improve peptide entity-subtype derivation

src/mol-model-formats/structure/basic/schema.ts

@@ -24,9 +24,9 @@ export type ChemComp = Table<mmCIF_chemComp_schema>
 export type ChemCompIdentifier = Table<mmCIF_Schema['pdbx_chem_comp_identifier']>
 export type AtomSite = Table<mmCIF_Schema['atom_site']>
 export type IhmSphereObjSite = Table<mmCIF_Schema['ihm_sphere_obj_site']>
-export type IhmGaussianObjSite =Table<mmCIF_Schema['ihm_gaussian_obj_site']>
-export type UnobsOrZeroOccResidues =Table<mmCIF_Schema['pdbx_unobs_or_zero_occ_residues']>
-export type Molecule =Table<mmCIF_Schema['pdbx_molecule']>
+export type IhmGaussianObjSite = Table<mmCIF_Schema['ihm_gaussian_obj_site']>
+export type UnobsOrZeroOccResidues = Table<mmCIF_Schema['pdbx_unobs_or_zero_occ_residues']>
+export type Molecule = Table<mmCIF_Schema['pdbx_molecule']>
 
 export const BasicSchema = {
     entry: mmCIF_Schema.entry,

src/mol-model/structure/model/properties/common.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -14,7 +14,8 @@ export type EntitySubtype = (
     mmCIF_Schema['entity_poly']['type']['T'] |
     mmCIF_Schema['pdbx_entity_branch']['type']['T'] |
     'ion' |
-    'lipid'
+    'lipid' |
+    'peptide-like'
 )
 export const EntitySubtype = Column.Schema.Aliased<EntitySubtype>(Column.Schema.Str(''));
 

src/mol-model/structure/model/types.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -192,7 +192,7 @@ export const ProteinTerminusComponentTypeNames = new Set([
     'L-PEPTIDE NH3 AMINO TERMINUS', 'L-PEPTIDE COOH CARBOXY TERMINUS'
 ]);
 
-/** Chemical component type names for pepdite-like protein */
+/** Chemical component type names for peptide-like protein */
 export const OtherProteinComponentTypeNames = new Set([
     'PEPTIDE LINKING', 'PEPTIDE-LIKE',
 ]);
@@ -416,6 +416,8 @@ export function getEntitySubtype(compId: string, compType: string): EntitySubtyp
         return 'ion';
     } else if (LipidComponentTypeNames.has(compType) || LipidNames.has(compId)) {
         return 'lipid';
+    } else if (OtherProteinComponentTypeNames.has(compType)) {
+        return 'peptide-like';
     } else {
         return 'other';
     }

src/mol-plugin-state/helpers/structure-selection-query.ts

@@ -92,7 +92,7 @@ const polymer = StructureSelectionQuery('Polymer', MS.struct.modifier.union([
         'entity-test': MS.core.logic.and([
             MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
             MS.core.str.match([
-                MS.re('(polypeptide|cyclic-pseudo-peptide|nucleotide|peptide nucleic acid)', 'i'),
+                MS.re('(polypeptide|cyclic-pseudo-peptide|peptide-like|nucleotide|peptide nucleic acid)', 'i'),
                 MS.ammp('entitySubtype')
             ])
         ])
@@ -122,7 +122,7 @@ const trace = StructureSelectionQuery('Trace', MS.struct.modifier.union([
 const _proteinEntityTest = MS.core.logic.and([
     MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
     MS.core.str.match([
-        MS.re('(polypeptide|cyclic-pseudo-peptide)', 'i'),
+        MS.re('(polypeptide|cyclic-pseudo-peptide|peptide-like)', 'i'),
         MS.ammp('entitySubtype')
     ])
 ]);