Author: bugman
Date: Thu Jan 28 13:23:15 2010
New Revision: 10498
URL: http://svn.gna.org/viewcvs/relax?rev=10498&view=rev
Log:
Deleted the gui_bieri.execution.calc_modelfree() function.
Modified:
branches/bieri_gui/gui_bieri/execution/calc_modelfree.py
Modified: branches/bieri_gui/gui_bieri/execution/calc_modelfree.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/execution/calc_modelfree.py?rev=10498&r1=10497&r2=10498&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/execution/calc_modelfree.py (original)
+++ branches/bieri_gui/gui_bieri/execution/calc_modelfree.py Thu Jan 28
13:23:15 2010
@@ -71,250 +71,6 @@
return result
-def start_model_free(self, model, automatic, global_setting, file_setting,
sequencefile, logpanel):
- # Number of Monte Carlo simulations
- global montecarlo
- montecarlo = int(global_setting[6])
-
- # value for progress bar during monte carlo simulation
- global progress
- progress = 5.0
-
- # redirect relax output and errors to relaxGUI - log panel
- redir=RedirectText(logpanel)
- sys.stdout=redir
- sys.stderr=redir
-
- wx.CallAfter(logpanel.log_panel.AppendText, ('Starting Model-free
calculation\n------------------------------------------\n\n') )
- time.sleep(0.5)
-
- # Set relax and file settings from dialog
- bondlength = converttofloat(global_setting[0])
- csa = converttofloat(global_setting[1])
- hetero = global_setting[2]
- prot = global_setting[3]
- gridinc = global_setting[4]
- minalgor = global_setting[5]
- intcol = int(file_setting[5])
- mol_name = int(file_setting[0])
- res_num = int(file_setting[1])
- res_name = int(file_setting[2])
- spin_num = int(file_setting[3])
- spin_name = int(file_setting[4])
-
- # get target directory, unresolved residues and NMR frequencies
- target_dir = str(self.resultsdir_r21_copy_2.GetValue())
- unres = str(self.unresolved_r21_copy_1_copy.GetValue())
- nmr_freq1 = str(self.modelfreefreq1.GetValue())
- nmr_freq2 = str(self.modelfreefreq2.GetValue())
- nmr_freq3 = str(self.modelfreefreq3.GetValue())
-
- # detect 2 or 3 field strength
- num_field = 3
- if self.modelfreefreq3.GetValue() == '':
- num_field = 2
- if self.m_noe_3.GetValue() == '':
- num_field = 2
- if self.m_r1_3.GetValue() == '':
- num_field = 2
- if self.m_r1_3.GetValue() == '':
- num_field = 2
-
- if self.aic.GetValue() == True:
- selection_mode = "AIC"
- if self.bic.GetValue() == True:
- selection_mode = "BIC"
-
- #create unresolved file
- if not unres == '':
- filename2 = target_dir + sep + 'unresolved'
- file = open(filename2, 'w')
- unres = replace(unres, ",", "\n")
- file.write(unres)
- file.close()
-
- # Create an empty file.
- else:
- filename2 = target_dir + sep + 'unresolved'
- file = open(filename2, 'w')
- file.write('')
- file.close()
-
- #create models list
- models = []
-
- if self.m0.GetValue() == True:
- models.append('m0')
- if self.m1.GetValue() == True:
- models.append('m1')
- if self.m2.GetValue() == True:
- models.append('m2')
- if self.m3.GetValue() == True:
- models.append('m3')
- if self.m4.GetValue() == True:
- models.append('m4')
- if self.m5.GetValue() == True:
- models.append('m5')
- if self.m6.GetValue() == True:
- models.append('m6')
- if self.m7.GetValue() == True:
- models.append('m7')
- if self.m8.GetValue() == True:
- models.append('m8')
- if self.m9.GetValue() == True:
- models.append('m9')
-
- #create tm models list
- tmodels = []
-
- if self.m0.GetValue() == True:
- tmodels.append('tm0')
- if self.m1.GetValue() == True:
- tmodels.append('tm1')
- if self.m2.GetValue() == True:
- tmodels.append('tm2')
- if self.m3.GetValue() == True:
- tmodels.append('tm3')
- if self.m4.GetValue() == True:
- tmodels.append('tm4')
- if self.m5.GetValue() == True:
- tmodels.append('tm5')
- if self.m6.GetValue() == True:
- tmodels.append('tm6')
- if self.m7.GetValue() == True:
- tmodels.append('tm7')
- if self.m8.GetValue() == True:
- tmodels.append('tm8')
- if self.m9.GetValue() == True:
- tmodels.append('tm9')
-
- MF_MODELS = models
- LOCAL_TM_MODELS = tmodels
-
- # User variables.
