From 7a61fd44fda2cac2e7996cd9ec23b20542c34a98 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Wed, 7 Sep 2022 18:32:43 -0700
Subject: [PATCH] remove rasmol transpiler
- functionallity integrated into jmol transpiler
---
CHANGELOG.md | 2 +-
src/mol-plugin-ui/controls/parameters.tsx | 2 +-
src/mol-script/script.ts | 2 -
.../transpilers/_spec/examples.spec.ts | 1 -
.../transpilers/_spec/rasmol.spec.ts | 64 ---
src/mol-script/transpilers/all.ts | 2 -
src/mol-script/transpilers/rasmol/examples.ts | 39 --
src/mol-script/transpilers/rasmol/keywords.ts | 390 ------------------
.../transpilers/rasmol/macroproperties.ts | 82 ----
.../transpilers/rasmol/markdown-docs.ts | 61 ---
.../transpilers/rasmol/operators.ts | 58 ---
src/mol-script/transpilers/rasmol/parser.ts | 387 -----------------
.../transpilers/rasmol/properties.ts | 131 ------
src/mol-script/transpilers/rasmol/symbols.ts | 38 --
14 files changed, 2 insertions(+), 1257 deletions(-)
delete mode 100644 src/mol-script/transpilers/_spec/rasmol.spec.ts
delete mode 100644 src/mol-script/transpilers/rasmol/examples.ts
delete mode 100644 src/mol-script/transpilers/rasmol/keywords.ts
delete mode 100644 src/mol-script/transpilers/rasmol/macroproperties.ts
delete mode 100644 src/mol-script/transpilers/rasmol/markdown-docs.ts
delete mode 100644 src/mol-script/transpilers/rasmol/operators.ts
delete mode 100644 src/mol-script/transpilers/rasmol/parser.ts
delete mode 100644 src/mol-script/transpilers/rasmol/properties.ts
delete mode 100644 src/mol-script/transpilers/rasmol/symbols.ts
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 105f71e7d..626de8e21 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Add custom labels to Confal pyramids
- Improve naming of some internal types in Confal pyramids extension coordinate
- Add example mmCIF file with categories necessary to display Confal pyramids
-- [Experimental] Add support for PyMOL, VMD, Jmol and RasMol atom expressions in selection scripts
+- [Experimental] Add support for PyMOL, VMD, and Jmol atom expressions in selection scripts
## [v3.13.0] - 2022-07-24
diff --git a/src/mol-plugin-ui/controls/parameters.tsx b/src/mol-plugin-ui/controls/parameters.tsx
index 46d78ae8c..4a5980197 100644
--- a/src/mol-plugin-ui/controls/parameters.tsx
+++ b/src/mol-plugin-ui/controls/parameters.tsx
@@ -1496,7 +1496,7 @@ export class ScriptControl extends React.PureComponent<ParamProps<PD.Script>> {
return <>
{select}
{this.props.value.language !== 'mol-script' && <div className='msp-help-text' style={{ padding: '10px' }}>
- <Icon svg={WarningSvg} /> Support for PyMOL, VMD, Jmol, and RasMol selections is an experimental feature and may not always work as intended.
+ <Icon svg={WarningSvg} /> Support for PyMOL, VMD, and Jmol selections is an experimental feature and may not always work as intended.
</div>}
{text}
</>;
diff --git a/src/mol-script/script.ts b/src/mol-script/script.ts
index a1e4e5d32..7497f49b8 100644
--- a/src/mol-script/script.ts
+++ b/src/mol-script/script.ts
@@ -27,7 +27,6 @@ namespace Script {
'pymol': 'PyMOL',
'vmd': 'VMD',
'jmol': 'Jmol',
- 'rasmol': 'RasMol'
};
export type Language = keyof typeof Info;
@@ -48,7 +47,6 @@ namespace Script {
case 'pymol':
case 'jmol':
case 'vmd':
- case 'rasmol':
return parse(script.language, script.expression);
default:
assertUnreachable(script.language);
diff --git a/src/mol-script/transpilers/_spec/examples.spec.ts b/src/mol-script/transpilers/_spec/examples.spec.ts
index 23ff1930b..ca45ce7e2 100644
--- a/src/mol-script/transpilers/_spec/examples.spec.ts
+++ b/src/mol-script/transpilers/_spec/examples.spec.ts
@@ -24,4 +24,3 @@ function testTranspilerExamples(name: string, transpiler: Transpiler) {
testTranspilerExamples('pymol', transpilers.pymol);
testTranspilerExamples('vmd', transpilers.vmd);
testTranspilerExamples('jmol', transpilers.jmol);
-testTranspilerExamples('rasmol', transpilers.rasmol);
diff --git a/src/mol-script/transpilers/_spec/rasmol.spec.ts b/src/mol-script/transpilers/_spec/rasmol.spec.ts
deleted file mode 100644
index 87865f3e3..000000000
--- a/src/mol-script/transpilers/_spec/rasmol.spec.ts
+++ /dev/null
@@ -1,64 +0,0 @@
-/**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
- */
-
-import * as u from './utils';
-import { transpiler } from '../rasmol/parser';
-import { keywords } from '../rasmol/keywords';
-import { properties } from '../rasmol/properties';
-import { operators } from '../rasmol/operators';
-
-const general = {
- supported: [
- // value comparison
- 'resno > 10',
- // atom expression
- '[LEU]100:A.CA',
- '[LEU]100:A',
- '[LEU]100:.CA',
- '[LEU]:A.CA',
- '[LEU].CA',
- // residue numbering
- '(1-10,15,21-30)',
- // within with parentheses
- '( within(5,[HEM]) ) and backbone',
- // trimming
- '[ALA] and [VAL] ',
- ' [ALA] and [VAL] ',
- ' [ALA] and [VAL]',
- // within with whitespaces
- 'within ( 5 , [HEM] ) ',
- // un-braketed residue name
- 'LEU and ILE',
- // un-parenthesized residue index range
- '100-120,220',
