/usr/include/libMUSCLE-3.7/libMUSCLE/gapscoredimer.h is in libmuscle-3.7-dev 3.7+4565-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | // source code generated by dimer.py
namespace muscle {
static SCORE GapScoreMM(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapOpen.get()*(PPA.m_LL*PPB.m_LG + PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_LG) +
g_scoreGapExtend.get()*(PPA.m_LL*PPB.m_GG + PPA.m_GG*PPB.m_LL) +
g_scoreGapAmbig.get()*(PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_GL);
}
static SCORE GapScoreMD(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapOpen.get()*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
g_scoreGapExtend.get()*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG) +
g_scoreGapAmbig.get()*(PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG);
}
static SCORE GapScoreMI(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapOpen.get()*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
g_scoreGapExtend.get()*(PPA.m_LG*PPB.m_LL + PPA.m_GG*PPB.m_LL) +
g_scoreGapAmbig.get()*(PPA.m_LG*PPB.m_GL + PPA.m_GG*PPB.m_GL);
}
static SCORE GapScoreDM(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapOpen.get()*(PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL) +
g_scoreGapExtend.get()*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG) +
g_scoreGapAmbig.get()*(PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_LL + PPA.m_GG*PPB.m_GL);
}
static SCORE GapScoreDD(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapExtend.get()*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GL + PPA.m_LL*PPB.m_GG) +
g_scoreGapAmbig.get()*(PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GL + PPA.m_GL*PPB.m_GG);
}
static SCORE GapScoreDI(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapOpen.get()*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
g_scoreGapAmbig.get()*(PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL + PPA.m_GG*PPB.m_LL + PPA.m_GG*PPB.m_GL);
}
static SCORE GapScoreIM(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapOpen.get()*(PPA.m_LL*PPB.m_LG + PPA.m_GL*PPB.m_LG) +
g_scoreGapExtend.get()*(PPA.m_LG*PPB.m_LL + PPA.m_GG*PPB.m_LL) +
g_scoreGapAmbig.get()*(PPA.m_LL*PPB.m_GG + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_GL);
}
static SCORE GapScoreID(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapOpen.get()*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
g_scoreGapAmbig.get()*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG + PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG);
}
static SCORE GapScoreII(const ProfPos &PPA, const ProfPos &PPB)
{
return
g_scoreGapExtend.get()*(PPA.m_LL*PPB.m_LL + PPA.m_LG*PPB.m_LL + PPA.m_GL*PPB.m_LL + PPA.m_GG*PPB.m_LL) +
g_scoreGapAmbig.get()*(PPA.m_LL*PPB.m_GL + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_GL + PPA.m_GG*PPB.m_GL);
}
} // namespace muscle
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