From ba78a8558cd73b6aee505e3275013c17b9a1e27a Mon Sep 17 00:00:00 2001
From: yakomaxa <47655565+yakomaxa@users.noreply.github.com>
Date: Sun, 21 Aug 2022 21:39:20 +0900
Subject: [PATCH] Finally enabled selection by negative-valued residue index
---
.../transpilers/rasmol/operators.ts | 32 +++----
src/mol-script/transpilers/rasmol/parser.ts | 94 ++++++++-----------
2 files changed, 55 insertions(+), 71 deletions(-)
diff --git a/src/mol-script/transpilers/rasmol/operators.ts b/src/mol-script/transpilers/rasmol/operators.ts
index 64b224810..8a1139af7 100644
--- a/src/mol-script/transpilers/rasmol/operators.ts
+++ b/src/mol-script/transpilers/rasmol/operators.ts
@@ -13,6 +13,22 @@ import { OperatorList } from '../types';
import { Expression } from '../../language/expression';
export const operators: OperatorList = [
+ {
+ '@desc': 'Selects atoms in s1 that are within X Angstroms of any atom in s2.',
+ '@examples': ['within(5.0, [HEM])'],
+ name: 'within',
+ type: h.prefixRemoveKet,
+ rule: h.prefixOpNoWhiteSpace(/within\s*\(\s*([-+]?[0-9]*\.?[0-9]+)\s*,/, 1).map((x: any) => {
+ return parseFloat(x);
+ }),
+ map: (radius: number, target: Expression) => {
+ return B.struct.filter.within({
+ 0: B.struct.generator.all(),
+ target,
+ 'max-radius': radius,
+ });
+ },
+ },
{
'@desc': 'Selects atoms that are not included in s1.',
'@examples': ['not [ARG]'],
@@ -38,21 +54,5 @@ export const operators: OperatorList = [
rule: P.MonadicParser.alt(h.infixOp(/OR|\||\|\||,/i)),
map: (op, s1, s2) => B.struct.combinator.merge([s1, s2])
},
- {
- '@desc': 'Selects atoms in s1 that are within X Angstroms of any atom in s2.',
- '@examples': ['within(5.0, [HEM])'],
- name: 'within',
- type: h.prefixRemoveKet,
- rule: h.prefixOpNoWhiteSpace(/within\s*\(\s*([-+]?[0-9]*\.?[0-9]+)\s*,/i, 1).map((x: any) => {
- return parseFloat(x);
- }),
- map: (radius: number, target: Expression) => {
- return B.struct.filter.within({
- 0: B.struct.generator.all(),
- target,
- 'max-radius': radius,
- });
- },
- },
];
diff --git a/src/mol-script/transpilers/rasmol/parser.ts b/src/mol-script/transpilers/rasmol/parser.ts
index ba6c74bd9..d51059b19 100644
--- a/src/mol-script/transpilers/rasmol/parser.ts
+++ b/src/mol-script/transpilers/rasmol/parser.ts
@@ -20,63 +20,61 @@ import { Transpiler } from '../transpiler';
function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/g, '')); }
function listOrRangeMap(x: string) {
- // cases
+ // cases
// case1: 1-100,200
- console.log(x)
if (x.includes('-') && x.includes(',')) {
const pSplit = x.split(',').map(x => x.replace(/^["']|["']$/g, ''));
const res: number[] = [];
pSplit.forEach(x => {
- if (x.includes('-') && !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)];
}
@@ -118,7 +116,7 @@ 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 [resnorange, inscode, chainname, atomname, altloc] = x[1];
const tests: AtomGroupArgs = {};
if (chainname) {
@@ -136,7 +134,6 @@ function atomExpressionQuery(x: any[]) {
const resProps: any = [];
if (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]));
@@ -152,14 +149,13 @@ function atomExpressionQuery(x: any[]) {
function resnorangeExpressionQuery(x: any[]) {
const [resnorange, chainname] = x;
- //const [resnorange, inscode, chainname, atomname, altloc] = x[1];
+ // 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) {
@@ -168,7 +164,7 @@ function resnorangeExpressionQuery(x: any[]) {
});
};
if (resnoRangeProps.length) tests['residue-test'] = h.orExpr(resnoRangeProps);
-
+
return B.struct.generator.atomGroups(tests);
}
@@ -191,27 +187,14 @@ 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)])
})),
r.Resname.map((x: string) => B.struct.generator.atomGroups({
'residue-test': B.core.rel.eq([B.ammp('label_comp_id'), x])
})),
+ r.ResnoRangeExpression.map(resnorangeExpressionQuery),
r.Object,
r.Object2,
);
@@ -343,7 +326,8 @@ 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));
+ //return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression));
},
AtomExpression: function (r: any) {
@@ -351,7 +335,7 @@ 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)),
@@ -365,11 +349,11 @@ const lang = P.MonadicParser.createLanguage({
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'),
+ Chainname: () => P.MonadicParser.regexp(/:([A-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'),
--
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