- // un-parenthesized residue index
- '20',
- // within in the head or the middle of sentence
- 'within ( 5 , [HEM] ) and backbone',
- ],
- unsupported: [
- ]
-};
-
-describe('rasmol general', () => {
- general.supported.forEach(str => {
- it(str, () => {
- transpiler(str);
- // compile(expr);
- });
- });
- general.unsupported.forEach(str => {
- it(str, () => {
- const transpileStr = () => transpiler(str);
- expect(transpileStr).toThrow();
- expect(transpileStr).not.toThrowError(RangeError);
- });
- });
-});
-
-describe('rasmol keywords', () => u.testKeywords(keywords, transpiler));
-describe('rasmol operators', () => u.testOperators(operators, transpiler));
-describe('rasmol properties', () => u.testProperties(properties, transpiler));
diff --git a/src/mol-script/transpilers/all.ts b/src/mol-script/transpilers/all.ts
index ad3f967f7..b1434278e 100644
--- a/src/mol-script/transpilers/all.ts
+++ b/src/mol-script/transpilers/all.ts
@@ -7,11 +7,9 @@
import { transpiler as jmol } from './jmol/parser';
import { transpiler as pymol } from './pymol/parser';
import { transpiler as vmd } from './vmd/parser';
-import { transpiler as rasmol } from './rasmol/parser';
export const _transpiler = {
pymol,
vmd,
jmol,
- rasmol
};
diff --git a/src/mol-script/transpilers/rasmol/examples.ts b/src/mol-script/transpilers/rasmol/examples.ts
deleted file mode 100644
index 2bfd3d6b9..000000000
--- a/src/mol-script/transpilers/rasmol/examples.ts
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- *
- */
-
-export const examples = [{
- name: 'Residue 50 or 135',
- value: '(50) or (135)'
-}, {
- name: 'Residue 50 or 135',
- value: '(50,135)'
-}, {
- name: 'Residue 20-22 or 8 or 2-16',
- value: '(20-22,8,2-16)'
-}, {
- name: 'Residue with the index more than 10',
- value: 'resno > 10'
-}, {
- name: 'Atoms assinged as backbone of protein or nucleic acid',
- value: 'backbone'
-}, {
- name: 'ALA, LEU, or aromatic residue within 10 angstrom from HEM ',
- value: '( [ALA] or [LEU] or aromatic ) and within( 10.0 ,[HEM])'
-}, {
- name: 'Residue within 10 angstrom from HEM but not HEM',
- value: 'not [HEM] and within(5, [HEM])'
-}, {
- name: 'Residue within 10 angstrom from HEM but not HEM',
- value: '( within(5, [HEM]) ) and not [HEM]'
-}, {
- name: 'C-beta atom ALA10 in chain A or all C-alpha atoms or all CG atoms from LYS',
- value: '[ALA]10:A.CB or :.CA or [LYS].CG'
-}, {
- name: 'Pyrimidine residues',
- value: 'pyrimidine'
-}];
diff --git a/src/mol-script/transpilers/rasmol/keywords.ts b/src/mol-script/transpilers/rasmol/keywords.ts
deleted file mode 100644
index 170846455..000000000
--- a/src/mol-script/transpilers/rasmol/keywords.ts
+++ /dev/null
@@ -1,390 +0,0 @@
-/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
-**/
-
-
-import { MolScriptBuilder } from '../../../mol-script/language/builder';
-const B = MolScriptBuilder;
-import * as h from '../helper';
-import { KeywordDict } from '../types';
-
-const Backbone = {
- nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*'],
- protein: ['C', 'N', 'CA', 'O']
-};
-
-
-function nucleicExpr() {
- return B.struct.combinator.merge([
- B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
- B.core.type.set(['G', 'C', 'A', 'T', 'U', 'I', 'DG', 'DC', 'DA', 'DT', 'DU', 'DI', '+G', '+C', '+A', '+T', '+U', '+I']),
- B.ammp('label_comp_id')
- ])
- }),
- B.struct.filter.pick({
- 0: B.struct.generator.atomGroups({
- 'group-by': B.ammp('residueKey')
- }),
- test: B.core.logic.and([
- B.core.set.isSubset([
- h.atomNameSet(['P']),
- B.ammpSet('label_atom_id')
- ]),
- ])
- }),
- B.struct.filter.pick({
- 0: B.struct.generator.atomGroups({
- 'group-by': B.ammp('residueKey')
- }),
- test: B.core.logic.or([
- B.core.set.isSubset([
- h.atomNameSet(["C1'", "C2'", "O3'", "C3'", "C4'", "C5'", "O5'"]),
- B.ammpSet('label_atom_id')
- ]),
- B.core.set.isSubset([
- h.atomNameSet(['C1*', 'C2*', 'O3*', 'C3*', 'C4*', 'C5*', 'O5*']),
- B.ammpSet('label_atom_id')
- ])
- ])
- })
- ]);
-}
-
-
-
-const ResDict = {
- 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'],
- acidic: ['ASP', 'GLU'],
- 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: ['A', 'C', 'T', 'G', 'U', 'DA', 'DC', 'DT', 'DG', 'DU'],
- protein: ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'CYX', 'GLN', 'GLU', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'ILE', 'LEU', 'LYS', 'MET', 'MSE', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL'],
- solvent: ['HOH', 'WAT', 'H20', 'TIP', 'SOL']
-};
-
-
-export const keywords: KeywordDict = {
- // general terms
- all: {
- '@desc': 'all atoms; same as *',
- abbr: ['*'],
- map: () => B.struct.generator.all()
- },
- none: {
- '@desc': 'no atoms',
- map: () => B.struct.generator.empty()
- },
- selected: {
- '@desc': 'atoms that have been selected; defaults to all when a file is first loaded'
- },
- unitcell: {
- '@desc': 'atoms within the current unitcell, which may be offset. This includes atoms on the faces and at the vertices of the unitcell.'
