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Originally posted by @mnaqvi-code in #4 (comment)

Hi
I am using the heteropolymer model and using the following fitting command:
ising.fit_heteropolymer(curves[0:12], topology1[0:12], popsize=10, maxiter= 10000)
I am getting the following error:

TypeError Traceback (most recent call last)
in
----> 1 ising.fit_heteropolymer(curves[0:12], topology1[0:12], popsize=10, maxiter= 10000)

~\anaconda3\lib\site-packages\pyfolding\ising.py in fit_heteropolymer(equilibrium_curves, topologies, popsize, tol, maxiter, **kwargs)
755 for protein, topology in zip(equilibrium_curves, topologies):
756 fit_func.append(protein, topology)
--> 757 print( '+ added {0:s} with topology {1:s}'.format(protein.ID, [d().name for d in topology]))
758
759 # do the fitting

TypeError: unsupported format string passed to list.format

Please inform me if you know how to fix it. It seems this is an issue with python 3 version? Thanks

When I am running the code and I am getting the following error
Automatic global fitting to the homozipper model

r_homo = ising.fit_homopolymer(proteins, n_helices)

ValueError Traceback (most recent call last)
in
1 # try with a one-liner which can also save out the curve fits via:"save='/Users/ergm/Desktop/test.csv'
----> 2 r_homo = ising.fit_homopolymer(proteins, n_helices) #, save='/Users/ergm/Desktop/test.csv')

~\anaconda3\lib\site-packages\pyfolding-1.0-py3.8.egg\pyfolding\ising.py in fit_homopolymer(equilibrium_curves, topologies, p0, bounds, **kwargs)
657 # do the global fit
658 # out, covar = global_fit.fit( p0=p0, bounds=((0,-1.,0.),(10.,1.,-10.)) )
--> 659 out, covar = global_fit.fit( p0=p0, bounds=bounds )
660
661

~\anaconda3\lib\site-packages\pyfolding-1.0-py3.8.egg\pyfolding\core.py in fit(self, p0, bounds)
776 # fit the data
777 if bounds:
--> 778 out, covar = optimize.curve_fit(self, x, y, p0=p0, bounds=bounds,
779 max_nfev=20000, absolute_sigma=True,
780 sigma=self.fit_weights)

~\anaconda3\lib\site-packages\scipy\optimize\minpack.py in curve_fit(f, xdata, ydata, p0, sigma, absolute_sigma, check_finite, bounds, method, jac, **kwargs)
793 kwargs['max_nfev'] = kwargs.pop('maxfev', None)
794
--> 795 res = least_squares(func, p0, jac=jac, bounds=bounds, method=method,
796 **kwargs)
797

~\anaconda3\lib\site-packages\scipy\optimize_lsq\least_squares.py in least_squares(fun, x0, jac, bounds, method, ftol, xtol, gtol, x_scale, loss, f_scale, diff_step, tr_solver, tr_options, jac_sparsity, max_nfev, verbose, args, kwargs)
789
790 if np.any(lb >= ub):
--> 791 raise ValueError("Each lower bound must be strictly less than each "
792 "upper bound.")
793

ValueError: Each lower bound must be strictly less than each upper bound.

The equation used for the model :TwoStateEquilibriumSloping is incorrect. The correct equation is :

Fnorm =[An + Bn + (Ad + Bd) exp(m(D-D50%)/RT )]/(1 + exp(m(D-D50%)/RT ))

There is a bracket [ ] missing in the equation currently used which is giving wrong fitting parameters. Please correct it. Thanks

Hello
Every time I try to use the command Equilm_FKBP12.save_fit('(test.csv') I get the error a bytes-like object is required, not 'str'. How do I fix this