From 151da1487c0d3c22dafbe995c687c673f7d8728c Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Wed, 7 Sep 2022 18:28:45 -0700
Subject: [PATCH] formatting
---
src/mol-script/transpilers/jmol/keywords.ts | 26 +++++-----
src/mol-script/transpilers/jmol/parser.ts | 2 +-
src/mol-script/transpilers/jmol/properties.ts | 2 +-
src/mol-script/transpilers/pymol/keywords.ts | 49 ++++++++++---------
src/mol-script/transpilers/pymol/parser.ts | 2 +-
.../transpilers/pymol/properties.ts | 36 +++++++-------
src/mol-script/transpilers/vmd/parser.ts | 26 +++++-----
7 files changed, 73 insertions(+), 70 deletions(-)
diff --git a/src/mol-script/transpilers/jmol/keywords.ts b/src/mol-script/transpilers/jmol/keywords.ts
index b1ea90609..1dc545721 100644
--- a/src/mol-script/transpilers/jmol/keywords.ts
+++ b/src/mol-script/transpilers/jmol/keywords.ts
@@ -32,7 +32,7 @@ const ResDict = {
const Backbone = {
nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*',
- "C2'", "C1'", "O4'", "O2'"],
+ "C2'", "C1'", "O4'", "O2'"],
protein: ['C', 'N', 'CA']
};
@@ -84,31 +84,31 @@ function proteinExpr() {
// TODO: improve, see keywords.backbone['@desc'] below
function backboneExpr() {
return B.struct.combinator.merge([
- B.struct.modifier.intersectBy({
+ 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')
+ 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({
+ B.struct.modifier.intersectBy({
0: B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
+ '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')
+ by: B.struct.generator.atomGroups({
+ 'atom-test': B.core.set.has([
+ B.core.type.set(Backbone.nucleic),
+ B.ammp('label_atom_id')
])
})
}),
diff --git a/src/mol-script/transpilers/jmol/parser.ts b/src/mol-script/transpilers/jmol/parser.ts
index bc814ed93..9af92200d 100644
--- a/src/mol-script/transpilers/jmol/parser.ts
+++ b/src/mol-script/transpilers/jmol/parser.ts
@@ -31,7 +31,7 @@ const valueOperators: OperatorList = [
rule: P.MonadicParser.regexp(/\s*(LIKE|>=|<=|=|!=|>|<)\s*/i, 1),
map: (op, e1, e2) => {
let expr;
- if (e1 === 'structure') {
+ 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)]);
diff --git a/src/mol-script/transpilers/jmol/properties.ts b/src/mol-script/transpilers/jmol/properties.ts
index f489c24d6..77fcf6792 100644
--- a/src/mol-script/transpilers/jmol/properties.ts
+++ b/src/mol-script/transpilers/jmol/properties.ts
@@ -13,7 +13,7 @@ const rePosInt = /[0-9]+/;
function str(x: string) { return x; }
-const structureDict: {[key: string]: string} = {
+const structureDict: { [key: string]: string } = {
none: 'none',
turn: 'turn',
sheet: 'beta',
diff --git a/src/mol-script/transpilers/pymol/keywords.ts b/src/mol-script/transpilers/pymol/keywords.ts
index 26ef52ef9..04471609f 100644
--- a/src/mol-script/transpilers/pymol/keywords.ts
+++ b/src/mol-script/transpilers/pymol/keywords.ts
@@ -18,36 +18,38 @@ const ResDict = {
const Backbone = {
nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*',
- "C2'", "C1'", "O4'", "O2'"],
+ "C2'", "C1'", "O4'", "O2'"],
protein: ['C', 'N', 'CA', 'O']
};
function backboneExpr() {
return B.struct.combinator.merge([
- B.struct.modifier.intersectBy(
- { 0: B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
+ B.struct.modifier.intersectBy({
+ 0: B.struct.generator.atomGroups({
+ 'residue-test': B.core.set.has([
B.core.type.set(ResDict.protein),
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([
+ 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')]) })
+ ])
}),
+ by: B.struct.generator.atomGroups({
+ 'atom-test': B.core.set.has([
+ B.core.type.set(Backbone.nucleic),
+ B.ammp('label_atom_id')])
+ })
+ }),
]);
}
@@ -98,13 +100,14 @@ export const keywords: KeywordDict = {
'@desc': 'Polymer non-backbone atoms (new in PyMOL 1.6.1)',
abbr: ['sc.'],
map: () => {
- return B.struct.modifier.exceptBy({
+ return B.struct.modifier.exceptBy({
'0': B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
+ 'residue-test': B.core.set.has([
B.core.type.set(ResDict.nucleic.concat(ResDict.protein)),
- B.ammp('label_comp_id')]) }),
+ B.ammp('label_comp_id')])
+ }),
by: backboneExpr()
- });
+ });
},
},
present: {
diff --git a/src/mol-script/transpilers/pymol/parser.ts b/src/mol-script/transpilers/pymol/parser.ts
index 43924f063..6f5ca1745 100644
