([e1, e2]);
- break;
- case '>':
- expr = B.core.rel.gr([e1, e2]);
- break;
- case '<':
- expr = B.core.rel.lt([e1, e2]);
- break;
- case '>=':
- expr = B.core.rel.gre([e1, e2]);
- break;
- case '<=':
- expr = B.core.rel.lte([e1, e2]);
- break;
- default: throw new Error(`value operator '${op}' not supported`);
- }
- }
- return B.struct.generator.atomGroups({ 'atom-test': expr });
- }
- }
-];
-
-function atomExpressionQuery(x: any[]) {
- const [resno, 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 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);
-}
-
const lang = P.MonadicParser.createLanguage({
Integer: () => P.MonadicParser.regexp(/-?[0-9]+/).map(Number).desc('integer'),
@@ -167,26 +77,10 @@ const lang = P.MonadicParser.createLanguage({
Expression: function (r: any) {
return P.MonadicParser.alt(
-// r.Keywords,
-// r.ValueQuery,
+ r.Keywords,
+ r.NamedAtomProperties,
r.AtomSelectionMacro.map(atomSelectionQuery2),
- r.AtomSelectionMacroResi.map(atomSelectionQuery2),
-// r.NamedAtomProperties,
-
-
- // 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.Atomno.lookahead(P.MonadicParser.regexp(/\s*(?!(LIKE|>=|<=|!=|[:^%/.=><]))/i)).map((x: any) => B.struct.generator.atomGroups({
- // 'atom-test': B.core.rel.eq([B.ammp('id'), x])
-// })),
-
-// r.Element.map((x: string) => B.struct.generator.atomGroups({
-// 'atom-test': B.core.rel.eq([B.acp('elementSymbol'), B.struct.type.elementSymbol(x)])
-// })),
-// r.Resname.map((x: string) => B.struct.generator.atomGroups({
-// 'residue-test': B.core.rel.eq([B.ammp('label_comp_id'), x])
-// })),
+ r.Object
);
},
@@ -201,6 +95,7 @@ const lang = P.MonadicParser.createLanguage({
// :.cg -> name ca
AtomSelectionMacro: function (r: any) {
return P.MonadicParser.alt(
+ // :A.CA :.CA
colon.then(P.MonadicParser.alt(
P.MonadicParser.seq(
orNull(propertiesDict.chain).skip(dot),
@@ -210,6 +105,7 @@ const lang = P.MonadicParser.createLanguage({
orNull(propertiesDict.name).skip(dot)
).map(x => { return {name: x[0] }; }),
)),
+ // *A.CA *.CA
star.then(P.MonadicParser.alt(
P.MonadicParser.seq(
orNull(propertiesDict.chain).skip(dot),
@@ -219,13 +115,14 @@ const lang = P.MonadicParser.createLanguage({
orNull(propertiesDict.name).skip(dot)
).map(x => { return {name: x[0] }; }),
)),
- // 1-100 lys:a.ca lys:a lys lys.ca
+ // 1-100+201
bra.then(P.MonadicParser.alt(
P.MonadicParser.alt(
P.MonadicParser.seq(
orNull(propertiesDict.resi).skip(ket),
).map(x => { return { resi: x[0] };})
))),
+ // lys:a.ca lys:a lys lys.ca
P.MonadicParser.alt(
P.MonadicParser.alt(
P.MonadicParser.seq(
@@ -260,23 +157,20 @@ const lang = P.MonadicParser.createLanguage({
},
- AtomSelectionMacroResi: function (r: any) {
- return P.MonadicParser.alt(
- P.MonadicParser.alt(
- P.MonadicParser.seq(
- orNull(propertiesDict.resi)
- ).map(x => { return { resi: x[0] };}),
- ),
- );
- },
-
ObjectProperty: () => {
const w = h.getReservedWords(special_properties, special_keywords, special_operators)
.sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
return P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i'));
},
+
+ ObjectProperty2: () => {
+ const w = h.getReservedWords(properties, keywords, operators)
+ .sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
+ return P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i'));
+ },
+
Object: (r: any) => {
- return r.ObjectProperty.notFollowedBy(slash)
+ return r.ObjectProperty2
.map((x: any) => { throw new Error(`property 'object' not supported, value '${x}'`); });
},
@@ -331,60 +225,18 @@ const lang = P.MonadicParser.createLanguage({
});
},
- Operator: function (r: any) {
- return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression));
- },
-
- AtomExpression: function (r: any) {
- 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.Atomno.or(P.MonadicParser.of(null)),
-// r.Resno2.or(P.MonadicParser.of(null)),
- r.Inscode.or(P.MonadicParser.of(null)),
- r.Chainname.or(P.MonadicParser.of(null)),
-// r.Chainname2.or(P.MonadicParser.of(null)),
- r.Atomname.or(P.MonadicParser.of(null)),
- r.Altloc.or(P.MonadicParser.of(null)),
- r.Model.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'),
