-2
저는 화학 연구를 위해이 스크립트를 실행하려고합니다.
http://pubs.acs.org/doi/suppl/10.1021/acs.analchem.5b02258__init__에 예상치 못한 키워드가 있습니다.
이 명령은 도움이 될 수 있습니다 :
이"fsolve_withPT.py는 두 가지 명령 줄 인수를 내가 제대로 여기에 스크립트를 복사하지 않은 경우
는 파일을 다운로드 할 수있는 링크입니다 "MamPol2_titration_data.txt"및 "Kaps_result.txt"의 출력 파일명 "
ㅁ 입력 파일명 나는이 오류 메시지가 ipython에서 스크립트 실행 도중 :
__init__() got an unexpected keyword argument 'step_max'
#University of California San Francisco
#Supplemental for
#
#A model for specific and nonspecific binding of ligand to multi-protein
#complexes by native mass spectrometry
#
#Shenheng Guan, et al
#2015
#
import sys
import math
import numpy
import warnings
from scipy.optimize import fsolve,fmin
import matplotlib.pyplot as plt
warnings.filterwarnings('ignore')
input_fn='MamPol2_titration_data.txt'
output_fn='Kaps_result1.txt'
##input_fn=sys.argv[1]
##output_fn=sys.argv[1]
fid=open(input_fn,'r')
line=fid.readline()
line=line.strip('\n')
no_mam=[float(x) for x in line.split('\t')[1:]]
line=fid.readline()
data=[]
conc=[]
for line in fid:
line=line.strip('\n')
tmp0=line.split('\t')
conc.append(float(tmp0[0]))
tmp1=[float(x) for x in tmp0[1:]]
data.append(tmp1)
fid.close()
class fsolve_withPT:
def __init__(self,conc,data):
self.conc = conc
self.data = data
def ff(self, x, Kas, LT, PT):#x[0]:[P];x[1]:[PL]...;x[n]:[PLn];x[-1]:[L] n+2 (10)
fc=[]
for j in range(0,len(x)-2):#setup equilibrium equations
fc.append(Kas[j]*x[j]*x[-1]-x[j+1])
#mass conservation for P
tmpP=0.0#[P]
for j in range(0,len(x)-1):#x[0] to x[8] or [P] to [PL8]
tmpP=tmpP+x[j]
fc.append(tmpP-PT)#PT equals to all P species combined
#mass conservation for L
tmpL=x[-1]#[L]
for j in range(1,len(x)-1):
tmpL=tmpL+j*x[j]
fc.append(tmpL-LT)
return fc
def error(self,w):
Kas=w[:-1]
PT=w[-1]
mySum=0.0
for m in range(0,len(self.conc)):#over conc (LT)
#print Kas,self.conc[m],PT
F=fsolve(self.ff, [1.0]*10, args=(Kas, self.conc[m], PT))
myPT=sum(F[:-1])
for k in range(0, len(no_mam)):#over # of Mam
mySum=mySum+(F[k]/myPT-self.data[m][k])**2
return mySum
w0=[8,7,6,5,4,3,2,1,0]
w0=numpy.array(w0)
w0=w0*3.01e4
w0[-1]=5.e-6
myFclass=fsolve_withPT(conc,data)
w, fopt, iter, funcalls, warnflag = fmin(myFclass.error, w0, maxiter=2000,
maxfun=2000, full_output=True,disp=True)
# http://nullege.com/codes/show/[email protected]@[email protected]@[email protected][email protected]_benchmarks.py/73/numdifftools.Hessian
import numdifftools as nd
#my_step_nom=[1.0e3]*8+[1.0e-6]*1
my_step_nom=w#*1.0e-3
hessian = nd.Hessian(myFclass.error,step_max=1.0e-2,step_nom=my_step_nom)#, step_max=1.0, step_nom=numpy.abs(w))
H = hessian(w)
covH=numpy.linalg.inv(H)
conc0=conc#numpy.linspace(0.0,6.0E-05,num=101).tolist()
y0=[]
for tmp in conc0:
F=fsolve(myFclass.ff, [1.0]*10, args=(w[:-1], tmp,w[-1]))
y0.append(F)
#y0=myFunc(conc0,w)
fid=open(output_fn,'w')
fid.write('Calculated complex conc. (M)\t'+str(w[-1])+'\n')
fid.write('# of Mam in Complex\t')
for j in no_mam:
fid.write(str(j)+'\t')
fid.write('\n')
fid.write('Associate constants (Kas)\t\t')
for j in no_mam[:-1]:
fid.write(str(w[j])+'\t')
fid.write('\n')
fid.write('Mam Conc. (M)\tSimulated abundances\n')
for k in range(0,len(y0)):
fid.write(str(conc0[k])+'\t')
yc=y0[k]
tmp=sum(yc[:-1])
for j in range(0,len(yc)-2):
fid.write(str(yc[j]/tmp)+'\t')
fid.write(str(yc[-2])+'\n')
fid.close()
from scipy import stats
SS=fopt
DF=len(data)*len(data[0])-len(w)
t_factor=stats.t.ppf(0.95, DF)
SE=[]
dw=[]
for j in range(0,len(w)):
SE.append(numpy.sqrt(SS/DF*numpy.abs(covH[j,j])))
for j in range(0,len(w)):
dw.append(SE[j]*t_factor)
어떤 줄이 오류를 나타 냅니까? – parsecer