Author: bugman
Date: Thu Jun 20 12:02:24 2013
New Revision: 20230
URL: http://svn.gna.org/viewcvs/relax?rev=20230&view=rev
Log:
Converted the relaxation dispersion chapter of the user manual to the
lstlisting environment.
This matches the changes occurring within the trunk.
Modified:
branches/relax_disp/docs/latex/relax_disp.tex
Modified: branches/relax_disp/docs/latex/relax_disp.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/relax_disp.tex?rev=20230&r1=20229&r2=20230&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/relax_disp.tex (original)
+++ branches/relax_disp/docs/latex/relax_disp.tex Thu Jun 20 12:02:24 2013
@@ -342,131 +342,131 @@
You will need to first copy this script to a dedicated analysis directory
containing peak lists, a sequence or PDB file and a file listing unresolved
spin systems, and then modify its contents to suit your specific analysis.
The script contents are:
-\begin{exampleenv}
-"""Script for performing a full relaxation dispersion analysis using
CPMG-type data.""" \\
- \\
- \\
-\# Python module imports. \\
-from os import sep \\
- \\
-\# relax module imports. \\
-from auto\_analyses.relax\_disp import Relax\_disp \\
- \\
- \\
-\# Analysis variables. \\
-\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# \\
- \\
-\# The dispersion models. \\
-MODELS = [`R2eff', `No Rex', `LM63', `CR72', `IT99'] \\
- \\
-\# The grid search size (the number of increments per dimension). \\
-GRID\_INC = 21 \\
- \\
-\# The number of Monte Carlo simulations to be used for error analysis at
the end of the analysis. \\
-MC\_NUM = 500 \\
- \\
-\# The model selection technique to use. \\
-MODSEL = `AIC' \\
- \\
- \\
-\# Set up the data pipe. \\
-\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# \\
- \\
-\# Create the data pipe. \\
-pipe\_name = `base pipe' \\
-pipe\_bundle = `relax\_disp' \\
-pipe.create(pipe\_name=pipe\_name, bundle=pipe\_bundle,
pipe\_type=`relax\_disp') \\
- \\
-\# Load the sequence. \\
-sequence.read(`fake\_sequence.in', res\_num\_col=1, res\_name\_col=2) \\
- \\
-\# Name the spins so they can be matched to the assignments, and the isotope
for field strength scaling. \\
-spin.name(name=`N') \\
-spin.isotope(isotope=`15N') \\
- \\
-\# Set the relaxation dispersion experiment type. \\
-relax\_disp.exp\_type(`cpmg fixed') \\
- \\
-\# The spectral data - spectrum ID, peak list file name, CPMG frequency
(Hz), spectrometer frequency in Hertz. \\
-data = [ \\
-\hspace*{4ex} [`500\_reference.in',
`500\_MHz'+sep+`reference.in\_sparky', None, 500e6], \\
-\hspace*{4ex} [`500\_66.667.in', `500\_MHz'+sep+`66.667.in\_sparky',
66.6666, 500e6], \\
-\hspace*{4ex} [`500\_133.33.in', `500\_MHz'+sep+`133.33.in\_sparky',
133.3333, 500e6], \\
-\hspace*{4ex} [`500\_133.33.in.bis',
`500\_MHz'+sep+`133.33.in.bis\_sparky', 133.3333, 500e6], \\
-\hspace*{4ex} [`500\_200.in', `500\_MHz'+sep+`200.in\_sparky',
200.0000, 500e6], \\
