inst/unitTests/test_extractPCMBLOSUM.R

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

test_extractPCMBLOSUM = function() {
    x = paste(
        'MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQHQSWLRP',
        'VLRSNRVEYCWCNSGRAQCHSVPVKSCSEPRCFNGGTCQQALYFSDFVCQCPEGFAGKCC',
        'EIDTRATCYEDQGISYRGTWSTAESGAECTNWNSSALAQKPYSGRRPDAIRLGLGNHNYC',
        'RNPDRDSKPWCYVFKAGKYSSEFCSTPACSEGNSDCYFGNGSAYRGTHSLTESGASCLPW',
        'NSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTC',
        'GLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCF',
        'QERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRC',
        'AQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQ',
        'HLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQ',
        'KDVPGVYTKVTNYLDWIRDNMRP', sep = '')
    blosum = extractPCMBLOSUM(x, submat = 'AABLOSUM62', k = 5, lag = 7,
                              scale = TRUE, silent = TRUE)
    pam = extractPCMBLOSUM(x, submat = 'AAPAM250', k = 3, lag = 9,
                           scale = TRUE, silent = TRUE)
    checkEquals(length(blosum), 175L)
    checkEquals(length(pam), 81L)
}