From 6dabe7300212065966328e0bc14f76ace1807dff Mon Sep 17 00:00:00 2001
From: yakomaxa <47655565+yakomaxa@users.noreply.github.com>
Date: Tue, 23 Aug 2022 17:16:10 +0900
Subject: [PATCH] Update pymol keywords and properties
---
src/mol-script/transpilers/pymol/keywords.ts | 60 +++++++++++++++----
.../transpilers/pymol/properties.ts | 6 ++
2 files changed, 54 insertions(+), 12 deletions(-)
diff --git a/src/mol-script/transpilers/pymol/keywords.ts b/src/mol-script/transpilers/pymol/keywords.ts
index e26990a41..556544447 100644
--- a/src/mol-script/transpilers/pymol/keywords.ts
+++ b/src/mol-script/transpilers/pymol/keywords.ts
@@ -17,10 +17,41 @@ const ResDict = {
};
const Backbone = {
- nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*'],
+ nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*',
+ "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.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([
+ 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 = {
all: {
@@ -65,6 +96,15 @@ export const keywords: KeywordDict = {
},
sidechain: {
'@desc': 'Polymer non-backbone atoms (new in PyMOL 1.6.1)',
+ abbr:['sc.'],
+ map: () => {
+ return B.struct.modifier.exceptBy({
+ '0': B.struct.generator.atomGroups({
+ 'residue-test': B.core.set.has([
+ B.core.type.set(ResDict.nucleic.concat(ResDict.protein)),
+ B.ammp('label_comp_id')])}),
+ by: backboneExpr()
+ })},
},
present: {
'@desc': 'All atoms with defined coordinates in the current state (used in creating movies)',
@@ -202,15 +242,11 @@ export const keywords: KeywordDict = {
},
backbone: {
'@desc': 'the C, N, CA, and O atoms of a protein and the equivalent atoms in a nucleic acid.',
- map: () => B.struct.generator.atomGroups({
- 'atom-test': B.core.set.has([
- B.core.type.set(Backbone.protein.concat(ResDict.protein)),
- B.ammp('label_atom_id')
- ])
- }),
- },
- proteinxxxxxx: {
- '@desc': 'protein................',
+ abbr: ['bb.'],
+ map: () => backboneExpr()
+ },
+ 'bFCLHMz55tjm16c9': {
+ '@desc': 'protein',
abbr: ['polymer.protein'],
map: () => B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
@@ -219,8 +255,8 @@ export const keywords: KeywordDict = {
])
})
},
- nucleicxxxxx: {
- '@desc': 'protein................',
+ 'bFCLHMz55tjm16c0': {
+ '@desc': 'nucleic acid',
abbr: ['polymer.nucleic'],
map: () => B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
diff --git a/src/mol-script/transpilers/pymol/properties.ts b/src/mol-script/transpilers/pymol/properties.ts
index 7b29db7bf..5b405187b 100644
--- a/src/mol-script/transpilers/pymol/properties.ts
+++ b/src/mol-script/transpilers/pymol/properties.ts
@@ -203,5 +203,11 @@ export const properties: PropertyDict = {
isNumeric: true,
abbr: ['pc.'], regex: reFloat, map: x => parseFloat(x),
level: 'atom-test'
+ },
+ elem: {
+ '@desc': 'str atomic element symbol string ("X" if undefined)',
+ '@examples': ['elem N'],
+ regex: /[a-zA-Z0-9]{1,3}/, map: x => B.es(x),
+ level: 'atom-test', property: B.acp('elementSymbol')
}
};
--
GitLab