Hi Ed, I was pretty sure there was something about this... Where whould the lower case names be in the code ? And where the mixed lower/upper case names should be ?
Also, this code is, for sure, not functionnal for now since I'll have to think about how the parameters are stored (etc) when selecting the slow- or fast-exchange regime... Of course, no model all parameters R2, Rex, kex, R2A, kA and dw... Regards, Séb :) Edward d'Auvergne wrote: > Hi, > > I think this change conflicts with the rest of relax. The parameters > like Rex as stored in the lower case data structures 'rex', etc. but > when a user is selecting models or asks for parameter values, the > natural mix of lower and upper case should be used. For example to > ask for the S2f parameter in model-free analysis, you use the string > 'S2f' in the value.write() user function. These strings are the > interface for the user, and hence the natural cases should be used. > Internally in relax it doesn't matter. > > Regards, > > Edward > > > On Fri, Jan 9, 2009 at 9:36 PM, <[email protected]> wrote: > >> Author: semor >> Date: Fri Jan 9 21:36:55 2009 >> New Revision: 8353 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=8353&view=rev >> Log: >> Corrected a few formatting issues and still added parameters for the slow- >> and fast-exchange regime. >> >> >> Modified: >> branches/relax_disp/specific_fns/relax_disp.py >> >> Modified: branches/relax_disp/specific_fns/relax_disp.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=8353&r1=8352&r2=8353&view=diff >> ============================================================================== >> --- branches/relax_disp/specific_fns/relax_disp.py (original) >> +++ branches/relax_disp/specific_fns/relax_disp.py Fri Jan 9 21:36:55 2009 >> @@ -62,7 +62,7 @@ >> # Loop over the model parameters. >> for i in xrange(len(spin.params)): >> # Transversal relaxation rate. >> - if spin.params[i] == 'R2': >> + if spin.params[i] == 'r2': >> if sim_index != None: >> param_vector.append(spin.r2_sim[sim_index]) >> elif spin.r2 == None: >> @@ -71,7 +71,7 @@ >> param_vector.append(spin.r2) >> >> # Chemical exchange contribution to 'R2'. >> - elif spin.params[i] == 'Rex': >> + elif spin.params[i] == 'rex': >> if sim_index != None: >> param_vector.append(spin.rex_sim[sim_index]) >> elif spin.rex == None: >> @@ -89,7 +89,7 @@ >> param_vector.append(spin.kex) >> >> # Relaxation rate for state A. >> - if spin.params[i] == 'R2A': >> + if spin.params[i] == 'r2a': >> if sim_index != None: >> param_vector.append(spin.r2a_sim[sim_index]) >> elif spin.r2a == None: >> @@ -334,11 +334,11 @@ >> The names are as follows: >> >> - 'params', an array of the parameter names associated with the >> model. >> - - 'R2', the transversal relaxation rate. >> - - 'Rex', the chemical exchange contribution to 'R2'. >> + - 'r2', the transversal relaxation rate. >> + - 'rex', the chemical exchange contribution to 'R2'. >> - 'kex', the exchange rate. >> - - 'R2A', the transversal relaxation rate for state A. >> - - 'kA', the exchange rate from state A to state B. >> + - 'r2a', the transversal relaxation rate for state A. >> + - 'ka', the exchange rate from state A to state B. >> - 'dw', the chemical shift difference between states A and B. >> - 'chi2', chi-squared value. >> - 'iter', iterations. >> @@ -419,15 +419,15 @@ >> | Data type | Object name >> | Value | >> >> |___________________________________________________|_______________|__________| >> | | >> | | >> - | Transversal relaxation rate | 'R2' >> | 8.0 | >> + | Transversal relaxation rate | 'r2' >> | 8.0 | >> | | >> | | >> - | Chemical exchange contribution to 'R2' | 'Rex' >> | 2.0 | >> + | Chemical exchange contribution to 'R2' | 'rex' >> | 2.0 | >> | | >> | | >> | Exchange rate | 'kex' >> | 10000.0 | >> | | >> | | >> - | Relaxation rate for state A | 'R2A' >> | 0.0 | >> + | Transversal relaxation rate for state A | 'r2a' >> | 8.0 | >> | | >> | | >> - | Exchange rate from state A to state B | 'kA' >> | 10000.0 | >> + | Exchange rate from state A to state B | 'ka' >> | 10000.0 | >> | | >> | | >> | Chemical shift difference between states A and B | 'dw' >> | 100 | >> | | >> | | >> @@ -435,17 +435,29 @@ >> >> """ >> >> - # Relaxation rate. >> - if param == 'rx': >> + # Transversal relaxation rate. >> + if param == 'r2': >> return 8.0 >> >> - # Initial intensity. >> - if param == 'i0': >> + # Chemical exchange contribution to 'R2'. >> + if param == 'rex': >> + return 2.0 >> + >> + # Exchange rate. >> + if param == 'kes': >> return 10000.0 >> >> - # Intensity at infinity. >> - if param == 'iinf': >> - return 0.0 >> + # Transversal relaxation rate for state A. >> + if param == 'r2a' : >> + return 8.0 >> + >> + # Exchange rate from state A to state B. >> + if param == 'ka' : >> + return 10000 >> + >> + # Chemical shift difference between states A and B. >> + if param == 'dw' : >> + return 100 >> >> >> def disassemble_param_vector(self, param_vector=None, spin=None, >> sim_index=None): >> @@ -1003,15 +1015,15 @@ >> | Data type | Object name | >> Patterns | >> >> |___________________________________________________|______________|__________________________| >> | | | >> | >> - | Transversal relaxation rate | 'R2' >> | '^[Rr]2$' | >> + | Transversal relaxation rate | 'r2' >> | '^[Rr]2$' | >> | | | >> | >> - | Chemical exchange contribution to 'R2' | 'Rex' >> | '^[Rr]ex$' | >> + | Chemical exchange contribution to 'R2' | 'rex' >> | '^[Rr]ex$' | >> | | | >> | >> | Exchange rate | 'kex' | >> '^[Kk]ex$' | >> | | | >> | >> - | Relaxation rate for state A | 'R2A' >> | '^[Rr]2A$' | >> + | Transversal relaxation rate for state A | 'r2a' >> | '^[Rr]2A$' | >> | | | >> | >> - | Exchange rate from state A to state B | 'kA' >> | '^[Kk]A$' | >> + | Exchange rate from state A to state B | 'ka' >> | '^[Kk]A$' | >> | | | >> | >> | Chemical shift difference between states A and B | 'dw' | >> '^[Dd]w$' | >> | | | >> | >> @@ -1103,12 +1115,12 @@ >> # Fast-exchange regime. >> if model == 'fast': >> print "Two parameter exponential fit." >> - params = ['R2', 'Rex', 'kex'] >> + params = ['r2', 'rex', 'kex'] >> >> # Slow-exchange regime. >> elif model == 'slow': >> print "Three parameter inversion recovery fit." >> - params = ['R2A', 'kA', 'dw'] >> + params = ['r2a', 'ka', 'dw'] >> >> # Invalid model. >> else: >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-commits mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-commits >> >> > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
