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jonrkarrjonrkarr
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fixing docs strings
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‎intro_to_wc_modeling/cell_modeling/model_composition.py

Lines changed: 94 additions & 94 deletions
Original file line numberDiff line numberDiff line change
@@ -23,100 +23,100 @@ class GlycolysisModel(object):
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Based on the `version from JWS Online <http://jjj.biochem.sun.ac.za/models/teusink/>`_
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Attributes:
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CPFKAMP (obj:`float`):
27-
CPFKATP (obj:`float`):
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CPFKF16BP (obj:`float`):
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CPFKF26BP (obj:`float`):
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CPFKF6P (obj:`float`):
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CiPFKATP (obj:`float`):
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F26BP (obj:`float`):
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KATPASE (obj:`float`):
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KGLYCOGEN (obj:`float`):
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KPFKAMP (obj:`float`):
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KPFKF16BP (obj:`float`):
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KPFKF26BP (obj:`float`):
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KSUCC (obj:`float`):
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KTREHALOSE (obj:`float`):
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KeqADH (obj:`float`):
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KeqAK (obj:`float`):
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KeqALD (obj:`float`):
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KeqENO (obj:`float`):
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KeqG3PDH (obj:`float`):
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KeqGLK (obj:`float`):
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KeqGLT (obj:`float`):
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KeqPGI (obj:`float`):
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KeqPGK (obj:`float`):
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KeqPGM (obj:`float`):
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KeqPYK (obj:`float`):
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KeqTPI (obj:`float`): ratio of GAP to DHAP at equilibrium
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KiADHACE (obj:`float`):
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KiADHETOH (obj:`float`):
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KiADHNAD (obj:`float`):
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KiADHNADH (obj:`float`):
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KiPFKATP (obj:`float`):
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KmADHACE (obj:`float`):
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KmADHETOH (obj:`float`):
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KmADHNAD (obj:`float`):
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KmADHNADH (obj:`float`):
61-
KmALDDHAP (obj:`float`):
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KmALDF16P (obj:`float`):
63-
KmALDGAP (obj:`float`):
64-
KmALDGAPi (obj:`float`):
65-
KmENOP2G (obj:`float`):
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KmENOPEP (obj:`float`):
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KmG3PDHDHAP (obj:`float`):
68-
KmG3PDHGLY (obj:`float`):
69-
KmG3PDHNAD (obj:`float`):
70-
KmG3PDHNADH (obj:`float`):
71-
KmGAPDHBPG (obj:`float`):
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KmGAPDHGAP (obj:`float`):
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KmGAPDHNAD (obj:`float`):
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KmGAPDHNADH (obj:`float`):
75-
KmGLKADP (obj:`float`):
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KmGLKATP (obj:`float`):
77-
KmGLKG6P (obj:`float`):
78-
KmGLKGLCi (obj:`float`):
79-
KmGLTGLCi (obj:`float`):
80-
KmGLTGLCo (obj:`float`):
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KmPDCPYR (obj:`float`):
82-
KmPFKATP (obj:`float`):
83-
KmPFKF6P (obj:`float`):
84-
KmPGIF6P (obj:`float`):
85-
KmPGIG6P (obj:`float`):
86-
KmPGKADP (obj:`float`):
