From ad684fdb3c739ca305cbe208c02bc965595d1348 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 13 Feb 2020 17:21:00 +0100
Subject: [PATCH] SCHWED-949: Updated tests for non-standard amino acids.
---
modules/conop/tests/test_amino_acids.cc | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/modules/conop/tests/test_amino_acids.cc b/modules/conop/tests/test_amino_acids.cc
index 2b05d2a0c..60b8ee3b9 100644
--- a/modules/conop/tests/test_amino_acids.cc
+++ b/modules/conop/tests/test_amino_acids.cc
@@ -76,7 +76,7 @@ BOOST_AUTO_TEST_CASE(test_one_letter_code_to_residue_name) {
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('W'), "TRP");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('Y'), "TYR");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('V'), "VAL");
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('a'), "ALA");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('r'), "ARG");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('n'), "ASN");
@@ -124,7 +124,7 @@ BOOST_AUTO_TEST_CASE(test_one_letter_code_to_amino_acid) {
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('W'), TRP);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('Y'), TYR);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('V'), VAL);
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('a'), ALA);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('r'), ARG);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('n'), ASN);
@@ -172,7 +172,7 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_one_letter_code) {
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("TRP"), 'W');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("TYR"), 'Y');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("VAL"), 'V');
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Ala"), 'A');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Arg"), 'R');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Asn"), 'N');
@@ -193,6 +193,11 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_one_letter_code) {
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Trp"), 'W');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Tyr"), 'Y');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Val"), 'V');
+ // non-standard amino acids
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("MSE"), 'X');
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("SEC"), 'X');
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("PYL"), 'X');
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("PCA"), 'X');
// unknown ones
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("MUH"), 'X');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("FOO"), 'X');
@@ -220,7 +225,7 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_amino_acid) {
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("TRP"), TRP);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("TYR"), TYR);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("VAL"), VAL);
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Ala"), ALA);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Arg"), ARG);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Asn"), ASN);
@@ -241,6 +246,11 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_amino_acid) {
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Trp"), TRP);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Tyr"), TYR);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Val"), VAL);
+ // non-standard amino acids
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("MSE"), XXX);
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("SEC"), XXX);
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("PYL"), XXX);
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("PCA"), XXX);
// unknown ones
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("MUH"), XXX);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("FOO"), XXX);
--
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