Author: bugman
Date: Wed May 19 10:49:53 2010
New Revision: 11206
URL: http://svn.gna.org/viewcvs/relax?rev=11206&view=rev
Log:
Created the rdc.corr_plot() and pcs_corr_plot() user functions.
These are for creating correlation plots of measured vs. back-calculated RDCs
and PCSs.
A couple of N-state model methods (return_grace_string() and return_units())
were added to allow the
user functions to work.
Modified:
1.3/generic_fns/pcs.py
1.3/generic_fns/rdc.py
1.3/prompt/pcs.py
1.3/prompt/rdc.py
1.3/specific_fns/n_state_model.py
Modified: 1.3/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pcs.py?rev=11206&r1=11205&r2=11206&view=diff
==============================================================================
--- 1.3/generic_fns/pcs.py (original)
+++ 1.3/generic_fns/pcs.py Wed May 19 10:49:53 2010
@@ -30,8 +30,8 @@
from warnings import warn
# relax module imports.
+from generic_fns import grace, pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
-from generic_fns import pipes
from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoSpinError
from relax_io import open_write_file, read_spin_data, write_spin_data
from relax_warnings import RelaxWarning
@@ -124,6 +124,69 @@
if verbosity:
print("\nUsing all paramagnetic positions.")
cdp.paramagnetic_centre = full_pos_list
+
+
+def corr_plot(format=None, file=None, dir=None, force=False):
+ """Generate a correlation plot of the measured vs. back-calculated PCSs.
+
+ @keyword format: The format for the plot file. The following values
are accepted: 'grace', a Grace plot; None, a plain text file.
+ @type format: str or None
+ @keyword file: The file name or object to write to.
+ @type file: str or file object
+ @keyword dir: The name of the directory to place the file into
(defaults to the current directory).
+ @type dir: str
+ @keyword force: A flag which if True will cause any pre-existing
file to be overwritten.
+ @type force: bool
+ """
+
+ # Test if the current pipe exists.
+ pipes.test()
+
+ # Test if the sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Does PCS data exist?
+ if not hasattr(cdp, 'pcs_ids') or not cdp.pcs_ids:
+ warn(RelaxWarning("No PCS data exists, skipping file creation."))
+ return
+
+ # Open the file for writing.
+ file = open_write_file(file, dir, force)
+
+ # Init.
+ data = []
+
+ # The diagonal.
+ data.append([[-100, -100], [100, 100]])
+
+ # Loop over the PCS data.
+ for align_id in cdp.pcs_ids:
+ # Append a new list for this alignment.
+ data.append([])
+
+ # Loop over the spins.
+ for spin, spin_id in spin_loop(return_id=True):
+ # Skip if data is missing.
+ if not hasattr(spin, 'pcs') or not hasattr(spin, 'pcs_bc') or
not align_id in spin.pcs.keys() or not align_id in spin.pcs_bc.keys():
+ continue
+
+ # Append the data.
+ data[-1].append([spin.pcs[align_id], spin.pcs_bc[align_id],
spin_id])
+
+ # The data size.
+ size = len(data)
+
+ # Only one data set.
+ data = [data]
+
+ # Grace file.
+ if format == 'grace':
+ # The header.
+ grace.write_xy_header(file=file, title="PCS correlation plot",
sets=size, set_names=[None]+cdp.pcs_ids, linestyle=[2]+[0]*size,
data_type=['pcs', 'pcs_bc'], axis_min=[-0.5, -0.5], axis_max=[0.5, 0.5],
legend_pos=[1, 0.5])
+
+ # The main data.
+ grace.write_xy_data(data=data, file=file, graph_type='xy')
def display(align_id=None):
@@ -300,7 +363,7 @@
errors.append(error)
# Print out.
- write_spin_data(file=sys.stdout, spin_ids=spin_ids, data=values,
data_name='RDCs', error=errors, error_name='RDC_error')
+ write_spin_data(file=sys.stdout, spin_ids=spin_ids, data=values,
data_name='PCSs', error=errors, error_name='PCS_error')
# Global (non-spin specific) data.
Modified: 1.3/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/rdc.py?rev=11206&r1=11205&r2=11206&view=diff
==============================================================================
--- 1.3/generic_fns/rdc.py (original)
+++ 1.3/generic_fns/rdc.py Wed May 19 10:49:53 2010
@@ -31,8 +31,8 @@
from warnings import warn
# relax module imports.
+from generic_fns import grace, pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
-from generic_fns import pipes
from maths_fns.rdc import ave_rdc_tensor
from physical_constants import dipolar_constant, return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxNoRDCError, RelaxNoSequenceError,
RelaxNoSpinError
@@ -80,6 +80,69 @@
# Calculate the RDC.
spin.rdc_bc = ave_rdc_tensor(dj, unit_vect, cdp.N,
cdp.align_tensors[i].A, weights=weights)
+
+
+def corr_plot(format=None, file=None, dir=None, force=False):
+ """Generate a correlation plot of the measured vs. back-calculated RDCs.
