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need catalyze table or simple convert table...

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1 parent ea2e11c commit daf8e51b3985dfa59b9f6cae3db4d082f6042baf Carlos Lopez committed Oct 8, 2012
Showing with 34 additions and 13 deletions.
  1. +13 −0 .gitignore
  2. +21 −13 egfr/chen_modules.py
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@@ -0,0 +1,13 @@
+*~
+.DS_Store
+*.swp
+*.pyc
+parser.out
+bng_files/*
+build/*
+dist/*
+doc/_build
+MANIFEST
+RELEASE-VERSION
+.idea
+.#*
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@@ -32,10 +32,10 @@ def erbb_reclayer_monomers():
"""
Monomer('EGF', ['bf']) # Epidermal Growth Factor ligand
Monomer('HRG', ['bf']) # Heregulin ligand
- Monomer('ERBB1', ['bf'])
- Monomer('ERBB2', ['bf'])
- Monomer('ERBB3', ['bf'])
- Monomer('ERBB4', ['bf'])
+ Monomer('erbb1', ['bf'])
+ Monomer('erbb2', ['bf'])
+ Monomer('erbb3', ['bf'])
+ Monomer('erbb4', ['bf'])
Monomer('DEP1', ['bf'])
Monomer('DEP2', ['bf'])
Monomer('DEP3', ['bf'])
@@ -47,17 +47,25 @@ def rec_events():
"""
# binding to receptors
bind_table([[ EGF, HRG],
- [ERBB1, (1.0,1.0), None],
- [ERBB3, None, (1.0,1.0)],
- [ERBB4, None, (1.0,1.0)],
+ [erbb1, (1.0,1.0), None],
+ [erbb3, None, (1.0,1.0)],
+ [erbb4, None, (1.0,1.0)],
])
# erbb dimerization
- bind_table([[ ERBB1, ERBB2, ERBB3, ERBB4],
- [ERBB1, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)],
- [ERBB2, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)],
- [ERBB3, (kdimf, kdimr), (kdimf, kdimr), None, (kdimf, kdimr)],
- [ERBB4, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)]
+ bind_table([[ erbb1, erbb2, erbb3, erbb4],
+ [erbb1, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)],
+ [erbb2, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)],
+ [erbb3, (kdimf, kdimr), (kdimf, kdimr), None, (kdimf, kdimr)],
+ [erbb4, (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr), (kdimf, kdimr)]
])
-
+ # ATP binding
+ bind_table([[ ATP],
+ [erbb1, (kf, kr)],
+ [erbb2, (kf, kr)],
+ [erbb4, (kf, kr)]
+ ])
+
+ # Receptor cross phosphorylation
+

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