Hi Edward
So as far as I understood, I have to prove that I can write scripts. As
already mentioned, I am not a programmer. To prove, I attach the
final_data_extraction.py script. i tested it with your code_validator.py
script and it seems to be ok.
I hope this can help.
Cheers
Michael
Edward d'Auvergne schrieb:
Hi,
Interesting that the subject of this message ist 'auf Deutsch'!
Unfortunately I cannot allow you to be a member of the relax project
straight away. Becoming a relax developer is a democratic process
which first requires a demonstration of basic coding ability (or more
precisely knowing your limits and not hurting other parts of the code)
and adherence to the principles of the project and the coding
conventions. This is all described in chapter 9 of the relax manual,
the development chapter, which should be read prior to joining the
project. Section 9.4.1 "Becoming a committer" details the steps for
joining. From the outside an open source project looks quite chaotic
but in reality it is highly structured and only code of the highest
quality - every line of code is checked by myself or others - is
accepted.
Cheers,
Edward
2009/11/12 Michael Bieri <michael.bieri@xxxxxx>:
Michael Bieri requested membership to the group relax
at Gna!
User Details:
-------------
Name: Michael Bieri
Login: michaelbieri
Email: michael.bieri@xxxxxx
Project Details:
----------------
Name: relax
Unix Name: relax
Main Page: https://gna.org/projects/relax
Message from user:
------------------
hello
Note:
-----
You receive this email because you are registered as an administrator of this
project and the system has been configured to send emails to administrators
when new users register.
Please login and go to the page
https://gna.org/project/admin/useradmin.php?group=relax
and approve or discard this membership request.
-- the Gna! team
_______________________________________________
Nachricht geschickt von/durch Gna!
http://gna.org/
#####################################################################################
# Script for Final Data Extraction after Model-free Analysis
#
# Michael Bieri
#
# 16.9.2009
#
#####################################################################################
# Extract Data to Table
#create a table file
# Python module imports.
from string import replace
# relax module imports.
from generic_fns.mol_res_spin import spin_loop
from generic_fns import pipes
pipe.create('Data_extraction', 'mf')
results.read()
#create file
self.file = open('Model-free_Results.txt', 'w')
self.file.write('Data Extraction by Michael Bieri')
self.file.write("\n")
self.file.write("\n")
self.file.write("Residue Model S2 Rex
[1/s] Te Relaxation Parameters\n")
self.file.write("\n")
for spin, spin_id in spin_loop(return_id=True):
# The spin ID string.
spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')]
spin_res = spin_id[spin_id.index('&')+2:spin_id.index('@')]
self.file.write((spin_res) + " " + (spin_no))
# The spin is not selected.
if not spin.select:
self.file.write("\n")
continue
# The model-free model.
if hasattr(spin, 'model'):
spin.model = spin.model[1:2]
self.file.write(" " + spin.model)
# S2.
if hasattr(spin, 's2'):
s2 = str(spin.s2)
s2_err = str(spin.s2_err)
if spin.s2 == None:
self.file.write("")
else:
self.file.write(" " + s2[0:5]+ " +/- " +
s2_err[0:4])
# Rex.
if hasattr(spin, 'rex'):
rex = str(spin.rex)
rex_err = str(spin.rex_err)
if spin.rex == None:
self.file.write(" ")
else:
rex_eff = spin.rex * (int(spin.frq_labels[1]) *
1000000 * 2 * 3.14159)**2
rex = str(rex_eff)
rex_err_eff = spin.rex_err * (int(spin.frq_labels[1])
* 1000000 * 2 * 3.14159)**2
rex_err = str(rex_err_eff)
self.file.write(" " + rex[0:5]+ " +/- "
+ rex_err[0:4])
# Te
if hasattr(spin, 'te'):
if spin.te == None:
self.file.write(" ")
else:
te_ps = spin.te * 1e-12
te = str(te_ps)
te_err = str(spin.te_err)
self.file.write(" " + te[0:5]+ " +/- "
+ te_err[0:4])
# Parameters.
if hasattr(spin, 'params'):
self.file.write(" " +
str(spin.params[0:len(spin.params)]))
else:
self.file.write("\\n")