+
+ @keyword format: The format for the plot file. The following values
are accepted: 'grace', a Grace plot; None, a plain text file.
+ @type format: str or None
+ @keyword file: The file name or object to write to.
+ @type file: str or file object
+ @keyword dir: The name of the directory to place the file into
(defaults to the current directory).
+ @type dir: str
+ @keyword force: A flag which if True will cause any pre-existing
file to be overwritten.
+ @type force: bool
+ """
+
+ # Test if the current pipe exists.
+ pipes.test()
+
+ # Test if the sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Does RDC data exist?
+ if not hasattr(cdp, 'rdc_ids') or not cdp.rdc_ids:
+ warn(RelaxWarning("No RDC data exists, skipping file creation."))
+ return
+
+ # Open the file for writing.
+ file = open_write_file(file, dir, force)
+
+ # Init.
+ data = []
+
+ # The diagonal.
+ data.append([[-100, -100], [100, 100]])
+
+ # Loop over the RDC data.
+ for align_id in cdp.rdc_ids:
+ # Append a new list for this alignment.
+ data.append([])
+
+ # Loop over the spins.
+ for spin, spin_id in spin_loop(return_id=True):
+ # Skip if data is missing.
+ if not hasattr(spin, 'rdc') or not hasattr(spin, 'rdc_bc') or
not align_id in spin.rdc.keys() or not align_id in spin.rdc_bc.keys():
+ continue
+
+ # Append the data.
+ data[-1].append([spin.rdc[align_id], spin.rdc_bc[align_id],
spin_id])
+
+ # The data size.
+ size = len(data)
+
+ # Only one data set.
+ data = [data]
+
+ # Grace file.
+ if format == 'grace':
+ # The header.
+ grace.write_xy_header(file=file, title="RDC correlation plot",
sets=size, set_names=[None]+cdp.rdc_ids, linestyle=[2]+[0]*size,
data_type=['rdc', 'rdc_bc'], axis_min=[-10, -10], axis_max=[10, 10],
legend_pos=[1, 0.5])
+
+ # The main data.
+ grace.write_xy_data(data=data, file=file, graph_type='xy')
def display(align_id=None):
Modified: 1.3/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/pcs.py?rev=11206&r1=11205&r2=11206&view=diff
==============================================================================
--- 1.3/prompt/pcs.py (original)
+++ 1.3/prompt/pcs.py Wed May 19 10:49:53 2010
@@ -75,7 +75,7 @@
Examples
~~~~~~~~
- To calculate the RDC Q-factor for only the spins '@H26', '@H27', and
'@H28', type one of:
+ To calculate the PCS Q-factor for only the spins '@H26', '@H27', and
'@H28', type one of:
relax> pcs.calc_q_factors('@H26 & @H27 & @H28')
relax> pcs.calc_q_factors(spin_id='@H26 & @H27 & @H28')
@@ -231,6 +231,62 @@
pcs.copy(pipe_from=pipe_from, pipe_to=pipe_to, align_id=align_id)
+ def corr_plot(self, format='grace', file='pcs_corr_plot.agr', dir=None,
force=False):
+ """Generate a correlation plot of the measured vs. the
back-calculated PCSs.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ format: The format of the plot data.
+
+ file: The name of the file.
+
+ dir: The directory name.
+
+ force: A flag which if True will cause the file to be overwritten.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ Two formats are currently supported. If format is set to 'grace',
then a Grace plot file
+ will be created. If the format arg is set to None, then a plain
text list of the measured
+ and back-calculated data will be created.