- },
- ions: {
- '@desc': '(specifically the PDB designations "PO4" and "SO4")'
- },
- ligand: {
- '@desc': '(originally "hetero and not solvent"; changed to "!(protein,nucleic,water,UREA)" for Jmol 12.2)'
- },
- nucleic: {
- '@desc': 'any group that (a) has one of the following group names: G, C, A, T, U, I, DG, DC, DA, DT, DU, DI, +G, +C, +A, +T, +U, +I; or (b) can be identified as a group that is only one atom, with name "P"; or (c) has all of the following atoms (prime, \', can replace * here): C1*, C2*, C3*, O3*, C4*, C5*, and O5*.',
- map: () => nucleicExpr()
- },
- purine: {
- '@desc': 'any nucleic group that (a) has one of the following group names: A, G, I, DA, DG, DI, +A, +G, or +I; or (b) also has atoms N7, C8, and N9.',
- map: () => B.struct.modifier.intersectBy({
- 0: nucleicExpr(),
- by: B.struct.combinator.merge([
- B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
- B.set(...['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']),
- B.ammp('label_comp_id')
- ])
- }),
- B.struct.filter.pick({
- 0: B.struct.generator.atomGroups({
- 'group-by': B.ammp('residueKey')
- }),
- test: B.core.set.isSubset([
- h.atomNameSet(['N7', 'C8', 'N9']),
- B.ammpSet('label_atom_id')
- ])
- })
- ])
- })
- },
- pyrimidine: {
- '@desc': 'any nucleic group that (a) has one of the following group names: C, T, U, DC, DT, DU, +C, +T, +U; or (b) also has atom O2.',
- map: () => B.struct.modifier.intersectBy({
- 0: nucleicExpr(),
- by: B.struct.combinator.merge([
- B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
- B.set(...['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']),
- B.ammp('label_comp_id')
- ])
- }),
- B.struct.filter.pick({
- 0: B.struct.generator.atomGroups({
- 'group-by': B.ammp('residueKey')
- }),
- test: B.core.logic.or([
- B.core.set.has([
- B.ammpSet('label_atom_id'),
- B.atomName('O2*')
- ]),
- B.core.set.has([
- B.ammpSet('label_atom_id'),
- B.atomName("O2'")
- ])
- ])
- })
- ])
- })
- },
- dna: {
- '@desc': 'any nucleic group that (a) has one of the following group names: DG, DC, DA, DT, DU, DI, T, +G, +C, +A, +T; or (b) has neither atom O2* or O2\'.',
- map: () => B.struct.modifier.intersectBy({
- 0: nucleicExpr(),
- by: B.struct.combinator.merge([
- B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
- B.set(...['DG', 'DC', 'DA', 'DT', 'DU', 'DI', 'T', '+G', '+C', '+A', '+T']),
- B.ammp('label_comp_id')
- ])
- }),
- B.struct.filter.pick({
- 0: B.struct.generator.atomGroups({
- 'group-by': B.ammp('residueKey')
- }),
- test: B.core.logic.not([
- B.core.logic.or([
- B.core.set.has([
- B.ammpSet('label_atom_id'),
- B.atomName('O2*')
- ]),
- B.core.set.has([
- B.ammpSet('label_atom_id'),
- B.atomName("O2'")
- ])
- ])
- ])
- })
- ])
- })
- },
- rna: {
- '@desc': 'any nucleic group that (a) has one of the following group names: G, C, A, U, I, +U, +I; or (b) has atom O2* or O2\'.',
- map: () => B.struct.modifier.intersectBy({
- 0: nucleicExpr(),
- by: B.struct.combinator.merge([
- B.struct.generator.atomGroups({
- 'residue-test': B.core.set.has([
- B.set(...['G', 'C', 'A', 'U', 'I', '+U', '+I']),
- B.ammp('label_comp_id')
- ])
- }),
- B.struct.filter.pick({
- 0: B.struct.generator.atomGroups({
- 'group-by': B.ammp('residueKey')
- }),
- test: B.core.logic.or([
- B.core.set.has([
- B.ammpSet('label_atom_id'),
- B.atomName('O2*')
- ]),
- B.core.set.has([
- B.ammpSet('label_atom_id'),
- B.atomName("O2'")
- ])
- ])
- })
- ])
- })
- },
- 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).',
- map: () => proteinExpr()
- },
- acidic: {
- '@desc': 'ASP GLU',
- map: () => h.resnameExpr(ResDict.acidic)
- },
- acyclic: {
- '@desc': 'amino and not cyclic',
- map: () => B.struct.modifier.intersectBy({
- 0: h.resnameExpr(ResDict.amino),
- by: h.invertExpr(h.resnameExpr(ResDict.cyclic))
- })
- },
- aliphatic: {
- '@desc': 'ALA GLY ILE LEU VAL',
- map: () => h.resnameExpr(ResDict.aliphatic)
- },
- amino: {
- '@desc': 'all twenty standard amino acids, plus ASX, GLX, UNK',
- map: () => h.resnameExpr(ResDict.amino)
- },
- aromatic: {
- '@desc': 'HIS PHE TRP TYR (see also "isaromatic" for aromatic bonds)',
- map: () => h.resnameExpr(ResDict.aromatic)
- },
- basic: {
- '@desc': 'ARG HIS LYS',
- map: () => h.resnameExpr(ResDict.basic)
- },
- buried: {
- '@desc': 'ALA CYS ILE LEU MET PHE TRP VAL',
- map: () => h.resnameExpr(ResDict.buried)
- },
- charged: {
- '@desc': 'same as acidic or basic -- ASP GLU, ARG HIS LYS',
- map: () => h.resnameExpr(ResDict.acidic.concat(ResDict.basic))
- },
- cyclic: {
- '@desc': 'HIS PHE PRO TRP TYR',
- map: () => h.resnameExpr(ResDict.cyclic)
- },
- helix: {
- '@desc': 'secondary structure-related.',
- map: () => B.struct.generator.atomGroups({
- 'residue-test': B.core.flags.hasAny([
- B.struct.type.secondaryStructureFlags(['helix']),
- B.ammp('secondaryStructureFlags')
- ])
- })
- },
- hetero: {