-\hspace*{4ex} [`500\_266.67.in', `500\_MHz'+sep+`266.67.in\_sparky',
266.6666, 500e6], \\
-\hspace*{4ex} [`500\_333.33.in', `500\_MHz'+sep+`333.33.in\_sparky',
333.3333, 500e6], \\
-\hspace*{4ex} [`500\_400.in', `500\_MHz'+sep+`400.in\_sparky',
400.0000, 500e6], \\
-\hspace*{4ex} [`500\_466.67.in', `500\_MHz'+sep+`466.67.in\_sparky',
466.6666, 500e6], \\
-\hspace*{4ex} [`500\_533.33.in', `500\_MHz'+sep+`533.33.in\_sparky',
533.3333, 500e6], \\
-\hspace*{4ex} [`500\_533.33.in.bis',
`500\_MHz'+sep+`533.33.in.bis\_sparky', 533.3333, 500e6], \\
-\hspace*{4ex} [`500\_600.in', `500\_MHz'+sep+`600.in\_sparky',
600.0000, 500e6], \\
-\hspace*{4ex} [`500\_666.67.in', `500\_MHz'+sep+`666.67.in\_sparky',
666.6666, 500e6], \\
-\hspace*{4ex} [`500\_733.33.in', `500\_MHz'+sep+`733.33.in\_sparky',
733.3333, 500e6], \\
-\hspace*{4ex} [`500\_800.in', `500\_MHz'+sep+`800.in\_sparky',
800.0000, 500e6], \\
-\hspace*{4ex} [`500\_866.67.in', `500\_MHz'+sep+`866.67.in\_sparky',
866.6666, 500e6], \\
-\hspace*{4ex} [`500\_933.33.in', `500\_MHz'+sep+`933.33.in\_sparky',
933.3333, 500e6], \\
-\hspace*{4ex} [`500\_933.33.in.bis',
`500\_MHz'+sep+`933.33.in.bis\_sparky', 933.3333, 500e6], \\
-\hspace*{4ex} [`500\_1000.in', `500\_MHz'+sep+`1000.in\_sparky',
1000.0000, 500e6], \\
-\hspace*{4ex} [`800\_reference.in',
`800\_MHz'+sep+`reference.in\_sparky', None, 800e6], \\
-\hspace*{4ex} [`800\_66.667.in', `800\_MHz'+sep+`66.667.in\_sparky',
66.6666, 800e6], \\
-\hspace*{4ex} [`800\_133.33.in', `800\_MHz'+sep+`133.33.in\_sparky',
133.3333, 800e6], \\
-\hspace*{4ex} [`800\_133.33.in.bis',
`800\_MHz'+sep+`133.33.in.bis\_sparky', 133.3333, 800e6], \\
-\hspace*{4ex} [`800\_200.in', `800\_MHz'+sep+`200.in\_sparky',
200.0000, 800e6], \\
-\hspace*{4ex} [`800\_266.67.in', `800\_MHz'+sep+`266.67.in\_sparky',
266.6666, 800e6], \\
-\hspace*{4ex} [`800\_333.33.in', `800\_MHz'+sep+`333.33.in\_sparky',
333.3333, 800e6], \\
-\hspace*{4ex} [`800\_400.in', `800\_MHz'+sep+`400.in\_sparky',
400.0000, 800e6], \\
-\hspace*{4ex} [`800\_466.67.in', `800\_MHz'+sep+`466.67.in\_sparky',
466.6666, 800e6], \\
-\hspace*{4ex} [`800\_533.33.in', `800\_MHz'+sep+`533.33.in\_sparky',
533.3333, 800e6], \\
-\hspace*{4ex} [`800\_533.33.in.bis',
`800\_MHz'+sep+`533.33.in.bis\_sparky', 533.3333, 800e6], \\
-\hspace*{4ex} [`800\_600.in', `800\_MHz'+sep+`600.in\_sparky',
600.0000, 800e6], \\
-\hspace*{4ex} [`800\_666.67.in', `800\_MHz'+sep+`666.67.in\_sparky',
666.6666, 800e6], \\
-\hspace*{4ex} [`800\_733.33.in', `800\_MHz'+sep+`733.33.in\_sparky',
733.3333, 800e6], \\
-\hspace*{4ex} [`800\_800.in', `800\_MHz'+sep+`800.in\_sparky',
800.0000, 800e6], \\
-\hspace*{4ex} [`800\_866.67.in', `800\_MHz'+sep+`866.67.in\_sparky',
866.6666, 800e6], \\
-\hspace*{4ex} [`800\_933.33.in', `800\_MHz'+sep+`933.33.in\_sparky',
933.3333, 800e6], \\
-\hspace*{4ex} [`800\_933.33.in.bis',
`800\_MHz'+sep+`933.33.in.bis\_sparky', 933.3333, 800e6], \\
