def calDeltaHS(qseq, hseq): """ Calculate deltaH and deltaS """ # Initial deltaH = 0 deltaS = 0 qseq = re.sub('[atcgn]+', '', qseq) hseq = re.sub('[atcgn]+', '', hseq) init_begin = 'init' + hseq[0] init_end = 'init' + hseq[-1] initH = TP.dH_full[init_begin] + TP.dH_full[init_end] initS = TP.dS_full[init_begin] + TP.dS_full[init_end] deltaH = deltaH + initH deltaS = deltaS + initS # Get the complement of a sequence hseq_complement = LS.seq(hseq).complement # Calculate the free Gibbs energy length = len(hseq) for i in range(length): if i > length - 2: break dinuc = qseq[i:(i + 2)] + hseq_complement[i:(i + 2)] if TP.dH_full.has_key(dinuc) and TP.dS_full.has_key(dinuc): deltaH = deltaH + TP.dH_full[dinuc] deltaS = deltaS + TP.dS_full[dinuc] return (deltaH, deltaS)
def calDeltaHS(qseq, hseq): """ Calculate deltaH and deltaS """ # Initial deltaH = 0 deltaS = 0 qseq = re.sub('[atcgn]+', '', qseq) hseq = re.sub('[atcgn]+', '', hseq) init_begin = 'init' + hseq[0] init_end = 'init' + hseq[-1] initH = TP.dH_full[init_begin] + TP.dH_full[init_end] initS = TP.dS_full[init_begin] + TP.dS_full[init_end] deltaH = deltaH + initH deltaS = deltaS + initS # Get the complement of a sequence hseq_complement = LS.seq(hseq).complement # Calculate the free Gibbs energy length = len(hseq) for i in range(length): if i > length - 2: break dinuc = qseq[i : (i+2)] + hseq_complement[i : (i+2)] if TP.dH_full.has_key(dinuc) and TP.dS_full.has_key(dinuc): deltaH = deltaH + TP.dH_full[dinuc] deltaS = deltaS + TP.dS_full[dinuc] return (deltaH, deltaS)
def test(): seq = 'CGTTGA' print LS.seq(seq).complement print '*' * 80 print seq