87-
KmPGKATP (obj:`float`):
88-
KmPGKBPG (obj:`float`):
89-
KmPGKP3G (obj:`float`):
90-
KmPGMP2G (obj:`float`):
91-
KmPGMP3G (obj:`float`):
92-
KmPYKADP (obj:`float`):
93-
KmPYKATP (obj:`float`):
94-
KmPYKPEP (obj:`float`):
95-
KmPYKPYR (obj:`float`):
96-
L0 (obj:`float`):
97-
SUMAXP (obj:`float`):
98-
VmADH (obj:`float`):
99-
VmALD (obj:`float`):
100-
VmENO (obj:`float`):
101-
VmG3PDH (obj:`float`):
102-
VmGAPDHf (obj:`float`):
103-
VmGAPDHr (obj:`float`):
104-
VmGLK (obj:`float`):
105-
VmGLT (obj:`float`):
106-
VmPDC (obj:`float`):
107-
VmPFK (obj:`float`):
108-
VmPGI (obj:`float`):
109-
VmPGK (obj:`float`):
110-
VmPGM (obj:`float`):
111-
VmPYK (obj:`float`):
112-
gR (obj:`float`):
113-
nPDC (obj:`float`):
114-
CO2 (obj:`float`):
115-
ETOH (obj:`float`):
116-
GLCo (obj:`float`):
117-
GLY (obj:`float`):
118-
SUCC (obj:`float`):
119-
Trh (obj:`float`):
26+
CPFKAMP (:obj:`float`):
27+
CPFKATP (:obj:`float`):
28+
CPFKF16BP (:obj:`float`):
29+
CPFKF26BP (:obj:`float`):
30+
CPFKF6P (:obj:`float`):
31+
CiPFKATP (:obj:`float`):
32+
F26BP (:obj:`float`):
33+
KATPASE (:obj:`float`):
34+
KGLYCOGEN (:obj:`float`):
35+
KPFKAMP (:obj:`float`):
36+
KPFKF16BP (:obj:`float`):
37+
KPFKF26BP (:obj:`float`):
38+
KSUCC (:obj:`float`):
39+
KTREHALOSE (:obj:`float`):
40+
KeqADH (:obj:`float`):
41+
KeqAK (:obj:`float`):
42+
KeqALD (:obj:`float`):
43+
KeqENO (:obj:`float`):
44+
KeqG3PDH (:obj:`float`):
45+
KeqGLK (:obj:`float`):
46+
KeqGLT (:obj:`float`):
47+
KeqPGI (:obj:`float`):
48+
KeqPGK (:obj:`float`):
49+
KeqPGM (:obj:`float`):
50+
KeqPYK (:obj:`float`):
51+
KeqTPI (:obj:`float`): ratio of GAP to DHAP at equilibrium
52+
KiADHACE (:obj:`float`):
53+
KiADHETOH (:obj:`float`):
54+
KiADHNAD (:obj:`float`):
55+
KiADHNADH (:obj:`float`):
56+
KiPFKATP (:obj:`float`):
57+
KmADHACE (:obj:`float`):
58+
KmADHETOH (:obj:`float`):
59+
KmADHNAD (:obj:`float`):
60+
KmADHNADH (:obj:`float`):
61+
KmALDDHAP (:obj:`float`):
62+
KmALDF16P (:obj:`float`):
63+
KmALDGAP (:obj:`float`):
64+
KmALDGAPi (:obj:`float`):
65+
KmENOP2G (:obj:`float`):
66+
KmENOPEP (:obj:`float`):
67+
KmG3PDHDHAP (:obj:`float`):
68+
KmG3PDHGLY (:obj:`float`):
69+
KmG3PDHNAD (:obj:`float`):
70+
KmG3PDHNADH (:obj:`float`):
71+
KmGAPDHBPG (:obj:`float`):
72+
KmGAPDHGAP (:obj:`float`):
73+
KmGAPDHNAD (:obj:`float`):
74+
KmGAPDHNADH (:obj:`float`):
75+
KmGLKADP (:obj:`float`):
76+
KmGLKATP (:obj:`float`):
77+
KmGLKG6P (:obj:`float`):
78+
KmGLKGLCi (:obj:`float`):
79+
KmGLTGLCi (:obj:`float`):
80+
KmGLTGLCo (:obj:`float`):
81+
KmPDCPYR (:obj:`float`):
82+
KmPFKATP (:obj:`float`):
83+
KmPFKF6P (:obj:`float`):
84+
KmPGIF6P (:obj:`float`):
85+
KmPGIG6P (:obj:`float`):
86+
KmPGKADP (:obj:`float`):
87+
KmPGKATP (:obj:`float`):
88+
KmPGKBPG (:obj:`float`):
89+
KmPGKP3G (:obj:`float`):
90+
KmPGMP2G (:obj:`float`):
91+
KmPGMP3G (:obj:`float`):
92+
KmPYKADP (:obj:`float`):
93+
KmPYKATP (:obj:`float`):
94+
KmPYKPEP (:obj:`float`):
95+
KmPYKPYR (:obj:`float`):
96+
L0 (:obj:`float`):
97+
SUMAXP (:obj:`float`):
98+
VmADH (:obj:`float`):
99+
VmALD (:obj:`float`):
100+
VmENO (:obj:`float`):
101+
VmG3PDH (:obj:`float`):
102+
VmGAPDHf (:obj:`float`):
103+
VmGAPDHr (:obj:`float`):
104+
VmGLK (:obj:`float`):
105+
VmGLT (:obj:`float`):
106+
VmPDC (:obj:`float`):
107+
VmPFK (:obj:`float`):
108+
VmPGI (:obj:`float`):
109+
VmPGK (:obj:`float`):
110+
VmPGM (:obj:`float`):
111+
VmPYK (:obj:`float`):
112+
gR (:obj:`float`):
113+
nPDC (:obj:`float`):
114+
CO2 (:obj:`float`):
115+
ETOH (:obj:`float`):
116+
GLCo (:obj:`float`):
117+
GLY (:obj:`float`):
118+
SUCC (:obj:`float`):
119+
Trh (:obj:`float`):
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ACE_0 (:obj:`float`): initial ACE concentration (mM)
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BPG_0 (:obj:`float`): initial BPG concentration (mM)

‎intro_to_wc_modeling/cell_modeling/simulation/ode.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ def d_conc_d_t(concs, time):
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(`BIOMD0000000003 <http://www.ebi.ac.uk/biomodels-main/BIOMD0000000003>`_)
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Args:
19-
time (obj:`float`): time
19+
time (:obj:`float`): time
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concs (:obj:`numpy.ndarray`): array of current concentrations
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Returns:

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