-\hspace*{4ex} [`800\_1000.in', `800\_MHz'+sep+`1000.in\_sparky',
1000.0000, 800e6] \\
-] \\
- \\
-\# Loop over the spectra. \\
-for id, file, cpmg\_frq, H\_frq in data: \\
-\hspace*{4ex} \# Load the peak intensities. \\
-\hspace*{4ex} spectrum.read\_intensities(file=file, spectrum\_id=id,
int\_method=`height') \\
- \\
-\hspace*{4ex} \# Set the relaxation dispersion CPMG frequencies. \\
-\hspace*{4ex} relax\_disp.cpmg\_frq(spectrum\_id=id, cpmg\_frq=cpmg\_frq) \\
- \\
-\hspace*{4ex} \# Set the NMR field strength of the spectrum. \\
-\hspace*{4ex} spectrometer.frequency(id=id, frq=H\_frq) \\
- \\
-\hspace*{4ex} \# Relaxation dispersion CPMG constant time delay T (in s). \\
-\hspace*{4ex} relax\_disp.relax\_time(spectrum\_id=id, time=0.030) \\
- \\
-\# Specify the duplicated spectra. \\
-spectrum.replicated(spectrum\_ids=[`500\_133.33.in', `500\_133.33.in.bis'])
\\
-spectrum.replicated(spectrum\_ids=[`500\_533.33.in', `500\_533.33.in.bis'])
\\
-spectrum.replicated(spectrum\_ids=[`500\_933.33.in', `500\_933.33.in.bis'])
\\
-spectrum.replicated(spectrum\_ids=[`800\_133.33.in', `800\_133.33.in.bis'])
\\
-spectrum.replicated(spectrum\_ids=[`800\_533.33.in', `800\_533.33.in.bis'])
\\
-spectrum.replicated(spectrum\_ids=[`800\_933.33.in', `800\_933.33.in.bis'])
\\
- \\
-\# Peak intensity error analysis. \\
-spectrum.error\_analysis(subset=[`500\_reference.in', `500\_66.667.in',
`500\_133.33.in', `500\_133.33\linebreak[0]{}.in.bis', `500\_200.in',
`500\_266.67.in', `500\_333.33.in', `500\_400.in', `500\_466.67.in',
`500\_533\linebreak[0]{}.33.in', `500\_533.33.in.bis', `500\_600.in',
`500\_666.67.in', `500\_733.33.in', `500\_800.in',
`500\linebreak[0]{}\_866.67.in', `500\_933.33.in', `500\_933.33.in.bis',
`500\_1000.in']) \\
-spectrum.error\_analysis(subset=[`800\_reference.in', `800\_66.667.in',
`800\_133.33.in', `800\_133.33\linebreak[0]{}.in.bis', `800\_200.in',
`800\_266.67.in', `800\_333.33.in', `800\_400.in', `800\_466.67.in',
`800\_533\linebreak[0]{}.33.in', `800\_533.33.in.bis', `800\_600.in',
`800\_666.67.in', `800\_733.33.in', `800\_800.in',
`800\linebreak[0]{}\_866.67.in', `800\_933.33.in', `800\_933.33.in.bis',
`800\_1000.in']) \\
- \\
-\# Deselect unresolved spins. \\
-deselect.read(file=`unresolved', dir=`500\_MHz', res\_num\_col=1) \\
-deselect.read(file=`unresolved', dir=`800\_MHz', res\_num\_col=1) \\
- \\
- \\
- \\
-\# Auto-analysis execution. \\
-\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# \\
- \\
-\# Do not change! \\
-Relax\_disp(pipe\_name=pipe\_name, pipe\_bundle=pipe\_bundle, models=MODELS,
grid\_inc=GRID\_INC, mc\_sim\linebreak[0]{}\_num=MC\_NUM, modsel=MODSEL) \\
-\end{exampleenv}
+\begin{lstlisting}
+"""Script for performing a full relaxation dispersion analysis using
CPMG-type data."""
+
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from auto_analyses.relax_disp import Relax_disp
+
+
+# Analysis variables.