--- a/src/mol-script/transpilers/pymol/parser.ts
+++ b/src/mol-script/transpilers/pymol/parser.ts
@@ -58,7 +58,7 @@ const lang = P.MonadicParser.createLanguage({
Expression: function (r: any) {
return P.MonadicParser.alt(
- r.Keywords,
+ r.Keywords,
r.AtomSelectionMacro.map(atomSelectionQuery),
r.NamedAtomProperties,
r.Pepseq,
diff --git a/src/mol-script/transpilers/pymol/properties.ts b/src/mol-script/transpilers/pymol/properties.ts
index cc3062cbd..0b318a5be 100644
--- a/src/mol-script/transpilers/pymol/properties.ts
+++ b/src/mol-script/transpilers/pymol/properties.ts
@@ -21,49 +21,49 @@ function listOrRangeMap(x: string) {
const pSplit = x.split('+').map(x => x.replace(/^["']|["']$/g, ''));
const res: number[] = [];
pSplit.forEach(x => {
- if (x.includes('-') && !x.startsWith('-')) {
- const [min, max] = x.split('-').map(x=>parseInt(x));
+ if (x.includes('-') && !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.includes('-') && x.startsWith('-') && x.match(/[0-9]+-[-0-9]+/)) {
+ } 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]);
+ max = -parseInt(x.split('-')[3]);
} else {
- max = parseInt(x.split('-')[2]);
+ max = parseInt(x.split('-')[2]);
}
for (let i = min; i <= max; i++) {
- res.push(i);
+ res.push(i);
}
- } else if (x.includes('-') && x.startsWith('-') && !x.match(/[0-9]+-[-0-9]+/)) {
+ } else if (x.includes('-') && x.startsWith('-') && !x.match(/[0-9]+-[-0-9]+/)) {
res.push(parseInt(x));
- } else {
+ } else {
res.push(parseInt(x));
- }
+ }
});
return res;
} else if (x.includes('-') && !x.includes('+')) {
const res: number[] = [];
if (!x.startsWith('-')) {
- const [min, max] = x.split('-').map(x=>parseInt(x));
+ const [min, max] = x.split('-').map(x => parseInt(x));
for (let i = min; i <= max; i++) {
res.push(i);
}
} else if (x.startsWith('-') && x.match(/[0-9]+-[-0-9]+/)) {
- const min = -parseInt(x.split('-')[1]);
- let max;
- if (x.includes('--')) {
+ const min = -parseInt(x.split('-')[1]);
+ let max;
+ if (x.includes('--')) {
max = -parseInt(x.split('-')[3]);
- } else {
+ } else {
max = parseInt(x.split('-')[2]);
- }
- for (let i = min; i <= max; i++) {
+ }
+ for (let i = min; i <= max; i++) {
res.push(i);
}
} else if (x.startsWith('-') && !x.match(/[0-9]+-[-0-9]+/)) {
- res.push(parseInt(x));
+ res.push(parseInt(x));
} else {
res.push(parseInt(x));
}
diff --git a/src/mol-script/transpilers/vmd/parser.ts b/src/mol-script/transpilers/vmd/parser.ts
index b79612248..eeecd0733 100644
--- a/src/mol-script/transpilers/vmd/parser.ts
+++ b/src/mol-script/transpilers/vmd/parser.ts
@@ -56,33 +56,33 @@ const valueOperators: OperatorList = [
rule: P.MonadicParser.alt(P.MonadicParser.regexp(/\s*(=~|==|>=|<=|=|!=|>|<)\s*/, 1), P.MonadicParser.whitespace.result('=')),
map: (op, e1, e2) => {
let expr;
- if (e1.head !== undefined) {
+ if (e1.head !== undefined) {
if (e1.head.name === 'structure-query.atom-property.macromolecular.secondary-structure-flags') {
- expr = B.core.flags.hasAny([e1, sstrucMap(e2)]);
+ expr = B.core.flags.hasAny([e1, sstrucMap(e2)]);
}
if (e1.head.name === 'core.type.regex') {
- expr = B.core.str.match([e1, B.core.type.str([e2])]);
+ expr = B.core.str.match([e1, B.core.type.str([e2])]);
}
- } else if (e2.head !== undefined) {
+ } else if (e2.head !== undefined) {
if (e2.head.name === 'structure-query.atom-property.macromolecular.secondary-structure-flags') {
- expr = B.core.flags.hasAny([e2, sstrucMap(e1)]);
+ expr = B.core.flags.hasAny([e2, sstrucMap(e1)]);
}
if (e2.head.name === 'core.type.regex') {
- expr = B.core.str.match([e2, B.core.type.str([e1])]);
+ expr = B.core.str.match([e2, B.core.type.str([e1])]);
}
- } else if (op === '=~') {
+ } else if (op === '=~') {
if (e1.head) {
- expr = B.core.str.match([
+ expr = B.core.str.match([
B.core.type.regex([`^${e2}$`, 'i']),
B.core.type.str([e1])
- ]);
+ ]);
} else {
- expr = B.core.str.match([
+ expr = B.core.str.match([
B.core.type.regex([`^${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);
@@ -179,7 +179,7 @@ const lang = P.MonadicParser.createLanguage({
test = rangeTest ? rangeTest : listTest;
}
- return B.struct.generator.atomGroups({ [h.testLevel(property)]: test });
+ return B.struct.generator.atomGroups({ [h.testLevel(property)]: test });
});
},
--
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