-// Chainname2: () => P.MonadicParser.regexp(/\*([A-Za-z]{1,3})/, 1).desc('chainname'),
- Model: () => P.MonadicParser.regexp(/\/([0-9]+)/, 1).map(Number).desc('model'),
- Element: () => P.MonadicParser.regexp(/_([A-Za-z]{1,3})/, 1).desc('element'),
- Atomname: () => P.MonadicParser.regexp(/\.([a-zA-Z0-9]{1,4})/, 1).map(B.atomName).desc('atomname'),
- Resname: () => P.MonadicParser.regexp(/[a-zA-Z0-9]{1,4}/).desc('resname'),
- Resno: (r: any) => r.Integer.desc('resno'),
- Atomno: (r: any) => r.Integer.desc('atomno'),
-// Resno2: (r: any) => r.split(',').Integer.desc('resno'),
- Altloc: () => P.MonadicParser.regexp(/%([a-zA-Z0-9])/, 1).desc('altloc'),
- Inscode: () => P.MonadicParser.regexp(/\^([a-zA-Z0-9])/, 1).desc('inscode'),
-
+// Operator: function (r: any) {
+// return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression));
+// },
- // function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/g, '')); }
-
-
-
- BracketedResname: function (r: any) {
- return P.MonadicParser.regexp(/\.([a-zA-Z0-9]{1,4})/, 1)
- .desc('bracketed-resname');
- // [0SD]
+ Operator: function (r: any) {
+ return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression, r.Operator));
},
- ResnoRange: function (r: any) {
- return P.MonadicParser.regexp(/\.([\s]){1,3}/, 1)
- .desc('resno-range');
- // 123-200
- // -12--3
- },
Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)),
+
Query: function (r: any) {
return P.MonadicParser.alt(
r.Operator,
@@ -413,45 +265,7 @@ const lang = P.MonadicParser.createLanguage({
return P.MonadicParser.alt(r.Number, r.String);
},
- ValueParens: function (r: any) {
- return P.MonadicParser.alt(
- r.ValueParens,
- r.ValueOperator,
- r.ValueExpressions
- ).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
- },
-
- ValuePropertyNames: function () {
- return P.MonadicParser.alt(...h.getPropertyNameRules(properties, /LIKE|>=|<=|=|!=|>|<|\)|\s/i));
- },
-
- ValueOperator: function (r: any) {
- return h.combineOperators(valueOperators, P.MonadicParser.alt(r.ValueParens, r.ValueExpressions));
- },
- ValueExpressions: function (r: any) {
- return P.MonadicParser.alt(
- r.Value,
- r.ValuePropertyNames
- );
- },
-
- ValueQuery: function (r: any) {
- return P.MonadicParser.alt(
- r.ValueOperator.map((x: any) => {
- if (x.head.name) {
- if (x.head.name.startsWith('structure-query.generator')) return x;
- } else {
- if (typeof x === 'string' && x.length <= 4) {
- return B.struct.generator.atomGroups({
- 'residue-test': B.core.rel.eq([B.ammp('label_comp_id'), x])
- });
- }
- }
- throw new Error(`values must be part of an comparison, value '${x}'`);
- })
- );
- }
});
export const transpiler: Transpiler = str => lang.Query.tryParse(str);
diff --git a/src/mol-script/transpilers/rasmol/special_properties.ts b/src/mol-script/transpilers/rasmol/special_properties.ts
index afe6a9e79..4ca944c6d 100644
--- a/src/mol-script/transpilers/rasmol/special_properties.ts
+++ b/src/mol-script/transpilers/rasmol/special_properties.ts
@@ -9,7 +9,7 @@ import { MolScriptBuilder } from '../../../mol-script/language/builder';
const B = MolScriptBuilder;
import { PropertyDict } from '../types';
-const reFloat = /[-+]?[0-9]*\.?[0-9]+/;
+//const reFloat = /[-+]?[0-9]*\.?[0-9]+/;
// const rePosInt = /[0-9]+/;
function atomNameListMap(x: string) { return x.split(',').map(B.atomName); }
@@ -44,18 +44,18 @@ function elementListMap(x: string) {
return x.split('+').map(B.struct.type.elementSymbol);
}
-const sstrucDict: { [k: string]: string } = {
- H: 'helix',
- S: 'beta',
- L: 'none'
-};
-function sstrucListMap(x: string) {
- return {
- flags: B.struct.type.secondaryStructureFlags(
- x.toUpperCase().split('+').map(ss => sstrucDict[ss] || 'none')
- )
- };
-}
+//const sstrucDict: { [k: string]: string } = {
+// H: 'helix',
+// S: 'beta',
+// L: 'none'
+//};
+//function sstrucListMap(x: string) {
+// return {
+// flags: B.struct.type.secondaryStructureFlags(
+// x.toUpperCase().split('+').map(ss => sstrucDict[ss] || 'none')
+// )
+// };
+//}
export const special_properties: PropertyDict = {
symbol: {
--
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