continue
# Start a new line.
self.file.write("\n")
##################################################################################################
#Create Single Data Files
value.write(param='rex', file='rex.txt', dir='final_results', force=True)
value.write(param='s2', file='s2.txt', dir='final_results', force=True)
value.write(param='s2f', file='s2f.txt', dir='final_results', force=True)
value.write(param='s2s', file='s2s.txt', dir='final_results', force=True)
value.write(param='te', file='te.txt', dir='final_results', force=True)
value.write(param='tf', file='tf.txt', dir='final_results', force=True)
value.write(param='ts', file='ts.txt', dir='final_results', force=True)
value.write(param='rex', file='rex.txt', dir='final_results', force=True)
value.write(param='r', file='r.txt', dir='final_results', force=True)
value.write(param='rex', file='rex.txt', dir='final_results', force=True)
value.write(param='csa', file='csa.txt', dir='final_results', force=True)
value.write(param='rex', file='rex.txt', dir='final_results', force=True)
value.write(param='local_tm', file='local_tm.txt', dir='final_results',
force=True)
##################################################################################################
#Create Grace Plots
grace.write(x_data_type='spin', y_data_type='s2', file='s2.agr', force=True)
grace.write(x_data_type='spin', y_data_type='te', file='te.agr', force=True)
grace.write(x_data_type='spin', y_data_type='s2f', file='s2f.agr', force=True)
grace.write(x_data_type='spin', y_data_type='s2s', file='s2s.agr', force=True)
grace.write(x_data_type='spin', y_data_type='ts', file='ts.agr', force=True)
grace.write(x_data_type='spin', y_data_type='tf', file='tf.agr', force=True)
grace.write(x_data_type='spin', y_data_type='csa', file='csa.agr', force=True)
grace.write(x_data_type='te', y_data_type='s2', file='s2-te.agr', force=True)
##################################################################################################
#Create Diffusion Tensor
# Display the diffusion tensor.
diffusion_tensor.display()
# Create the tensor PDB file.
tensor_file = 'tensor.pdb'
structure.create_diff_tensor_pdb(file=tensor_file, force=True)
##################################################################################################
# Create S2 Macro for PyMol
# Python module imports.
from string import replace
# relax module imports.
from generic_fns.mol_res_spin import spin_loop
from generic_fns import pipes
#create file
self.file = open('s2.pml', 'w')
self.file.write("bg_color white\n")
self.file.write("color gray90\n")
self.file.write("hide all\n")
self.file.write("show ribbon\n")
for spin, spin_id in spin_loop(return_id=True):
#select residue
spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')]
#ribbon color
if hasattr(spin, 's2'):
s2 = str(spin.s2)
if spin.s2 == None:
self.file.write("")
else:
width = ((1-spin.s2) * 2)
green = 1 - ((spin.s2)**3)
green = green * green * green #* green * green
green = 1 - green
self.file.write("set_color resicolor" + spin_no + ",
[1, " + str(green) + ", 0]\n")
self.file.write("color resicolor" + spin_no + ", resi
" + spin_no + "\n")
self.file.write("set_bond stick_radius, " +
str(width) + ", resi " + spin_no + "\n")
self.file.write("hide all\n")
self.file.write("show sticks, name C+N+CA\n")
self.file.write("set stick_quality, 10\n")
self.file.write("ray\n")
##################################################################################################
# Create Rex Macro for PyMol
#create file
self.file = open('rex.pml', 'w')
self.file.write("bg_color white\n")
self.file.write("color gray90\n")
self.file.write("hide all\n")
self.file.write("show ribbon\n")
max_rex = 0
#find max Rex
for spin, spin_id in spin_loop(return_id=True):
if hasattr(spin, 'rex'):
if not spin.rex == None:
if spin.rex > max_rex:
max_rex = spin.rex
for spin, spin_id in spin_loop(return_id=True):
#select residue
spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')]
#ribbon color
if hasattr(spin, 'rex'):
rex = str(spin.rex)
if spin.rex == None:
self.file.write("")
else:
rel_rex = spin.rex / max_rex
width = ((rel_rex) * 2)
green = ((rel_rex))
green = green * green * green #* green * green
green = 1 - green
self.file.write("set_color resicolor" + spin_no + ",
[1 ," + str(green) + ", 0]\n")
self.file.write("color resicolor" + spin_no + ", resi
" + spin_no + "\n")
self.file.write("set_bond stick_radius, " +
str(width) + ", resi " + spin_no + "\n")
self.file.write("hide all\n")
self.file.write("show sticks, name C+N+CA\n")
self.file.write("set stick_quality, 10\n")
self.file.write("ray\n")
##################################################################################################
print ""
print ""
print " ---------- done ----------------"
print ""
print ""
print "Grace Plots are in Folder /grace/"
print ""
print "Signle Text Files for Relaxation Parameters are in Folder
/final_results/"
print ""
print "Diffusion Tensor is in current Folder"
print ""
print "PyMol Macros are in current Folder - execute in PyMol with Command:"
print "@rex.pml and @s2.pml"
Re: Mitgliedsantrag für die Gruppe relax