+
+
+ Examples
+ ~~~~~~~~
+
+ To create a Grace plot of the data, type:
+
+ relax> pcs.corr_plot()
+
+
+ To create a plain text list of the measured and back-calculated
data, type one of:
+
+ relax> pcs.corr_plot(None)
+ relax> pcs.corr_plot(format=None)
+ """
+
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "pcs.corr_plot("
+ text = text + "format=" + repr(format)
+ text = text + ", file=" + repr(file)
+ text = text + ", dir=" + repr(dir)
+ text = text + ", force=" + repr(force) + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str(format, 'format', can_be_none=True)
+ arg_check.is_str(file, 'file name')
+ arg_check.is_str(dir, 'directory name', can_be_none=True)
+ arg_check.is_bool(force, 'force flag')
+
+ # Execute the functional code.
+ pcs.corr_plot(format=format, file=file, dir=dir, force=force)
+
+
def delete(self, align_id=None):
"""Delete the PCS data corresponding to the alignment ID.
@@ -316,7 +372,7 @@
spin_name_col: The spin name column (alternative to the
spin_id_col).
- data_col: The RDC data column.
+ data_col: The PCS data column.
error_col: The experimental error column.
Modified: 1.3/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/rdc.py?rev=11206&r1=11205&r2=11206&view=diff
==============================================================================
--- 1.3/prompt/rdc.py (original)
+++ 1.3/prompt/rdc.py Wed May 19 10:49:53 2010
@@ -149,6 +149,62 @@
# Execute the functional code.
rdc.copy(pipe_from=pipe_from, pipe_to=pipe_to, align_id=align_id)
+
+
+ def corr_plot(self, format='grace', file='rdc_corr_plot.agr', dir=None,
force=False):
+ """Generate a correlation plot of the measured vs. the
back-calculated RDCs.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ format: The format of the plot data.
+
+ file: The name of the file.
+
+ dir: The directory name.
+
+ force: A flag which if True will cause the file to be overwritten.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ Two formats are currently supported. If format is set to 'grace',
then a Grace plot file
+ will be created. If the format arg is set to None, then a plain
text list of the measured
+ and back-calculated data will be created.
+
+
+ Examples
+ ~~~~~~~~
+
+ To create a Grace plot of the data, type:
+
+ relax> rdc.corr_plot()
+
+
+ To create a plain text list of the measured and back-calculated
data, type one of:
+
+ relax> rdc.corr_plot(None)
+ relax> rdc.corr_plot(format=None)
+ """
+
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "rdc.corr_plot("
+ text = text + "format=" + repr(format)
+ text = text + ", file=" + repr(file)
+ text = text + ", dir=" + repr(dir)
+ text = text + ", force=" + repr(force) + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str(format, 'format', can_be_none=True)
+ arg_check.is_str(file, 'file name')
+ arg_check.is_str(dir, 'directory name', can_be_none=True)
+ arg_check.is_bool(force, 'force flag')
+
+ # Execute the functional code.
+ rdc.corr_plot(format=format, file=file, dir=dir, force=force)
def delete(self, align_id=None):
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=11206&r1=11205&r2=11206&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Wed May 19 10:49:53 2010
@@ -1829,6 +1829,56 @@
return 'proton_type'
+ def return_grace_string(self, param):
+ """Return the Grace string representation of the parameter.
+
+ This is used for axis labelling.
+
+ @param param: The specific analysis parameter.
+ @type param: str
+ @return: The Grace string representation of the parameter.
+ @rtype: str
+ """
+
+ # The measured PCS.
+ if param == 'pcs':
+ return "Measured PCS"
+
+ # The back-calculated PCS.
+ if param == 'pcs_bc':
+ return "Back-calculated PCS"
+
+ # The measured RDC.
+ if param == 'rdc':
+ return "Measured RDC"
+
+ # The back-calculated RDC.
+ if param == 'rdc_bc':
+ return "Back-calculated RDC"
+
+
+ def return_units(self, param, spin=None, spin_id=None):
+ """Return a string representing the parameters units.
+
+ @param param: The name of the parameter to return the units string
for.
+ @type param: str
+ @param spin: The spin container (unused).
+ @type spin: None
+ @param spin_id: The spin identification string (unused).
+ @type spin_id: None
+ @return: The parameter units string.
+ @rtype: str
+ """
+
+ # PCSs.
+ if param == 'pcs' or param == 'pcs_bc':
+ return 'ppm'
+
+ # RDCs.
+ if param == 'rdc' or param == 'rdc_bc':
+ return 'Hz'
+
+
set_doc = """
N-state model set details
~~~~~~~~~~~~~~~~~~~~~~~~~
r11206 - in /1.3: generic_fns/pcs.py generic_fns/rdc.py prompt/pcs.py prompt/rdc.py specific_fns/n_state_model.py