- '@desc': 'PDB atoms designated as HETATM',
- map: () => B.struct.generator.atomGroups({
- 'atom-test': B.ammp('isHet')
- })
- },
- hydrophobic: {
- '@desc': 'ALA GLY ILE LEU MET PHE PRO TRP TYR VAL',
- map: () => h.resnameExpr(ResDict.hydrophobic)
- },
- large: {
- '@desc': 'ARG GLU GLN HIS ILE LEU LYS MET PHE TRP TYR',
- map: () => h.resnameExpr(ResDict.large)
- },
- medium: {
- '@desc': 'ASN ASP CYS PRO THR VAL',
- map: () => h.resnameExpr(ResDict.medium)
- },
- negative: {
- '@desc': 'same as acidic -- ASP GLU',
- map: () => h.resnameExpr(ResDict.acidic)
- },
- neutral: {
- '@desc': 'amino and not (acidic or basic)',
- map: () => B.struct.modifier.intersectBy({
- 0: h.resnameExpr(ResDict.amino),
- by: h.invertExpr(h.resnameExpr(ResDict.acidic.concat(ResDict.basic)))
- })
- },
- polar: {
- '@desc': 'amino and not hydrophobic',
- map: () => B.struct.modifier.intersectBy({
- 0: h.resnameExpr(ResDict.amino),
- by: h.invertExpr(h.resnameExpr(ResDict.hydrophobic))
- })
- },
- positive: {
- '@desc': 'same as basic -- ARG HIS LYS',
- map: () => h.resnameExpr(ResDict.basic)
- },
- sheet: {
- '@desc': 'secondary structure-related',
- map: () => B.struct.generator.atomGroups({
- 'residue-test': B.core.flags.hasAny([
- B.struct.type.secondaryStructureFlags(['sheet']),
- B.ammp('secondaryStructureFlags')
- ])
- })
- },
- small: {
- '@desc': 'ALA GLY SER',
- map: () => h.resnameExpr(ResDict.small)
- },
- turn: {
- '@desc': 'secondary structure-related',
- map: () => B.struct.generator.atomGroups({
- 'residue-test': B.core.flags.hasAny([
- B.struct.type.secondaryStructureFlags(['turn']),
- B.ammp('secondaryStructureFlags')
- ])
- })
- },
- alpha: {
- '@desc': '(*.CA)',
- map: () => B.struct.generator.atomGroups({
- 'atom-test': B.core.rel.eq([
- B.atomName('CA'),
- B.ammp('label_atom_id')
- ])
- })
- },
- base: {
- '@desc': '(nucleic bases)'
- },
- backbone: {
- '@desc': '(*.C, *.CA, *.N, and all nucleic other than the bases themselves)',
- abbr: ['mainchain'],
- map: () => backboneExpr()
- },
- sidechain: {
- '@desc': '((protein or nucleic) and not backbone)'
- },
- solvent: {
- '@desc': 'PDB "HOH", water, also the connected set of H-O-H in any model',
- map: () => h.resnameExpr(ResDict.solvent)
- },
-};
-
-function backboneExpr() {
- return B.struct.combinator.merge([
- B.struct.generator.queryInSelection({
- 0: proteinExpr(),
- query: B.struct.generator.atomGroups({
- 'atom-test': B.core.set.has([
- h.atomNameSet(Backbone.protein),
- B.ammp('label_atom_id')
- ])
- })
- }),
- B.struct.generator.queryInSelection({
- 0: nucleicExpr(),
- query: B.struct.generator.atomGroups({
- 'atom-test': B.core.set.has([
- h.atomNameSet(Backbone.nucleic),
- B.ammp('label_atom_id')
- ])
- })
- })
- ]);
-}
-
-function proteinExpr() {
- return B.struct.filter.pick({
- 0: B.struct.generator.atomGroups({
- 'group-by': B.ammp('residueKey')
- }),
- test: B.core.set.isSubset([
- h.atomNameSet(['C', 'N', 'CA', 'O']),
- B.ammpSet('label_atom_id')
- ])
- });
-}
-
diff --git a/src/mol-script/transpilers/rasmol/macroproperties.ts b/src/mol-script/transpilers/rasmol/macroproperties.ts
deleted file mode 100644
index f991e2ed9..000000000
--- a/src/mol-script/transpilers/rasmol/macroproperties.ts
+++ /dev/null
@@ -1,82 +0,0 @@
-/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
- */
-
-import { MolScriptBuilder } from '../../../mol-script/language/builder';
-const B = MolScriptBuilder;
-import { PropertyDict } from '../types';
-
-function atomNameListMap(x: string) { return x.split(',').map(B.atomName); }
-function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/g, '')); }
-function rangeMap(x: string) {
- const [min, max] = x.split('-').map(x => parseInt(x));
- return { min, max };
-}
-function listOrRangeMap(x: string) {
- if (x.includes('-') && x.includes(',')) {
- const pSplit = x.split(',').map(x => x.replace(/^["']|["']$/g, ''));
- const res: number[] = [];
- pSplit.forEach(x => {
- if (x.includes('-')) {
- const [min, max] = x.split('-').map(x=>parseInt(x));
- for (let i = min; i <= max; i++) {
- res.push(i);
- }
- } else {
- res.push(parseInt(x));
- }
- });
- return res;
- } else if (x.includes('-') && !x.includes(',')) {
- return rangeMap(x);
- } else if (!x.includes('-') && x.includes(',')) {
- return listMap(x).map(x => parseInt(x));
- } else {
- return parseInt(x);
- }
-}
-function elementListMap(x: string) {
- return x.split(',').map(B.struct.type.elementSymbol);
-}
-
-export const macroproperties: PropertyDict = {
- symbol: {
- '@desc': 'chemical-symbol-list: list of 1- or 2-letter chemical symbols from the periodic table',
- '@examples': ['symbol O+N'],
- abbr: ['e.'], regex: /[a-zA-Z'",]+/, map: elementListMap,
- level: 'atom-test', property: B.acp('elementSymbol')
- },
- name: {
- '@desc': 'atom-name-list: list of up to 4-letter codes for atoms in proteins or nucleic acids',
