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Commit 278dcb88 authored by yakomaxa's avatar yakomaxa
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added all and polymer.protein to keywords of pymol

parent 2ccfdb12
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...@@ -16,11 +16,17 @@ const ResDict = { ...@@ -16,11 +16,17 @@ const ResDict = {
solvent: ['HOH', 'WAT', 'H20', 'TIP', 'SOL'] solvent: ['HOH', 'WAT', 'H20', 'TIP', 'SOL']
}; };
const Backbone = {
nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*'],
protein: ['C', 'N', 'CA', 'O']
};
export const keywords: KeywordDict = { export const keywords: KeywordDict = {
all: { all: {
'@desc': 'All atoms currently loaded into PyMOL', '@desc': 'All atoms currently loaded into PyMOL',
abbr: ['*'], abbr: ['*'],
map: () => B.struct.generator.atomGroups() map: () => B.struct.generator.all()
}, },
none: { none: {
'@desc': 'No atoms (empty selection)', '@desc': 'No atoms (empty selection)',
...@@ -57,10 +63,6 @@ export const keywords: KeywordDict = { ...@@ -57,10 +63,6 @@ export const keywords: KeywordDict = {
]) ])
}) })
}, },
backbone: {
'@desc': 'Polymer backbone atoms (new in PyMOL 1.6.1)',
abbr: ['bb.']
},
sidechain: { sidechain: {
'@desc': 'Polymer non-backbone atoms (new in PyMOL 1.6.1)', '@desc': 'Polymer non-backbone atoms (new in PyMOL 1.6.1)',
abbr: ['sc.'] abbr: ['sc.']
...@@ -198,5 +200,80 @@ export const keywords: KeywordDict = { ...@@ -198,5 +200,80 @@ export const keywords: KeywordDict = {
}, },
metals: { metals: {
'@desc': 'All metal atoms (new in PyMOL 1.6.1)' '@desc': 'All metal atoms (new in PyMOL 1.6.1)'
},
backbone: {
'@desc': 'the C, N, CA, and O atoms of a protein and the equivalent atoms in a nucleic acid.',
map: () => backboneExpr()
},
protein: {
'@desc': 'protein',
abbr: ['polymer.protein'],
map: () => B.struct.generator.atomGroups({
'residue-test': B.core.set.has([
B.core.type.set(ResDict.protein),
B.ammp('label_comp_id')
])
})
} }
}; };
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')
])
});
}
function nucleicExpr() {
return B.struct.filter.pick({
0: B.struct.generator.atomGroups({
'group-by': B.ammp('residueKey')
}),
test: B.core.logic.and([
B.core.set.isSubset([
// B.core.type.set([ 'P', 'O1P', 'O2P' ]),
h.atomNameSet(['P']),
B.ammpSet('label_atom_id')
]),
B.core.logic.or([
B.core.set.isSubset([
h.atomNameSet(["O3'", "C3'", "C4'", "C5'", "O5'"]),
B.ammpSet('label_atom_id')
]),
B.core.set.isSubset([
h.atomNameSet(['O3*', 'C3*', 'C4*', 'C5*', 'O5*']),
B.ammpSet('label_atom_id')
])
])
])
});
}
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