00001 import sys
00002 import ScrumPy
00003 from ScrumPy.Util import Format
00004
00005
00006 TOL=1e-6
00007
00008
00009
00010 def MakeSM(smx):
00011
00012 sm = smx.Copy()
00013 for met in smx.Externs:
00014 sm.DelRow(met)
00015 sm.Externs = smx.Externs[:]
00016
00017 return sm
00018
00019
00020 def AreOrthogonal(a,b,tol=TOL ):
00021
00022 theta = abs(ScrumPy.Util.Seq.CosTheta(a,b))
00023
00024 return abs(theta) <tol
00025
00026
00027 def FindDeads(m, txs=[], tol=TOL):
00028 """ identify dead reactions as those that are orthogonal to all transporters in txs.
00029 See Poolman et al 2008 JTB """
00030
00031
00032 k = m.sm.OrthNullSpace()
00033 lentxs = len(txs)
00034 rv = []
00035
00036 for reac in k.rnames:
00037 if not reac in txs:
00038 dead = max(map(abs, k[reac])) < tol
00039 nchecked = 0
00040
00041 while not dead and nchecked < lentxs:
00042 tx = txs[nchecked]
00043 nchecked +=1
00044 dead = AreOrthogonal(k[tx],k[reac],tol)
00045
00046 if dead:
00047 rv.append(reac)
00048
00049 return rv
00050
00051
00052 def DelDeads(m,txs=[],tol = TOL):
00053
00054 deads = FindDeads(m, txs, tol)
00055 m.DelReactions(deads)
00056
00057 return deads
00058
00059
00060
00061 def HasSubsets(ess):
00062
00063 for ss in ess:
00064 if len(ess[ss]) >1:
00065 return True
00066 return False
00067
00068 def RenameEss(ess,sfx):
00069
00070 for k in ess.keys():
00071 if len(ess[k])>1:
00072 ess[k+"_"+str(sfx)] = ess[k]
00073 del ess[k]
00074
00075
00076
00077 def _Condense(m, IsosEss):
00078
00079 isos = m.DelIsoforms()
00080 e = m.EnzSubsets()
00081 del e["DeadReacs"]
00082 nits = len(IsosEss)
00083 RenameEss(e, nits)
00084
00085 IsosEss.append([isos,e])
00086 print nits
00087
00088
00089 emtx = e.ToMtx()
00090
00091 smx = m.smexterns.Mul(emtx)
00092 smx.Externs = m.sm.Externs[:]
00093 smx.ZapZeroes()
00094 smx.Irrevs = e.Irrev_ss()
00095
00096 m.smexterns=smx
00097 m.sm = MakeSM(smx)
00098
00099 CanCondense = len(isos) >0 or HasSubsets(e)
00100 CanCondense = CanCondense and len(m.sm) >0
00101
00102
00103 if CanCondense:
00104 _Condense(m,IsosEss)
00105
00106
00107
00108 def Condense(m,txs=[],tol=TOL):
00109
00110 deads = DelDeads(m, txs,tol)
00111 print len(deads), "dead"
00112
00113 m.sm.ReQuote()
00114 m.smexterns.ReQuote()
00115 IsosEss = []
00116 _Condense(m, IsosEss)
00117 IsosEss[0][1]["DeadReacs"] = deads
00118
00119
00120 m.smexterns.ToScrumPy(m.ModelName+"_Condensed.spy")
00121
00122 open(m.ModelName+"_Condensed.py","w").write(Format.FormatNested(IsosEss,Quoted=False))
00123
00124 m.sm.DeQuote()
00125 m.smexterns.DeQuote()
00126
00127
00128
00129
00130 return IsosEss
00131
00132
00133
00134
00135
00136
00137
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00140