+#####################
+
+# The dispersion models.
+MODELS = ['R2eff', 'No Rex', 'LM63', 'CR72', 'IT99']
+
+# The grid search size (the number of increments per dimension).
+GRID_INC = 21
+
+# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
+MC_NUM = 500
+
+# The model selection technique to use.
+MODSEL = 'AIC'
+
+
+# Set up the data pipe.
+#######################
+
+# Create the data pipe.
+pipe_name = 'base pipe'
+pipe_bundle = 'relax_disp'
+pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
+
+# Load the sequence.
+sequence.read('fake_sequence.in', res_num_col=1, res_name_col=2)
+
+# Name the spins so they can be matched to the assignments, and the isotope
for field strength scaling.
+spin.name(name='N')
+spin.isotope(isotope='15N')
+
+# Set the relaxation dispersion experiment type.
+relax_disp.exp_type('cpmg fixed')
+
+# The spectral data - spectrum ID, peak list file name, CPMG frequency (Hz),
spectrometer frequency in Hertz.
+data = [
+ ['500_reference.in', '500_MHz'+sep+'reference.in_sparky',
None, 500e6],
+ ['500_66.667.in', '500_MHz'+sep+'66.667.in_sparky',
66.6666, 500e6],
+ ['500_133.33.in', '500_MHz'+sep+'133.33.in_sparky',
133.3333, 500e6],
+ ['500_133.33.in.bis', '500_MHz'+sep+'133.33.in.bis_sparky',
133.3333, 500e6],
+ ['500_200.in', '500_MHz'+sep+'200.in_sparky',
200.0000, 500e6],
+ ['500_266.67.in', '500_MHz'+sep+'266.67.in_sparky',
266.6666, 500e6],
+ ['500_333.33.in', '500_MHz'+sep+'333.33.in_sparky',
333.3333, 500e6],
+ ['500_400.in', '500_MHz'+sep+'400.in_sparky',
400.0000, 500e6],
+ ['500_466.67.in', '500_MHz'+sep+'466.67.in_sparky',
466.6666, 500e6],
+ ['500_533.33.in', '500_MHz'+sep+'533.33.in_sparky',
533.3333, 500e6],
+ ['500_533.33.in.bis', '500_MHz'+sep+'533.33.in.bis_sparky',
533.3333, 500e6],
+ ['500_600.in', '500_MHz'+sep+'600.in_sparky',
600.0000, 500e6],
+ ['500_666.67.in', '500_MHz'+sep+'666.67.in_sparky',
666.6666, 500e6],
+ ['500_733.33.in', '500_MHz'+sep+'733.33.in_sparky',
733.3333, 500e6],
+ ['500_800.in', '500_MHz'+sep+'800.in_sparky',
800.0000, 500e6],
+ ['500_866.67.in', '500_MHz'+sep+'866.67.in_sparky',
866.6666, 500e6],
+ ['500_933.33.in', '500_MHz'+sep+'933.33.in_sparky',
933.3333, 500e6],
+ ['500_933.33.in.bis', '500_MHz'+sep+'933.33.in.bis_sparky',
933.3333, 500e6],
+ ['500_1000.in', '500_MHz'+sep+'1000.in_sparky',
1000.0000, 500e6],
+ ['800_reference.in', '800_MHz'+sep+'reference.in_sparky',
None, 800e6],
+ ['800_66.667.in', '800_MHz'+sep+'66.667.in_sparky',
66.6666, 800e6],
+ ['800_133.33.in', '800_MHz'+sep+'133.33.in_sparky',
133.3333, 800e6],
+ ['800_133.33.in.bis', '800_MHz'+sep+'133.33.in.bis_sparky',
133.3333, 800e6],
+ ['800_200.in', '800_MHz'+sep+'200.in_sparky',
200.0000, 800e6],
+ ['800_266.67.in', '800_MHz'+sep+'266.67.in_sparky',
266.6666, 800e6],
+ ['800_333.33.in', '800_MHz'+sep+'333.33.in_sparky',
333.3333, 800e6],
+ ['800_400.in', '800_MHz'+sep+'400.in_sparky',
400.0000, 800e6],
+ ['800_466.67.in', '800_MHz'+sep+'466.67.in_sparky',