- '@examples': ['name CA+CB+CG+CD'],
- abbr: ['n.'], regex: /[a-zA-Z0-9'",]+/, map: atomNameListMap,
- level: 'atom-test', property: B.ammp('label_atom_id')
- },
- resn: {
- '@desc': 'residue-name-list: list of 3-letter codes for amino acids or list of up to 2-letter codes for nucleic acids',
- '@examples': ['resn ASP+GLU+ASN+GLN', 'resn A+G'],
- abbr: ['resname', 'r.'], regex: /[a-zA-Z0-9'",]+/, map: listMap,
- level: 'residue-test', property: B.ammp('label_comp_id')
- },
- resi: {
- '@desc': 'residue-identifier-list list of up to 4-digit residue numbers or residue-identifier-range',
- '@examples': ['resi 1+10+100+1000', 'resi 1-10'],
- abbr: ['resident', 'residue', 'resid', 'i.'], regex: /[0-9,-]+/, map: listOrRangeMap,
- level: 'residue-test', property: B.ammp('auth_seq_id')
- },
- alt: {
- '@desc': 'alternate-conformation-identifier-list list of single letters',
- '@examples': ['alt A+B', 'alt ""', 'alt ""+A'],
- abbr: [], regex: /[a-zA-Z0-9'",]+/, map: listMap,
- level: 'atom-test', property: B.ammp('label_alt_id')
- },
- chain: {
- '@desc': 'chain-identifier-list list of single letters or sometimes numbers',
- '@examples': ['chain A'],
- abbr: ['c.'], regex: /[a-zA-Z0-9'",]+/, map: listMap,
- level: 'chain-test', property: B.ammp('auth_asym_id')
- },
-
-};
diff --git a/src/mol-script/transpilers/rasmol/markdown-docs.ts b/src/mol-script/transpilers/rasmol/markdown-docs.ts
deleted file mode 100644
index ea4dc8203..000000000
--- a/src/mol-script/transpilers/rasmol/markdown-docs.ts
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
-*/
-
-import { properties } from './properties';
-import { operators } from './operators';
-import { keywords } from './keywords';
-
-
-const _docs: string[] = [
- 'RasMol',
- '============',
- '--------------------------------',
- ''
-];
-
-_docs.push(`## Properties\n\n`);
-_docs.push('--------------------------------\n');
-for (const name in properties) {
- if (properties[name].isUnsupported) continue;
-
- const names = [name];
- if (properties[name].abbr) names.push(...properties[name].abbr!);
- _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
-
- if (properties[name]['@desc']) {
- _docs.push(`*${properties[name]['@desc']}*\n`);
- }
-}
-
-_docs.push(`## Operators\n\n`);
-_docs.push('--------------------------------\n');
-operators.forEach(o => {
- if (o.isUnsupported) return;
-
- const names = [o.name];
- if (o.abbr) names.push(...o.abbr!);
- _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
-
- if (o['@desc']) {
- _docs.push(`*${o['@desc']}*\n`);
- }
-});
-
-_docs.push(`## Keywords\n\n`);
-_docs.push('--------------------------------\n');
-for (const name in keywords) {
- if (!keywords[name].map) continue;
-
- const names = [name];
- if (keywords[name].abbr) names.push(...keywords[name].abbr!);
- _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
-
- if (keywords[name]['@desc']) {
- _docs.push(`*${keywords[name]['@desc']}*\n`);
- }
-}
-
-export const docs = _docs.join('\n');
diff --git a/src/mol-script/transpilers/rasmol/operators.ts b/src/mol-script/transpilers/rasmol/operators.ts
deleted file mode 100644
index 8a1139af7..000000000
--- a/src/mol-script/transpilers/rasmol/operators.ts
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
- */
-
-
-import * as P from '../../../mol-util/monadic-parser';
-import * as h from '../helper';
-import { MolScriptBuilder } from '../../../mol-script/language/builder';
-const B = MolScriptBuilder;
-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]'],
- name: 'not',
- type: h.prefix,
- rule: P.MonadicParser.alt(P.MonadicParser.regex(/NOT/i).skip(P.MonadicParser.whitespace), P.MonadicParser.string('!').skip(P.MonadicParser.optWhitespace)),
- map: (op, selection) => h.invertExpr(selection),
- },
- {
- '@desc': 'Selects atoms included in both s1 and s2.',
- '@examples': ['[ASP] and :.CA'],
- name: 'and',
- type: h.binaryLeft,
- rule: P.MonadicParser.alt(h.infixOp(/AND|&/i)),
- map: (op, selection, by) => B.struct.modifier.intersectBy({ 0: selection, by })
- },
- {
- '@desc': 'Selects atoms included in either s1 or s2.',
- '@examples': ['[ASP] or [GLU]'],
- name: 'or',
- abbr: [','],
- type: h.binaryLeft,
- rule: P.MonadicParser.alt(h.infixOp(/OR|\||\|\||,/i)),
- map: (op, s1, s2) => B.struct.combinator.merge([s1, s2])
- },
-];
-
diff --git a/src/mol-script/transpilers/rasmol/parser.ts b/src/mol-script/transpilers/rasmol/parser.ts
deleted file mode 100644
index e44fce0e2..000000000
--- a/src/mol-script/transpilers/rasmol/parser.ts
+++ /dev/null
@@ -1,387 +0,0 @@
-/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
- **/
-
-
-import * as P from '../../../mol-util/monadic-parser';
-import * as h from '../helper';
-import { MolScriptBuilder } from '../../../mol-script/language/builder';
-const B = MolScriptBuilder;
-import { properties } from './properties';
