Or open the relax prompt
Ctrl+p
And write:
script("script.py")
------------ OUT COME ---------
script = 'script.py'
----------------------------------------------------------------------------------------------------
# Python module imports.
from numpy import float64, zeros
# relax module imports.
from lib.auto_relaxation.ri_comps import calc_fixed_csa,
calc_fixed_dip, comp_csa_const_func, comp_dip_const_func
from lib.physical_constants import h_bar, mu0, return_gyromagnetic_ratio
class Data:
"""Dummy class for storing data."""
# Initialise the data container.
data = Data()
# The spectrometer frequency (Hz).
frq = 500e6
# The dynamically averaged bond length (m) and chemical shift tensor anisotropy.
r = 1.02e-10
csa = -172e-6
# Add the needed physical constants to the data storage.
data.gx = return_gyromagnetic_ratio('15N')
data.gh = return_gyromagnetic_ratio('1H')
data.mu0 = mu0
data.h_bar = h_bar
# The number of frequencies.
data.num_frq = 1
# Initialise dipolar and CSA data structures.
data.dip_const_fixed = 0.0
data.csa_const_fixed = [0.0]
data.dip_const_func = 0.0
data.csa_const_func = zeros(1, float64)
# Nuclear frequencies.
frq = frq * 2 * pi
frqX = frq * data.gx / data.gh
# Calculate the five frequencies which cause R1, R2, and NOE relaxation.
data.frq_list = zeros((1, 5), float64)
data.frq_list[0, 1] = frqX
data.frq_list[0, 2] = frq - frqX
data.frq_list[0, 3] = frq
data.frq_list[0, 4] = frq + frqX
data.frq_sqrd_list = data.frq_list ** 2
# Calculate the fixed component of the dipolar and CSA constants.
calc_fixed_dip(data)
calc_fixed_csa(data)
# Calculate the dipolar and CSA constants.
comp_dip_const_func(data, r)
comp_csa_const_func(data, csa)
# Rename the dipolar and CSA constants.
d = data.dip_const_func
c = data.csa_const_func[0]
# Printout.
print("d: %s" % d)
print("c: %s" % c)
--------------------------------------------------------------------------------------------------
d: 1300116668.53
c: 1000661534.67
2014-03-18 17:15 GMT+01:00 Edward d'Auvergne <[email protected]>:
> Hi Stefano,
>
> When running relax, you should avoid putting any files in the relax
> source code directories. These should be kept separate at all times -
> otherwise the result could be severe problems that are very difficult
> to understand. To see the output of the script when running in GUI
> mode, you will have to open the relax controller window were all
> messages are displayed. To do this, perform one of:
>
> - Select the 'View->Controller' menu item.
> - Click on the 'relax controller' button in the toolbar.
> - Type Ctrl-Z.
>
> The two numbers should be printed at the bottom. If you see errors,
> then there is likely to be word wrapping problems - one line has been
> split into two in the email text.
>
> Regards,
>
> Edward
>
>
> On 18 March 2014 17:06, Stefano Luciano Ciurli <[email protected]>
> wrote:
>> Hi Edward,
>> thank you for the exhaustive answer.
>> I have saved the script as a filename.py file in the
>> /relax/Contents/Resources/user_functions directory and tried to run in from
>> within relax using the menu user functions (n-z) -> script
>> However, it does not appear to do anything.
>> Any hint?
>> Stefano
>>
>> On Mar 18, 2014, at 10:04 AM, Edward d'Auvergne wrote:
>>
>> # Python module imports.
>> from numpy import float64, zeros
>>
>> # relax module imports.
>> from lib.auto_relaxation.ri_comps import calc_fixed_csa,
>> calc_fixed_dip, comp_csa_const_func, comp_dip_const_func
>> from lib.physical_constants import h_bar, mu0, return_gyromagnetic_ratio
>>
>>
>> class Data:
>> """Dummy class for storing data."""
>>
>> # Initialise the data container.
>> data = Data()
>>
>> # The spectrometer frequency (Hz).
>> frq = 500e6
>>
>> # The dynamically averaged bond length (m) and chemical shift tensor
>> anisotropy.
>> r = 1.02e-10
>> csa = -172e-6
>>
>> # Add the needed physical constants to the data storage.
>> data.gx = return_gyromagnetic_ratio('15N')
>> data.gh = return_gyromagnetic_ratio('1H')
>> data.mu0 = mu0
>> data.h_bar = h_bar
>>
>> # The number of frequencies.
>> data.num_frq = 1
>>
>> # Initialise dipolar and CSA data structures.
>> data.dip_const_fixed = 0.0
>> data.csa_const_fixed = [0.0]
>> data.dip_const_func = 0.0
>> data.csa_const_func = zeros(1, float64)
>>
>> # Nuclear frequencies.
>> frq = frq * 2 * pi
>> frqX = frq * data.gx / data.gh
>>
>> # Calculate the five frequencies which cause R1, R2, and NOE relaxation.
>> data.frq_list = zeros((1, 5), float64)
>> data.frq_list[0, 1] = frqX
>> data.frq_list[0, 2] = frq - frqX
>> data.frq_list[0, 3] = frq
>> data.frq_list[0, 4] = frq + frqX
>> data.frq_sqrd_list = data.frq_list ** 2
>>
>> # Calculate the fixed component of the dipolar and CSA constants.
>> calc_fixed_dip(data)
>> calc_fixed_csa(data)
>>
>> # Calculate the dipolar and CSA constants.
>> comp_dip_const_func(data, r)
>> comp_csa_const_func(data, csa)
>>
>> # Rename the dipolar and CSA constants.
>> d = data.dip_const_func
>> c = data.csa_const_func[0]
>>
>> # Printout.
>> print("d: %s" % d)
>> print("c: %s" % c)
>>
>
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