- #################
-
- PDB_FILE = str(self.structure_r21_copy_1_copy.GetValue())
- gracedir = target_dir + sep + 'grace'
- resultsdir = target_dir + sep
- m_method = selection_mode
-
- if selection_mode == "AIC":
- msel = "aic"
- if selection_mode == "BIC":
- msel = "bic"
- modelselection = msel
-
- #parameter files
- noe_1 = str(self.m_noe_1.GetValue())
- r1_1 = str(self.m_r1_1.GetValue())
- r2_1 = str(self.m_r2_1.GetValue())
- noe_2 = str(self.m_noe_2.GetValue())
- r1_2 = str(self.m_r1_2.GetValue())
- r2_2 = str(self.m_r2_2.GetValue())
- noe_3 = str(self.m_noe_3.GetValue())
- r1_3 = str(self.m_r1_3.GetValue())
- r2_3 = str(self.m_r2_3.GetValue())
-
- nmr_freq1 = int(self.modelfreefreq1.GetValue())
- nmr_freq2 = int(self.modelfreefreq2.GetValue())
- if num_field == 3:
- nmr_freq3 = int(self.modelfreefreq3.GetValue())
-
- # (data type, frequency label, frequency, file name, dir,
mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col,
data_col, error_col, sep)
-
- if num_field == 2:
- RELAX_DATA = [['R1', str(nmr_freq1), nmr_freq1 * 1e6, r1_1, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['R2', str(nmr_freq1), nmr_freq1 * 1e6, r2_1, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['NOE', str(nmr_freq1), nmr_freq1 * 1e6, noe_1,
None, None, 2, 3, 4, 5, 6, 7, None],
- ['R1', str(nmr_freq2), nmr_freq2 * 1e6, r1_2, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['NOE', str(nmr_freq2), nmr_freq2 * 1e6, noe_2,
None, None, 2, 3, 4, 5, 6, 7, None] ]
-
- if num_field == 3:
- RELAX_DATA = [['R1', str(nmr_freq1), nmr_freq1 * 1e6, r1_1, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['R2', str(nmr_freq1), nmr_freq1 * 1e6, r2_1, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['NOE', str(nmr_freq1), nmr_freq1 * 1e6, noe_1,
None, None, 2, 3, 4, 5, 6, 7, None],
- ['R1', str(nmr_freq2), nmr_freq2 * 1e6, r1_2, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['R2', str(nmr_freq2), nmr_freq2 * 1e6, r2_2, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['NOE', str(nmr_freq2), nmr_freq2 * 1e6, noe_2,
None, None, 2, 3, 4, 5, 7, 6, None],
- ['R1', str(nmr_freq3), nmr_freq3 * 1e6, r1_3, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['R2', str(nmr_freq3), nmr_freq3 * 1e6, r2_3, None,
None, 2, 3, 4, 5, 6, 7, None],
- ['NOE', str(nmr_freq3), nmr_freq3 * 1e6, noe_3,
None, None, 2, 3, 4, 5, 6, 7, None]]
-
- HETNUC = hetero
-
- # [file name, dir, mol_name_col, res_num_col, res_name_col,
spin_num_col, spin_name_col, sep]
- SEQ_ARGS = [noe_1, None, None, 2, 3, 4, 5, None]
-
- # The diffusion model.
- DIFF_MODEL = model
-
- # The heteronucleus atom name corresponding to that of the PDB file
(used if the spin name is not in the sequence data).
- HET_NAME = hetero
-
- # The file containing the list of unresolved spins to exclude from the
analysis (set this to None if no spin is to be excluded).
- UNRES = resultsdir + 'unresolved'
-
- # A file containing a list of spins which can be dynamically excluded at
any point within the analysis (when set to None, this variable is not used).
- EXCLUDE = None
-
- # The bond length, CSA values, heteronucleus type, and proton type.
- BOND_LENGTH = 1.02 * 1e-10
- CSA = -172 * 1e-6
- HETNUC = '15N'
- PROTON = '1H'
-
- # The grid search size (the number of increments per dimension).
- GRID_INC = 11
-
- # The optimisation technique.
- MIN_ALGOR = 'newton'
-
- # Minimisation Options
- MIN_OPT = ('back', 'gmw')
-
- # The number of Monte Carlo simulations to be used for error analysis at
the end of the analysis.
- MC_NUM = 500
-
- # Automatic looping over all rounds until convergence (must be a boolean
value of True or False).
- CONV_LOOP = True
-
- # Execute the automatic model-free protocol.
- dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME, relax_data=RELAX_DATA, unres=UNRES, exclude=EXCLUDE,
bond_length=BOND_LENGTH, csa=CSA, hetnuc=HETNUC, proton=PROTON,
grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
-
- #create results file
- if model == 'final':
- results_analysis = model_free_results(self)
- return results_analysis # return data for results table dialog
-
- # return successful value to automatic mode to proceed to next step
- if automatic == True:
- return 'successful'
-
- # Feedback about successful Calculation in manual mode and after final
calculation in autamatic mode
- if not automatic:
- if model == 'local_tm':
- print ('Local Tm calculation was successful !')
-
- # enable m1 - m5 to choose for calculation
- return True
-
- if model == 'sphere':
- print ('Sphere calculation was successful !')
- if model == 'prolate':
- print ('Prolate calculation was successful !')
- if model == 'oblate':
- print ('Oblate calculation was successful !')
- if model == 'ellipsoid':
- print ('Ellipsoid calculation was successful !')
- if model == 'Final':
- print ('Final Model-free calculation was successful !')
-
- # Close thread.
- return
-
-
-
class RedirectText(object):
"""Class to redirect relax output to relaxGUI - log panel and progress
bar."""
r10498 - /branches/bieri_gui/gui_bieri/execution/calc_modelfree.py