-import { macroproperties } from './macroproperties';
-import { operators } from './operators';
-import { keywords } from './keywords';
-import { AtomGroupArgs } from '../types';
-import { Transpiler } from '../transpiler';
-
-
-function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/g, '')); }
-
-function listOrRangeMap(x: string) {
- // cases
- // case1: 1-100,200
- if (x.includes('-') && x.includes(',')) {
- const pSplit = x.split(',').map(x => x.replace(/^["']|["']$/g, ''));
- const res: number[] = [];
- pSplit.forEach(x => {
- if (x.includes('-') && !x.startsWith('-')) {
- 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]);
- 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 {
- 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));
- 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('--')) {
- 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(parseInt(x));
- } else {
- res.push(parseInt(x));
- }
- return res;
- } else if (!x.includes('-') && x.includes(',')) {
- return listMap(x).map(x => parseInt(x));
- } else {
- return [parseInt(x)];
- }
-}
-
-
-const propertiesDict = h.getPropertyRules(macroproperties);
-
-const dot = P.MonadicParser.string('.');
-const colon = P.MonadicParser.string(':');
-const star = P.MonadicParser.string('*');
-const commu = P.MonadicParser.string('[');
-const tator = P.MonadicParser.string(']');
-
-function orNull(rule: P.MonadicParser<any>) {
- return rule.or(P.MonadicParser.of(null));
-}
-
-function atomSelectionQuery2(x: any) {
- const tests: AtomGroupArgs = {};
- const props: { [k: string]: any[] } = {};
-
- for (const k in x) {
- const ps = macroproperties[k];
- if (!ps) {
- throw new Error(`property '${k}' not supported, value '${x[k]}'`);
- }
- if (x[k] === null) continue;
- if (!props[ps.level]) props[ps.level] = [];
- props[ps.level].push(x[k]);
- }
-
- for (const p in props) {
- tests[p] = h.andExpr(props[p]);
- }
-
- return B.struct.generator.atomGroups(tests);
-}
-
-function atomExpressionQuery(x: any[]) {
- const [resnorange, resno, 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) {
- resnorange.forEach((x: number) =>{
- resnoRangeProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), x]));
- });
- };
- if (resnoRangeProps.length) tests['residue-test'] = h.orExpr(resnoRangeProps);
-
- const resProps: any = [];
- if (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]));
- if (resProps.length) tests['residue-test'] = h.andExpr(resProps);
-
- const atomProps = [];
- if (atomname) atomProps.push(B.core.rel.eq([B.ammp('auth_atom_id'), atomname]));
- if (altloc) atomProps.push(B.core.rel.eq([B.ammp('label_alt_id'), altloc]));
- if (atomProps.length) tests['atom-test'] = h.andExpr(atomProps);
-
- return B.struct.generator.atomGroups(tests);
-}
-
-function resnorangeExpressionQuery(x: any[]) {
- const [resnorange, chainname] = x;
- 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) {
- resnorange.forEach((x: number) =>{
- resnoRangeProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), x]));
- });
- };
- if (resnoRangeProps.length) tests['residue-test'] = h.orExpr(resnoRangeProps);
-
- return B.struct.generator.atomGroups(tests);
-}
-
-
-const lang = P.MonadicParser.createLanguage({
-
- Integer: () => P.MonadicParser.regexp(/-?[0-9]+/).map(Number).desc('integer'),
-
- Parens: function (r: any) {
- return P.MonadicParser.alt(
- r.Parens,
- r.Operator,
- r.Expression
- ).wrap(P.MonadicParser.regexp(/\(\s*/), P.MonadicParser.regexp(/\s*\)/));
- },
-
- Expression: function (r: any) {
- return P.MonadicParser.alt(
- // order matters
- r.Keywords,
- r.NamedAtomProperties,
- r.AtomSelectionMacro.map(atomSelectionQuery2),
- r.AtomExpression.map(atomExpressionQuery),
- 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,
- );
- },
-
- // lys:a.ca -> resn lys and chain A and name ca
- // lys*a.ca -> resn lys and chain A and name ca
- //
- // :a.ca -> chain A and name ca
- // *a.ca -> chain A and name ca
- //
- // *.cg -> name ca
- // :.cg -> name ca
- AtomSelectionMacro: function (r: any) {
- return P.MonadicParser.alt(
- // :A.CA :.CA :A
- colon.then(P.MonadicParser.alt(
- P.MonadicParser.seq(
- orNull(propertiesDict.chain).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { chain: x[0], name: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.name).skip(dot)
- ).map(x => { return { name: x[0] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.chain)
- ).map(x => { return { chain: x[0] }; }),
- )),
- // *A.CA *.CA
- star.then(P.MonadicParser.alt(
- P.MonadicParser.seq(
- orNull(propertiesDict.chain).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { chain: x[0], name: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.name).skip(dot)
- ).map(x => { return { name: x[0] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.chain)
- ).map(x => { return { chain: x[0] }; }),
