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Commit e3f6dfad authored by Alexander Rose's avatar Alexander Rose
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improve jmol transpiler 

- add basic within function
- add basic backbone and protein keyword
- allow withspace in parans
parent 32080ce9
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src/mol-script/transpilers/_spec/jmol.spec.ts
+ 7
− 4
View file @ e3f6dfad
/**
* Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Koya Sakuma <koya.sakuma.work@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
......@@ -62,14 +62,17 @@ const general = {
'100, 42, ALA',
// residue numbering
'(1-10,15,21-30)',
// within
'within(5,[HEM])',
// within with parentheses
// '( within(5,[HEM]) ) and backbone',
'(within(5,[HEM])) and backbone',
'( within(5,[HEM]) ) and backbone',
// trimming
'[ALA] and [VAL] ',
' [ALA] and [VAL] ',
' [ALA] and [VAL]',
// within with whitespaces
// 'within ( 5 , [HEM] ) ',
'within ( 5 , [HEM] ) ',
// un-braketed residue name
'LEU and ILE',
// un-parenthesized residue index range
......@@ -77,7 +80,7 @@ const general = {
// un-parenthesized residue index
'20',
// within in the head or the middle of sentence
// 'within ( 5 , [HEM] ) and backbone',
'within ( 5 , [HEM] ) and backbone',
],
unsupported: [
// values outside of comparisons
......
src/mol-script/transpilers/jmol/keywords.ts
+ 75
− 19
View file @ e3f6dfad
/**
* Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Koya Sakuma <koya.sakuma.work@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*
* Adapted from MolQL project
**/
*/
import { MolScriptBuilder } from '../../../mol-script/language/builder';
......@@ -10,12 +13,34 @@ const B = MolScriptBuilder;
import * as h from '../helper';
import { KeywordDict } from '../types';
const ResDict = {
acidic: ['ASP', 'GLU'],
aliphatic: ['ALA', 'GLY', 'ILE', 'LEU', 'VAL'],
amino: ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'ASX', 'GLX', 'UNK'],
aromatic: ['HIS', 'PHE', 'TRP', 'TYR'],
basic: ['ARG', 'HIS', 'LYS'],
buried: ['ALA', 'CYS', 'ILE', 'LEU', 'MET', 'PHE', 'TRP', 'VAL'],
cg: ['CYT', 'C', 'GUA', 'G'],
cyclic: ['HIS', 'PHE', 'PRO', 'TRP', 'TYR'],
hydrophobic: ['ALA', 'GLY', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'TYR', 'VAL'],
large: ['ARG', 'GLU', 'GLN', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'TRP', 'TYR'],
medium: ['ASN', 'ASP', 'CYS', 'PRO', 'THR', 'VAL'],
small: ['ALA', 'GLY', 'SER'],
nucleic: ['G', 'C', 'A', 'T', 'U', 'I', 'DG', 'DC', 'DA', 'DT', 'DU', 'DI', '+G', '+C', '+A', '+T', '+U', '+I']
};
const Backbone = {
nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*',
"C2'", "C1'", "O4'", "O2'"],
protein: ['C', 'N', 'CA']
};
function nucleicExpr() {
return B.struct.combinator.merge([
B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
B.set(...['G', 'C', 'A', 'T', 'U', 'I', 'DG', 'DC', 'DA', 'DT', 'DU', 'DI', '+G', '+C', '+A', '+T', '+U', '+I']),
B.set(...ResDict.nucleic),
B.ammp('label_comp_id')
])
}),
......@@ -46,20 +71,49 @@ function nucleicExpr() {
]);
}
const ResDict = {
acidic: ['ASP', 'GLU'],
aliphatic: ['ALA', 'GLY', 'ILE', 'LEU', 'VAL'],
amino: ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'ASX', 'GLX', 'UNK'],
aromatic: ['HIS', 'PHE', 'TRP', 'TYR'],
basic: ['ARG', 'HIS', 'LYS'],
buried: ['ALA', 'CYS', 'ILE', 'LEU', 'MET', 'PHE', 'TRP', 'VAL'],
cg: ['CYT', 'C', 'GUA', 'G'],
cyclic: ['HIS', 'PHE', 'PRO', 'TRP', 'TYR'],
hydrophobic: ['ALA', 'GLY', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'TYR', 'VAL'],
large: ['ARG', 'GLU', 'GLN', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'TRP', 'TYR'],
medium: ['ASN', 'ASP', 'CYS', 'PRO', 'THR', 'VAL'],
small: ['ALA', 'GLY', 'SER'],
};
// TODO: improve, see keywords.protein['@desc'] below
function proteinExpr() {
return B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
B.set(...ResDict.amino),
B.ammp('label_comp_id')
])
});
}
