Python create_sequence Examples, opt_tm_fns.create_sequence Python Examples

Example #1

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File: opt_tm6_grid.py Project: tlinnet/relax

# Module docstring.
"""Set up the data pipe for testing optimisation against tm6 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data


# The model-free parameters.
tm = [2e-9, 10e-9]          
s2 = [0.2, 0.8]             
s2f = [0.7, 0.8]            
tf = [2e-12, 40e-12]        
ts = [2e-11, 1.8e-9]        

# Create the sequence.
create_sequence(len(tm)*len(s2)*len(s2f)*len(tf)*len(ts))

# Set up the data.
setup_data(dir='tm6_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for ts_index in range(len(ts)):
    for tf_index in range(len(tf)):
        for s2f_index in range(len(s2f)):
            for s2_index in range(len(s2)):
                for tm_index in range(len(tm)):
                    # Optimise and validate.
                    opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm[tm_index], s2=s2[s2_index], s2f=s2f[s2f_index], tf=tf[tf_index], ts=ts[ts_index])

Example #2

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File: opt_tm4_grid.py Project: tlinnet/relax

###############################################################################

# Module docstring.
"""Set up the data pipe for testing optimisation against tm4 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data

# The model-free parameters.
tm = [2e-9, 10e-9, 21e-9]
s2 = [0.2, 0.8, 0.95]
te = [2e-12, 40e-12]
rex = [0.5, 4]

# Create the sequence.
create_sequence(len(tm) * len(s2) * len(te) * len(rex))

# Set up the data.
setup_data(dir='tm4_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for rex_index in range(len(rex)):
    for te_index in range(len(te)):
        for s2_index in range(len(s2)):
            for tm_index in range(len(tm)):
                # Optimise and validate.
                opt_and_check(spin=cdp.mol[0].res[res_index].spin[0],
                              tm=tm[tm_index],

Example #3

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File: opt_tm7_grid.py Project: tlinnet/relax

# Module docstring.
"""Set up the data pipe for testing optimisation against tm7 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data

# The model-free parameters.
tm = [2e-9, 10e-9]
s2 = [0.2, 0.8]
s2f = [0.7, 0.8]
ts = [2e-12, 40e-12]
rex = [0.5, 4]

# Create the sequence.
create_sequence(len(tm) * len(s2) * len(s2f) * len(ts) * len(rex))

# Set up the data.
setup_data(dir='tm7_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for rex_index in range(len(rex)):
    for ts_index in range(len(ts)):
        for s2f_index in range(len(s2f)):
            for s2_index in range(len(s2)):
                for tm_index in range(len(tm)):
                    # Optimise and validate.
                    opt_and_check(spin=cdp.mol[0].res[res_index].spin[0],

Example #4

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File: opt_tm1_grid.py Project: tlinnet/relax

# along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
#                                                                             #
###############################################################################

# Module docstring.
"""Set up the data pipe for testing optimisation against tm1 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data

# The model-free parameters.
tm = [2e-9, 10e-9, 21e-9]
s2 = [0.2, 0.8, 0.95]

# Create the sequence.
create_sequence(len(tm) * len(s2))

# Set up the data.
setup_data(dir='tm1_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for s2_index in range(3):
    for tm_index in range(3):
        # Optimise and validate.
        opt_and_check(spin=cdp.mol[0].res[res_index].spin[0],
                      tm=tm[tm_index],
                      s2=s2[s2_index])

Example #5

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File: opt_tm9_grid.py Project: belisario21/relax_trunk

# along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
#                                                                             #
###############################################################################

"""Set up the data pipe for testing optimisation against tm9 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data


# The model-free parameters.
tm = [2e-9, 10e-9, 80e-9]   
rex = [0.5, 4, 20]

# Create the sequence.
create_sequence(len(tm)*len(rex))

# Set up the data.
setup_data(dir='tm9_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for rex_index in range(len(rex)):
    for tm_index in range(len(tm)):
        # Optimise and validate.
        opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm[tm_index], rex=rex[rex_index])

