Again, awesome work Seb! A perfect and complete set of changes to shift this function to the new relax design.
Cheers, Edward On Thu, Apr 3, 2008 at 4:35 AM, <[EMAIL PROTECTED]> wrote: > Author: semor > Date: Thu Apr 3 04:35:30 2008 > New Revision: 5250 > > URL: http://svn.gna.org/viewcvs/relax?rev=5250&view=rev > Log: > Modified the calculate() function from specific_fns.jw_mapping to the new > design. > > > Modified: > 1.3/specific_fns/jw_mapping.py > > Modified: 1.3/specific_fns/jw_mapping.py > URL: > http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=5250&r1=5249&r2=5250&view=diff > > ============================================================================== > --- 1.3/specific_fns/jw_mapping.py (original) > +++ 1.3/specific_fns/jw_mapping.py Thu Apr 3 04:35:30 2008 > @@ -37,55 +37,50 @@ > """Class containing functions specific to reduced spectral density > mapping.""" > > > - def calculate(self, run=None, verbosity=1, sim_index=None): > + def calculate(self, verbosity=1, sim_index=None): > """Calculation of the spectral density values.""" > > - # Run argument. > - self.run = run > + # Alias the current data pipe. > + cdp = relax_data_store[relax_data_store.current_pipe] > > # Test if the frequency has been set. > - if not hasattr(relax_data_store, 'jw_frq') or not > relax_data_store.jw_frq.has_key(self.run) or > type(relax_data_store.jw_frq[self.run]) != float: > - raise RelaxError, "The frequency for the run " + `self.run` + " > has not been set up." > - > - # Test if the nucleus type has been set. > - if not hasattr(relax_data_store, 'gx'): > - raise RelaxNucleusError > + if not hasattr(cdp, 'jw_frq') or type(cdp.jw_frq) != float: > + raise RelaxError, "The frequency has not been set up." > > # Test if the sequence data is loaded. > - if not relax_data_store.res.has_key(self.run): > - raise RelaxNoSequenceError, self.run > + if not exists_mol_res_spin_data(): > + raise RelaxNoSequenceError > > # Test if the CSA and bond length values have been set. > - for i in xrange(len(relax_data_store.res[self.run])): > + for spin in spin_loop(spin_id): > + > # Skip unselected residues. > - if not relax_data_store.res[self.run][i].select: > + if not spin.select: > continue > > # CSA value. > - if not hasattr(relax_data_store.res[self.run][i], 'csa') or > relax_data_store.res[self.run][i].csa == None: > + if not hasattr(spin, 'csa') or spin.csa == None: > raise RelaxNoValueError, "CSA" > > # Bond length value. > - if not hasattr(relax_data_store.res[self.run][i], 'r') or > relax_data_store.res[self.run][i].r == None: > + if not hasattr(spin, 'r') or spin.r == None: > raise RelaxNoValueError, "bond length" > > # Frequency index. > - if relax_data_store.jw_frq[self.run] not in > relax_data_store.frq[self.run]: > - raise RelaxError, "No relaxation data corresponding to the > frequency " + `relax_data_store.jw_frq[self.run]` + " has been loaded." > + if cdp.jw_frq not in cdp.frq: > + raise RelaxError, "No relaxation data corresponding to the > frequency " + `cdp.jw_frq` + " has been loaded." > > # Reduced spectral density mapping. > - for i in xrange(len(relax_data_store.res[self.run])): > - # Reassign data structure. > - data = relax_data_store.res[self.run][i] > + for spin in spin_loop(spin_id): > > # Skip unselected residues. > - if not data.select: > + if not spin.select: > continue > > # Residue specific frequency index. > frq_index = None > - for j in xrange(data.num_frq): > - if data.frq[j] == relax_data_store.jw_frq[self.run]: > + for j in xrange(spin.num_frq): > + if spin.frq[j] == cdp.jw_frq: > frq_index = j > if frq_index == None: > continue > @@ -96,57 +91,57 @@ > noe = None > > # Get the R1, R2, and NOE values corresponding to the set > frequency. > - for j in xrange(data.num_ri): > + for j in xrange(spin.num_ri): > # R1. > - if data.remap_table[j] == frq_index and data.ri_labels[j] > == 'R1': > + if spin.remap_table[j] == frq_index and spin.ri_labels[j] > == 'R1': > if sim_index == None: > - r1 = data.relax_data[j] > + r1 = spin.relax_data[j] > else: > - r1 = data.relax_sim_data[sim_index][j] > + r1 = spin.relax_sim_data[sim_index][j] > > # R2. > - if data.remap_table[j] == frq_index and data.ri_labels[j] > == 'R2': > + if spin.remap_table[j] == frq_index and spin.ri_labels[j] > == 'R2': > if sim_index == None: > - r2 = data.relax_data[j] > + r2 = spin.relax_data[j] > else: > - r2 = data.relax_sim_data[sim_index][j] > + r2 = spin.relax_sim_data[sim_index][j] > > # NOE. > - if data.remap_table[j] == frq_index and data.ri_labels[j] > == 'NOE': > + if spin.remap_table[j] == frq_index and spin.ri_labels[j] > == 'NOE': > if sim_index == None: > - noe = data.relax_data[j] > + noe = spin.relax_data[j] > else: > - noe = data.relax_sim_data[sim_index][j] > + noe = spin.relax_sim_data[sim_index][j] > > # Skip the residue if not all of the three value exist. > if r1 == None or r2 == None or noe == None: > continue > > # Initialise the function to calculate. > - self.jw = Mapping(frq=relax_data_store.jw_frq[self.run], > gx=relax_data_store.gx, gh=relax_data_store.gh, mu0=relax_data_store.mu0, > h_bar=relax_data_store.h_bar) > + self.jw = Mapping(frq=cdp.jw_frq, gx=spin.gx, gh=spin.gh, > mu0=spin.mu0, h_bar=spin.h_bar) > > # Calculate the spectral density values. > - j0, jwx, jwh = self.jw.func(r=data.r, csa=data.csa, r1=r1, > r2=r2, noe=noe) > + j0, jwx, jwh = self.jw.func(r=spin.r, csa=spin.csa, r1=r1, > r2=r2, noe=noe) > > # Reduced spectral density values. > if sim_index == None: > - data.j0 = j0 > - data.jwx = jwx > - data.jwh = jwh > + spin.j0 = j0 > + spin.jwx = jwx > + spin.jwh = jwh > > # Monte Carlo simulated reduced spectral density values. > else: > # Initialise the simulation data structures. > - self.data_init(data, sim=1) > - if data.j0_sim == None: > - data.j0_sim = [] > - data.jwx_sim = [] > - data.jwh_sim = [] > + self.spin_init(spin, sim=1) > + if spin.j0_sim == None: > + spin.j0_sim = [] > + spin.jwx_sim = [] > + spin.jwh_sim = [] > > # Reduced spectral density values. > - data.j0_sim.append(j0) > - data.jwx_sim.append(jwx) > - data.jwh_sim.append(jwh) > + spin.j0_sim.append(j0) > + spin.jwx_sim.append(jwx) > + spin.jwh_sim.append(jwh) > > > def data_init(self, data, sim=0): > > > _______________________________________________ > 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
