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Commit b4bde3f5 authored by yakomaxa's avatar yakomaxa
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Rasmol parser WIP 5

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src/mol-script/transpilers/pymol/properties.ts
+ 1
− 1
View file @ b4bde3f5
......@@ -32,7 +32,7 @@ function listOrRangeMap(x: string) {
res.push(parseInt(x));
}
});
console.log(res)
// console.log(res)
return res;
}else if(x.includes('-') && !x.includes('+')){
return rangeMap(x)
......
src/mol-script/transpilers/rasmol/special_properties.ts
+ 13
− 87
View file @ b4bde3f5
......@@ -12,15 +12,15 @@ import { PropertyDict } from '../types';
const reFloat = /[-+]?[0-9]*\.?[0-9]+/;
// const rePosInt = /[0-9]+/;
function atomNameListMap(x: string) { return x.split('+').map(B.atomName); }
function listMap(x: string) { return x.split('+').map(x => x.replace(/^["']|["']$/g, '')); }
function atomNameListMap(x: string) { return x.split(',').map(B.atomName); }
function listMap(x: string) { return x.split(',').map(x => x.replace(/^["']|["']$/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(/^["']|["']$/g, ''));
if (x.includes('-') && x.includes(',')){
const pSplit = x.split(',').map(x => x.replace(/^["']|["']$/g, ''));
const res : number[] =[];
pSplit.forEach( x => {
if (x.includes('-')){
......@@ -32,11 +32,11 @@ function listOrRangeMap(x: string) {
res.push(parseInt(x));
}
});
console.log(res)
// console.log(res)
return res;
}else if(x.includes('-') && !x.includes('+')){
}else if(x.includes('-') && !x.includes(',')){
return rangeMap(x)
}else if(!x.includes('-') && x.includes('+')){
}else if(!x.includes('-') && x.includes(',')){
return listMap(x)
}
}
......@@ -61,112 +61,38 @@ export const special_properties: 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,
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,
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,
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,
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,
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,
abbr: ['c.'], regex: /[a-zA-Z0-9'",]+/, map: listMap,
level: 'chain-test', property: B.ammp('auth_asym_id')
},
segi: {
'@desc': 'segment-identifier-list list of up to 4 letter identifiers',
'@examples': ['segi lig'],
abbr: ['segid', 's.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
level: 'chain-test', property: B.ammp('label_asym_id')
},
flag: {
'@desc': 'flag-number a single integer from 0 to 31',
'@examples': ['flag 0'],
isUnsupported: true,
abbr: ['f.'], regex: /[0-9]+/, map: x => parseInt(x),
level: 'atom-test'
},
numeric_type: {
'@desc': 'type-number a single integer',
'@examples': ['nt. 5'],
isUnsupported: true,
abbr: ['nt.'], regex: /[0-9]+/, map: x => parseInt(x),
level: 'atom-test'
},
text_type: {
'@desc': 'type-string a list of up to 4 letter codes',
'@examples': ['text_type HA+HC'],
isUnsupported: true,
abbr: ['tt.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
level: 'atom-test'
},
id: {
'@desc': 'external-index-number a single integer',
'@examples': ['id 23'],
regex: /[0-9+-]+/, map: listOrRangeMap,
level: 'atom-test', property: B.ammp('id')
},
index: {
'@desc': 'internal-index-number a single integer',
'@examples': ['index 11'],
regex: /[0-9+-]+/, map: listOrRangeMap,
level: 'atom-test', property: B.ammp('id')
},
ss: {
'@desc': 'secondary-structure-type list of single letters. Helical regions should be assigned H and sheet regions S. Loop regions can either be assigned L or be blank.',
'@examples': ['ss H+S+L', 'ss S+""'],
abbr: [], regex: /[a-zA-Z'"+]+/, map: sstrucListMap,
level: 'residue-test', property: B.ammp('secondaryStructureFlags')
},
b: {
'@desc': 'comparison-operator b-factor-value a real number',
'@examples': ['b > 10'],
isNumeric: true,
abbr: [], regex: reFloat, map: x => parseFloat(x),
level: 'atom-test', property: B.ammp('B_iso_or_equiv')
},
q: {
'@desc': 'comparison-operator occupancy-value a real number',
'@examples': ['q <0.50'],
isNumeric: true,
abbr: [], regex: reFloat, map: x => parseFloat(x),
level: 'atom-test', property: B.ammp('occupancy')
},
formal_charge: {
'@desc': 'comparison-operator formal charge-value an integer',
'@examples': ['fc. = -1'],
isNumeric: true,
abbr: ['fc.'], regex: reFloat, map: x => parseFloat(x),
level: 'atom-test', property: B.ammp('pdbx_formal_charge')
},
partial_charge: {
'@desc': 'comparison-operator partial charge-value a real number',
'@examples': ['pc. > 1'],
isUnsupported: true,
isNumeric: true,
abbr: ['pc.'], regex: reFloat, map: x => parseFloat(x),
level: 'atom-test'
}
};
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