466.6666, 800e6],
+ ['800_533.33.in', '800_MHz'+sep+'533.33.in_sparky',
533.3333, 800e6],
+ ['800_533.33.in.bis', '800_MHz'+sep+'533.33.in.bis_sparky',
533.3333, 800e6],
+ ['800_600.in', '800_MHz'+sep+'600.in_sparky',
600.0000, 800e6],
+ ['800_666.67.in', '800_MHz'+sep+'666.67.in_sparky',
666.6666, 800e6],
+ ['800_733.33.in', '800_MHz'+sep+'733.33.in_sparky',
733.3333, 800e6],
+ ['800_800.in', '800_MHz'+sep+'800.in_sparky',
800.0000, 800e6],
+ ['800_866.67.in', '800_MHz'+sep+'866.67.in_sparky',
866.6666, 800e6],
+ ['800_933.33.in', '800_MHz'+sep+'933.33.in_sparky',
933.3333, 800e6],
+ ['800_933.33.in.bis', '800_MHz'+sep+'933.33.in.bis_sparky',
933.3333, 800e6],
+ ['800_1000.in', '800_MHz'+sep+'1000.in_sparky',
1000.0000, 800e6]
+]
+
+# Loop over the spectra.
+for id, file, cpmg_frq, H_frq in data:
+ # Load the peak intensities.
+ spectrum.read_intensities(file=file, spectrum_id=id, int_method='height')
+
+ # Set the relaxation dispersion CPMG frequencies.
+ relax_disp.cpmg_frq(spectrum_id=id, cpmg_frq=cpmg_frq)
+
+ # Set the NMR field strength of the spectrum.
+ spectrometer.frequency(id=id, frq=H_frq)
+
+ # Relaxation dispersion CPMG constant time delay T (in s).
+ relax_disp.relax_time(spectrum_id=id, time=0.030)
+
+# Specify the duplicated spectra.
+spectrum.replicated(spectrum_ids=['500_133.33.in', '500_133.33.in.bis'])
+spectrum.replicated(spectrum_ids=['500_533.33.in', '500_533.33.in.bis'])
+spectrum.replicated(spectrum_ids=['500_933.33.in', '500_933.33.in.bis'])
+spectrum.replicated(spectrum_ids=['800_133.33.in', '800_133.33.in.bis'])
+spectrum.replicated(spectrum_ids=['800_533.33.in', '800_533.33.in.bis'])
+spectrum.replicated(spectrum_ids=['800_933.33.in', '800_933.33.in.bis'])
+
+# Peak intensity error analysis.
+spectrum.error_analysis(subset=['500_reference.in', '500_66.667.in',
'500_133.33.in', '500_133.33.in.bis', '500_200.in', '500_266.67.in',
'500_333.33.in', '500_400.in', '500_466.67.in', '500_533.33.in',
'500_533.33.in.bis', '500_600.in', '500_666.67.in', '500_733.33.in',
'500_800.in', '500_866.67.in', '500_933.33.in', '500_933.33.in.bis',
'500_1000.in'])
+spectrum.error_analysis(subset=['800_reference.in', '800_66.667.in',
'800_133.33.in', '800_133.33.in.bis', '800_200.in', '800_266.67.in',
'800_333.33.in', '800_400.in', '800_466.67.in', '800_533.33.in',
'800_533.33.in.bis', '800_600.in', '800_666.67.in', '800_733.33.in',
'800_800.in', '800_866.67.in', '800_933.33.in', '800_933.33.in.bis',
'800_1000.in'])
+
+# Deselect unresolved spins.
+deselect.read(file='unresolved', dir='500_MHz', res_num_col=1)
+deselect.read(file='unresolved', dir='800_MHz', res_num_col=1)
+
+
+
+# Auto-analysis execution.
+##########################
+
+# Do not change!
+Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, models=MODELS,
grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL)
+\end{lstlisting}
r20230 - /branches/relax_disp/docs/latex/relax_disp.tex