// TODO: improve, see keywords.backbone['@desc'] below
function backboneExpr() {
return B.struct.combinator.merge([
B.struct.modifier.intersectBy({
0: B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
B.core.type.set(ResDict.amino),
B.ammp('label_comp_id')
])
}),
by: B.struct.generator.atomGroups({
'atom-test': B.core.set.has([
B.core.type.set(Backbone.protein),
B.ammp('label_atom_id')
])
})
}),
B.struct.modifier.intersectBy({
0: B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
B.core.type.set(ResDict.nucleic),
B.ammp('label_comp_id')
])
}),
by: B.struct.generator.atomGroups({
'atom-test': B.core.set.has([
B.core.type.set(Backbone.nucleic),
B.ammp('label_atom_id')
])
})
}),
]);
}
export const keywords: KeywordDict = {
// general terms
......@@ -336,7 +390,8 @@ export const keywords: KeywordDict = {
})
},
protein: {
'@desc': 'defined as a group that (a) has one of the following group names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, or UNK; or (b) contains PDB atom designations [C, O, CA, and N] bonded correctly; or (c) does not contain "O" but contains [C, CA, and N] bonded correctly; or (d) has only one atom, which has name CA and does not have the group name CA (indicating a calcium atom).'
'@desc': 'defined as a group that (a) has one of the following group names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, or UNK; or (b) contains PDB atom designations [C, O, CA, and N] bonded correctly; or (c) does not contain "O" but contains [C, CA, and N] bonded correctly; or (d) has only one atom, which has name CA and does not have the group name CA (indicating a calcium atom).',
map: () => proteinExpr()
},
acidic: {
'@desc': 'ASP GLU',
......@@ -496,7 +551,8 @@ export const keywords: KeywordDict = {
},
backbone: {
'@desc': '(*.C, *.CA, *.N, and all nucleic other than the bases themselves)',
abbr: ['mainchain']
abbr: ['mainchain'],
map: () => backboneExpr()
},
sidechain: {
'@desc': '((protein or nucleic) and not backbone)'
......
src/mol-script/transpilers/jmol/parser.ts
+ 14
− 3
View file @ e3f6dfad
/**
* Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Koya Sakuma < koya.sakuma.work@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
......@@ -18,6 +18,7 @@ import { keywords } from './keywords';
import { AtomGroupArgs } from '../types';
import { Transpiler } from '../transpiler';
import { OperatorList } from '../types';
import { Expression } from '../../language/expression';
// <, <=, =, >=, >, !=, and LIKE
const valueOperators: OperatorList = [
......@@ -116,7 +117,7 @@ const lang = P.MonadicParser.createLanguage({
r.Parens,
r.Operator,
r.Expression
).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
).wrap(P.MonadicParser.regexp(/\(\s*/), P.MonadicParser.regexp(/\s*\)/));
},
Expression: function (r: any) {
......@@ -129,11 +130,12 @@ const lang = P.MonadicParser.createLanguage({
B.core.rel.lte([B.ammp('auth_seq_id'), x[1]])
])
})),
r.Resno.lookahead(P.MonadicParser.regexp(/\s*(?!(LIKE|>=|<=|!=|[\[:^%/.=><]))/i)).map((x: any) => B.struct.generator.atomGroups({
r.Resno.lookahead(P.MonadicParser.regexp(/\s*(?!(LIKE|>=|<=|!=|[\[:^%/.=><]))/i)).map((x: number) => B.struct.generator.atomGroups({
'residue-test': B.core.rel.eq([B.ammp('auth_seq_id'), x])
})),
r.AtomExpression.map(atomExpressionQuery),
r.Within.map((x: [number, Expression]) => B.struct.modifier.includeSurroundings({ 0: x[1], radius: x[0] })),
r.ValueQuery,
r.Element.map((x: string) => B.struct.generator.atomGroups({
......@@ -186,6 +188,15 @@ const lang = P.MonadicParser.createLanguage({
r.Integer
).desc('resno-range');
},
Within: (r: any) => {
return P.MonadicParser.regexp(/within/i)
.skip(P.MonadicParser.regexp(/\s*\(\s*/))
.then(P.MonadicParser.seq(
r.Integer.skip(P.MonadicParser.regexp(/\s*,\s*/)),
r.Query
))
.skip(P.MonadicParser.regexp(/\)/));
},
Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)).desc('keyword'),
......
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