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root/osprai/osprai/trunk/modelbasic_varyC.py
Revision: 25
Committed: Wed Apr 28 20:22:24 2010 UTC (8 years, 11 months ago) by rjaynes
File size: 4130 byte(s)
Log Message:
Add py and obj files to allow modeling of more SPR experiments with converter and curvefitting modules.  This is the work of Yuhang Wan and Rui Hou.

1. In "converter.py": 
      Add the saving and reading function for the sprclass data object.
      Also add function "keyfile_read_fake" to provide default information for SPRit and ICM formats in case of the bug when do background_subtract.
      Fix the bugs in "background_subtract".
      Tested by DAM and ICM formats.
2. In model modules:
      "modelclass.py" is the parent class for all the other model classes that performs the theoretical simulating, loading and saving of the parameter or simulated data. Rui and I also add some other model modules like competing model, twostate model, parallel model, and the time variable concentrated models, where the simulated result is compared with Clamp's simulation to make sure the equations are correct. 
       The basicmodel and basicmodel_varyC class are tested. 
3. In "curvefitting.py":
      Add typical pipeline for operation. The examples are packed with the file. 
      Add function to show the Elapsed time for each fitting.
Line File contents
1 """
2 Provide the model for curvefitting.
3 This is a BASIC 1:1 REACTION model with time variable concentration.
4 The reaction equations are:
5 L + A ==ka=> LA
6 L + A <=kd== LA
7
8 Yuhang Wan, Rui Hou
9 Last modified on 100427 (yymmdd) by YW
10
11 Typical Pipeline:(work together with "modelclass.py" the father class):
12 >import modelbasic_varyC as mbvc
13 >m = mbvc.basicmodel_varyC()
14 >m.check_attribute()
15 >m.load_conc('example_conc.txt') or m.create_conc(t)
16 >m.wizard() or m.load_model('model.obj')
17 >m.simulate(t)
18 >m.save_model('newmodel')
19 >m.save_parainfo('parainfo.txt')
20 >m.save_sim_data('sim.dat')
21
22 """
23 __version__ = "100427"
24
25 import numpy as np
26 import pylab as plt
27 import copy
28 import os
29 import pickle
30 from modelclass import *
31
32
33 class basicmodel_varyC(modelclass):
34 """The data attributes of the class:
35 parainfo: the parameter information
36 sim_data: the simulated data
37 conc: the time variable concentration data
38 """
39
40 def __init__ (self, parainfo=[], sim_data=[], conc=[] ):
41 modelclass.__init__(self,parainfo,sim_data)
42 self.conc = conc
43
44 ##------------ not finished yet---------------
45 def load_conc(self, fname):
46 ##fp = file(fname, 'r+')
47 conc = np.loadtxt(fname)
48 self.conc = conc
49 return
50
51 def create_conc(self, t):
52 # create a step-function as concentration curve for debugging now
53 c = np.zeros(len(t), dtype=float)
54 conc = np.zeros((2,len(t)), dtype=float)
55 t = np.array(t)
56 t1 = input("start time:")
57 t2 = input("end time:")
58 ind = plt.find((t>t1-(t[1]-t[0]))&(t<t2-(t[1]-t[0])))
59 c[ind] = 1
60 conc[0] = t
61 conc[1] = c
62 self.conc = conc
63 plt.plot(t,c,'.')
64 plt.show()
65 return
66
67 ##----------------for debugging now------------
68
69 def wizard(self, ):
70 '''This function helps you to create a parameter information list.
71 This is a basic 1:1 reaction model, where there are 4 parameters:
72 rmax: Maximum analyte binding capacity(RU),
73 ka: Association rate constant(M-1S-1),
74 kd: Dissociation rate constant(S-1),
75 ca: Analyte concentration(M).'''
76 print ('')
77 pname = ['rmax','ka','kd','ca']
78 parainfo = []
79 for i in range(4):
80 print i
81 tmp={}
82 tmp['name'] = pname[i]
83 vstr = raw_input("input the value of parameter '%s', if a series, seperate with ',': " %pname[i])
84 vtmp = vstr.strip().split(',')
85 tmp['number'] = len(vtmp)
86 if len(vtmp) == 1:
87 vtmp = float(vtmp[0])
88 else:
89 vtmp = map(float, vtmp)
90 tmp['value'] = vtmp
91 tmp['fixed'] = bool(input("Is '%s' fixed? (1/0): " %pname[i]))
92
93 parainfo.append(tmp)
94 ##parainfo.append({'name':'', 'value':0., 'fixed':0, 'number':0})
95 self.parainfo = parainfo
96
97 return
98
99 def function(self, t, paralist):
100 '''This function calculates the theoretical curve through the
101 parameter list you give.
102 '''
103 # for the basic 1:1 model
104 ## Assign the parameters to calculate the curve
105 conc = copy.deepcopy(self.conc)
106 C = np.interp(t,conc[0],conc[1])
107 for p in paralist:
108 if p['name'] == 'rmax': rmax = p['value']
109 elif p['name'] == 'ka': ka = p['value']
110 elif p['name'] == 'kd': kd = p['value']
111 elif p['name'] == 'ca': ca = p['value']
112 else: print p['name'], p['value']
113 if type(ca) == list:
114 print "Error: This function can only generate data for a single concentration."
115 return
116
117 ## Must iterate through data, numerical integration.
118 g = np.zeros(len(C), dtype=float)
119
120 for i in range(1,len(C)):
121 dG = ka*ca*C[i-1]*(rmax-g[i-1]) - kd*g[i-1]
122 if (abs(g[i]) > 999999999): dG = 0
123
124 g[i] = g[i-1] + dG * (t[i] - t[i-1])
125
126 return g
127