        # Increment the residue index.
        res_index += 1

Example #6

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File: opt_tm0_grid.py Project: belisario21/relax_trunk

# You should have received a copy of the GNU General Public License           #
# along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
#                                                                             #
###############################################################################

"""Set up the data pipe for testing optimisation against tm0 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data


# The model-free parameters.
tm = [2e-9, 10e-9, 80e-9]

# Create the sequence.
create_sequence(len(tm))

# Set up the data.
setup_data(dir='tm0_grid')

# Residue index.
res_index = 0

# Loop over tm.
for tm_index in range(len(tm)):
    # Optimise and validate.
    opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm[tm_index])

    # Increment the residue index.
    res_index += 1

Example #7

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File: opt_tm1_grid.py Project: belisario21/relax_trunk

# along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
#                                                                             #
###############################################################################

"""Set up the data pipe for testing optimisation against tm1 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data


# The model-free parameters.
tm = [2e-9, 10e-9, 21e-9]
s2 = [0.2, 0.8, 0.95]

# Create the sequence.
create_sequence(len(tm)*len(s2))

# Set up the data.
setup_data(dir='tm1_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for s2_index in range(3):
    for tm_index in range(3):
        # Optimise and validate.
        opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm[tm_index], s2=s2[s2_index])

        # Increment the residue index.
        res_index += 1

Example #8

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File: opt_tm7_grid.py Project: belisario21/relax_trunk

"""Set up the data pipe for testing optimisation against tm7 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data


# The model-free parameters.
tm = [2e-9, 10e-9]          
s2 = [0.2, 0.8]             
s2f = [0.7, 0.8]            
ts = [2e-12, 40e-12]        
rex = [0.5, 4]              

# Create the sequence.
create_sequence(len(tm)*len(s2)*len(s2f)*len(ts)*len(rex))

# Set up the data.
setup_data(dir='tm7_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for rex_index in range(len(rex)):
    for ts_index in range(len(ts)):
        for s2f_index in range(len(s2f)):
            for s2_index in range(len(s2)):
                for tm_index in range(len(tm)):
                    # Optimise and validate.
                    opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm[tm_index], s2=s2[s2_index], s2f=s2f[s2f_index], ts=ts[ts_index], rex=rex[rex_index])

Example #9

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File: opt_tm6_grid.py Project: belisario21/relax_trunk

"""Set up the data pipe for testing optimisation against tm6 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data


# The model-free parameters.
tm = [2e-9, 10e-9]          
s2 = [0.2, 0.8]             
s2f = [0.7, 0.8]            
tf = [2e-12, 40e-12]        
ts = [2e-11, 1.8e-9]        

# Create the sequence.
create_sequence(len(tm)*len(s2)*len(s2f)*len(tf)*len(ts))

# Set up the data.
setup_data(dir='tm6_grid')

# Residue index.
res_index = 0

# Loop over the parameters.
for ts_index in range(len(ts)):
    for tf_index in range(len(tf)):
        for s2f_index in range(len(s2f)):
            for s2_index in range(len(s2)):
                for tm_index in range(len(tm)):
                    # Optimise and validate.
                    opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm[tm_index], s2=s2[s2_index], s2f=s2f[s2f_index], tf=tf[tf_index], ts=ts[ts_index])

Example #10

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File: opt_tm0_grid.py Project: tlinnet/relax

# You should have received a copy of the GNU General Public License           #
# along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
#                                                                             #
###############################################################################

# Module docstring.
"""Set up the data pipe for testing optimisation against tm0 relaxation data."""

# relax module imports.
from opt_tm_fns import create_sequence, opt_and_check, setup_data

# The model-free parameters.
tm = [2e-9, 10e-9, 80e-9]

# Create the sequence.
create_sequence(len(tm))

# Set up the data.
setup_data(dir='tm0_grid')

# Residue index.
res_index = 0

# Loop over tm.
for tm_index in range(len(tm)):
    # Optimise and validate.
    opt_and_check(spin=cdp.mol[0].res[res_index].spin[0], tm=tm[tm_index])

    # Increment the residue index.
    res_index += 1