def test_l_peptide_chem_comp(self):
"""Test LPeptideChemComp class"""
cc1 = ihm.LPeptideChemComp(id='MET', code='M', code_canonical='M')
self.assertEqual(cc1.type, 'L-peptide linking')
# IHM contains definitions for standard amino and nucleic acids, plus
# a few common non-standard residues such as MSE and UNK.
# To create a new non-standard residue, we first need to create a chemical
# component for it. In this case, we add a definition for norvaline, an
# isomer of valine. IHM provides a ChemComp class for this purpose and a
# number of more specialized subclasses. Since norvaline is a chiral peptide,
# here we define it in its L- form using the LPeptideChemComp class.
#
# 'id' should match the officially defined name of the component, as defined
# in the chemical component dictionary: https://www.wwpdb.org/data/ccd
# (See also https://www3.rcsb.org/ligand/NVA)
# 'code' is used to populate the primary sequence in the output mmCIF file.
# For non-standard residues it should normally match 'id'.
# 'code_canonical' is the the one-letter code of the closest standard residue.
# Here we use 'V', valine.
norvaline = ihm.LPeptideChemComp(id='NVA', code='NVA', code_canonical='V',
name='NORVALINE', formula='C5 H11 N O2')
# The Entity constructor takes a sequence of either or both one-letter codes
# and ChemComp objects, so now we can make a sequence containing both
# alanine and norvaline:
entity1 = ihm.Entity(['A', 'A', norvaline, 'A'], description='First entity')
# If a particular non-standard residue is commonly used in your own software,
# and you have assigned a one-letter code for it, you can subclass
# the ihm Alphabet class appropriately. Here we extend the normal set of
# one-letter codes (uppercase) for standard L- amino acids to add 'n' for
# norvaline:
class MyAlphabet(ihm.LPeptideAlphabet):
# Alphabet contains a _comps dictionary that is a simple mapping from
# codes (usually one-letter) to ChemComp objects