add common non-standard amino-acids

src/mol-model-formats/structure/common/component.ts

@@ -54,6 +54,12 @@ const StandardComponents = (function() {
         { id: 'SEC', name: 'SELENOCYSTEINE', type: 'L-peptide linking' },
         { id: 'PYL', name: 'PYRROLYSINE', type: 'L-peptide linking' },
 
+        { id: 'MSE', name: 'SELENOMETHIONINE', type: 'L-peptide linking' },
+        { id: 'SEP', name: 'PHOSPHOSERINE', type: 'L-peptide linking' },
+        { id: 'TPO', name: 'PHOSPHOTHREONINE', type: 'L-peptide linking' },
+        { id: 'PTR', name: 'O-PHOSPHOTYROSINE', type: 'L-peptide linking' },
+        { id: 'PCA', name: 'PYROGLUTAMIC ACID', type: 'L-peptide linking' },
+
         { id: 'A', name: 'ADENOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
         { id: 'C', name: 'CYTIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
         { id: 'T', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },

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

@@ -245,7 +245,9 @@ export const WaterNames = new Set([
 export const AminoAcidNamesL = new Set([
     'HIS', 'ARG', 'LYS', 'ILE', 'PHE', 'LEU', 'TRP', 'ALA', 'MET', 'PRO', 'CYS',
     'ASN', 'VAL', 'GLY', 'SER', 'GLN', 'TYR', 'ASP', 'GLU', 'THR', 'SEC', 'PYL',
-    'UNK' // unknown amino acid from CCD
+    'UNK', // unknown amino acid from CCD
+    'MSE', 'SEP', 'TPO', 'PTR', 'PCA' // common
+
 ]);
 export const AminoAcidNamesD = new Set([
     'DAL', // D-ALANINE