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Commit ba78a855 authored by yakomaxa's avatar yakomaxa
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Finally enabled selection by negative-valued residue index

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src/mol-script/transpilers/rasmol/operators.ts
+ 16
− 16
View file @ ba78a855
......@@ -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,
});
},
},
];
src/mol-script/transpilers/rasmol/parser.ts
+ 39
− 55
View file @ ba78a855
......@@ -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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