- )),
- // [lys]10:a.ca [lys]10:a [lys]10 [lys]10.ca
- // [lys]:a.ca [lys]:a [lys] [lys].ca
- commu.then(P.MonadicParser.alt(
- P.MonadicParser.alt(
- P.MonadicParser.alt(
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator),
- orNull(propertiesDict.resi).skip(colon),
- orNull(propertiesDict.chain).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { resn: x[0], resi: x[1], chain: x[2], name: x[3] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator),
- orNull(propertiesDict.resi).skip(colon),
- orNull(propertiesDict.chain)
- ).map(x => { return { resn: x[0], resi: x[1], chain: x[2] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator),
- orNull(propertiesDict.resi).skip(colon).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { resn: x[0], resi: x[1], name: x[2] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator),
- orNull(propertiesDict.resi).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { resn: x[0], resi: x[1], name: x[2] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator),
- orNull(propertiesDict.resi)
- ).map(x => { return { resn: x[0], resi: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator).skip(colon),
- orNull(propertiesDict.chain).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { resn: x[0], chain: x[1], name: x[2] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator).skip(star),
- orNull(propertiesDict.chain).skip(dot),
- orNull(propertiesDict.name)
- ).map(x => { return { resn: x[0], chain: x[1], name: x[2] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator).skip(colon),
- orNull(propertiesDict.chain),
- ).map(x => { return { resn: x[0], chain: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator).skip(star),
- orNull(propertiesDict.chain),
- ).map(x => { return { resn: x[0], chain: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator).skip(dot),
- orNull(propertiesDict.name),
- ).map(x => { return { resn: x[0], name: x[1] }; }),
- P.MonadicParser.seq(
- orNull(propertiesDict.resn).skip(tator),
- ).map(x => { return { resn: x[0] }; })
- )
- )
- )
- )
- );
- },
-
- ObjectProperty: () => {
- const w = h.getReservedWords(macroproperties, keywords, operators)
- .sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
- return P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i'));
- },
-
- Object: (r: any) => {
- return r.ObjectProperty
- .map((x: any) => { throw new Error(`property 'object' not supported, value '${x}'`); });
- },
-
-
- ObjectProperty2: () => {
- const w = h.getReservedWords(properties, keywords, operators)
- .sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
- return P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i'));
- },
-
- Object2: (r: any) => {
- return r.ObjectProperty2
- .map((x: any) => { throw new Error(`property 'object' not supported, value '${x}'`); });
- },
-
- NamedAtomProperties: function () {
- return P.MonadicParser.alt(...h.getNamedPropertyRules(properties));
- },
-
- Operator: function (r: any) {
- return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression, r.Operator));
- },
-
- AtomExpression: function (r: any) {
- return P.MonadicParser.seq(
- P.MonadicParser.lookahead(r.AtomPrefix),
- P.MonadicParser.seq(
- r.ResnoRange.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)),
- r.Altloc.or(P.MonadicParser.of(null)),
- r.Model.or(P.MonadicParser.of(null))
- )
- );
- },
-
- ResnoRangeExpression: function (r: any) {
- 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-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'),
- Resname: () => P.MonadicParser.regexp(/[A-Z0-9]{1,4}/).desc('resname'),
- Resno: (r: any) => r.Integer.desc('resno'),
- Altloc: () => P.MonadicParser.regexp(/%([a-zA-Z0-9])/, 1).desc('altloc'),
- Inscode: () => P.MonadicParser.regexp(/\^([a-zA-Z0-9])/, 1).desc('inscode'),
-
- Number: function () {
- return P.MonadicParser.regexp(/-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/)
- .map(Number)
- .desc('number');
- },
-
-
- ResnoRange: function (r: any) {
- return P.MonadicParser.regex(/-?[0-9,-]+/).map(listOrRangeMap).desc('resnorange');
- // // 123-200
- // // -12--3
- },
-
- Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)),
-
- Query: function (r: any) {
- return P.MonadicParser.alt(
- r.Operator,
- r.Parens,
- r.Expression
- ).trim(P.MonadicParser.optWhitespace);
- }
-
-});
-
-export const transpiler: Transpiler = str => lang.Query.tryParse(str);
diff --git a/src/mol-script/transpilers/rasmol/properties.ts b/src/mol-script/transpilers/rasmol/properties.ts
deleted file mode 100644
index 37ed627bc..000000000
--- a/src/mol-script/transpilers/rasmol/properties.ts
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
-*/
-
-import { MolScriptBuilder } from '../../../mol-script/language/builder';
-const B = MolScriptBuilder;
-import { PropertyDict } from '../types';
-
-const reFloat = /[-+]?[0-9]*\.?[0-9]+/;
-const rePosInt = /[0-9]+/;
-
-export function sstrucMap(x: string) {
- return B.struct.type.secondaryStructureFlags(
- [structureDict[x.toUpperCase()] || 'none']
- );
-}
-
-
-export const structureDict: {[key: string]: string} = {
- none: 'none',
- turn: 'turn',
- sheet: 'beta',
- helix: 'helix',
- dna: 'dna',
- rna: 'rna',
-
- 0: 'none',
- 1: 'turn',
- 2: 'beta',
- 3: 'helix',
- 4: 'dna',
- 5: 'rna',
- 6: 'carbohydrate',
- 7: '3-10',
- 8: 'alpha',
- 9: 'pi',
-};
-export function structureMap(x: any) {
- if (x.head && x.head === 'core.type.regex') x = x.args[0].replace(/^\^|\$$/g, '');
- x = structureDict[x.toString().toLowerCase()] || 'none';
- if (['dna', 'rna', 'carbohydrate'].indexOf(x) !== -1) {
- throw new Error("values 'dna', 'rna', 'carbohydrate' not yet supported for 'structure' property");
- } else {
- return B.struct.type.secondaryStructureFlags([x]);
- }
-}
-
-export const properties: PropertyDict = {
- atomno: {
- '@desc': 'sequential number; you can use "@" instead of "atomno=" -- for example, select @33 or Var x = @33 or @35',
- '@examples': ['atomno = 10'],
- isNumeric: true,
- regex: rePosInt, map: x => parseInt(x),
- level: 'atom-test', property: B.ammp('id')
- },
- atomX: {
- '@desc': 'Cartesian X coordinate (or just X)',
- '@examples': ['x = 4.2'],
- abbr: ['X'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.acp('x')
- },
- atomY: {
- '@desc': 'Cartesian Y coordinate (or just Y)',
- '@examples': ['y < 42'],
- abbr: ['Y'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.acp('y')
- },
- atomZ: {
- '@desc': 'Cartesian Z coordinate (or just Z)',
- '@examples': ['Z > 10'],
- abbr: ['Z'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.acp('z')
- },
- elemno: {
- '@desc': 'atomic element number',
- '@examples': ['elemno=8'],
- isNumeric: true,
- regex: /[0-9\s{}-]+/, map: x => parseInt(x),
- level: 'atom-test', property: B.acp('atomicNumber')
- },
- formalCharge: {
- '@desc': 'formal charge',
- '@examples': ['formalCharge=1'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.ammp('pdbx_formal_charge')
- },
- mass: {
- '@desc': 'atomic mass -- especially useful with appended .max or .sum',
- '@examples': ['mass > 13'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.acp('mass')
- },
- occupancy: {
- '@desc': 'CIF file site occupancy. In SELECT command comparisons ("select occupancy < 90"), an integer n implies measurement on a 0-100 scale; also, in the context %[occupancy] or %q for a label, the reported number is a percentage. In all other cases, such as when %Q is used in a label or when a decimal number is used in a comparison, the scale is 0.0 - 1.0.',
- '@examples': ['occupancy < 1'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.ammp('occupancy')
- },
- resno: {
- '@desc': 'PDB residue number, not including insertion code (see also seqcode, below)',
- '@examples': ['resno = 100'],
- isNumeric: true,
- regex: /-?[0-9]+/, map: x => parseInt(x),
- level: 'residue-test', property: B.ammp('auth_seq_id')
- },
- temperature: {
- '@desc': 'yes yes temperature factor (B-factor)',
- '@examples': ['temperature >= 20'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.ammp('B_iso_or_equiv')
- },
- vanderwaals: {
- '@desc': 'van der Waals radius',
- '@examples': ['vanderwaals >2'],
- isNumeric: true,
- regex: reFloat, map: x => parseFloat(x),
- level: 'atom-test', property: B.acp('vdw')
- },
-};
diff --git a/src/mol-script/transpilers/rasmol/symbols.ts b/src/mol-script/transpilers/rasmol/symbols.ts
deleted file mode 100644
index a13dbb288..000000000
--- a/src/mol-script/transpilers/rasmol/symbols.ts
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Koya Sakuma <koya.sakuma.work@gmail.com>
-*/
-
-import { properties } from './properties';
-import { macroproperties } from './macroproperties';
-import { operators } from './operators';
-import { keywords } from './keywords';
-
-export const Properties: string[] = [];
-for (const name in properties) {
- if (properties[name].isUnsupported) continue;
- Properties.push(name);
- if (properties[name].abbr) Properties.push(...properties[name].abbr!);
-}
-for (const name in macroproperties) {
- if (macroproperties[name].isUnsupported) continue;
- Properties.push(name);
- if (macroproperties[name].abbr) Properties.push(...macroproperties[name].abbr!);
-}
-
-export const Operators: string[] = [];
-operators.forEach(o => {
- if (o.isUnsupported) return;
- Operators.push(o.name);
- if (o.abbr) Operators.push(...o.abbr);
-});
-
-export const Keywords: string[] = [];
-for (const name in keywords) {
- if (!keywords[name].map) continue;
- Keywords.push(name);
- if (keywords[name].abbr) Keywords.push(...keywords[name].abbr!);
-}
-
-export const _all = { Properties, Operators, Keywords };
--
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