Author: bugman
Date: Tue Jul 8 21:36:00 2008
New Revision: 6848
URL: http://svn.gna.org/viewcvs/relax?rev=6848&view=rev
Log:
Converted all of the rdc user functions from the relax_data code.
Modified:
branches/rdc_analysis/prompt/rdc.py
Modified: branches/rdc_analysis/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/prompt/rdc.py?rev=6848&r1=6847&r2=6848&view=diff
==============================================================================
--- branches/rdc_analysis/prompt/rdc.py (original)
+++ branches/rdc_analysis/prompt/rdc.py Tue Jul 8 21:36:00 2008
@@ -19,6 +19,9 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
#
###############################################################################
+
+# Module docstring.
+"""User functions involved with RDCs."""
# Python module imports.
import sys
@@ -42,82 +45,63 @@
self.__relax__ = relax
- def back_calc(self, id=None, frq_label=None, frq=None):
- """Function for back calculating relaxation data.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
-
- frq_label: The field strength label.
-
- frq: The spectrometer frequency in Hz.
-
+ def back_calc(self, id=None):
+ """Back calculate RDCs.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The RDC identification string.
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "rdc.back_calc("
- text = text + "id=" + `id`
- text = text + ", frq_label=" + `frq_label`
- text = text + ", frq=" + `frq` + ")"
- print text
-
- # Relaxation data type.
- if type(id) != str:
- raise RelaxStrError, ('relaxation label', id)
-
- # Frequency label.
- if type(frq_label) != str:
- raise RelaxStrError, ('frequency label', frq_label)
-
- # Frequency.
- if type(frq) != float:
- raise RelaxFloatError, ('frequency', frq)
-
- # Execute the functional code.
- rdc.back_calc(id=id, frq_label=frq_label, frq=frq)
-
-
- def copy(self, pipe_from=None, pipe_to=None, id=None, frq_label=None):
- """Function for copying relaxation data from pipe_from to pipe_to.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- pipe_from: The name of the pipe to copy the relaxation data from.
-
- pipe_to: The name of the pipe to copy the relaxation data to.
-
- id: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
-
- frq_label: The field strength label.
+ text = text + "id=" + `id` + ")"
+ print text
+
+ # Identification string.
+ if type(id) != str:
+ raise RelaxStrError, ('identification string', id)
+
+ # Execute the functional code.
+ rdc.back_calc(id=id)
+
+
+ def copy(self, pipe_from=None, pipe_to=None, id=None):
+ """Copy RDC data from pipe_from to pipe_to.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ pipe_from: The name of the pipe to copy the RDC data from.
+
+ pipe_to: The name of the pipe to copy the RDC data to.
+
+ id: The RDC identification string.
Description
~~~~~~~~~~~
- This function will copy relaxation data from 'pipe_from' to
'pipe_to'. If id and frq_label
- are not given then all relaxation data will be copied, otherwise
only a specific data set
- will be copied.
+ This function will copy RDC data from 'pipe_from' to 'pipe_to'. If
id is not given then all
+ RDC data will be copied, otherwise only a specific data set will be.
Examples
~~~~~~~~
- To copy all relaxation data from pipe 'm1' to pipe 'm9', type one of:
+ To copy all RDC data from pipe 'm1' to pipe 'm9', type one of:
relax> rdc.copy('m1', 'm9')
relax> rdc.copy(pipe_from='m1', pipe_to='m9')
- relax> rdc.copy('m1', 'm9', None, None)
- relax> rdc.copy(pipe_from='m1', pipe_to='m9', id=None,
frq_label=None)
-
- To copy only the NOE relaxation data with the frq_label of '800'
from 'm3' to 'm6', type one
- of:
-
- relax> rdc.copy('m3', 'm6', 'NOE', '800')
- relax> rdc.copy(pipe_from='m3', pipe_to='m6', id='NOE',
frq_label='800')
+ relax> rdc.copy('m1', 'm9', None)
+ relax> rdc.copy(pipe_from='m1', pipe_to='m9', id=None)
+
+ To copy only the 'Th' RDC data from 'm3' to 'm6', type one of:
+
+ relax> rdc.copy('m3', 'm6', 'Th')
+ relax> rdc.copy(pipe_from='m3', pipe_to='m6', id='Th')
"""
# Function intro text.
@@ -125,8 +109,7 @@
text = sys.ps3 + "rdc.copy("
text = text + "pipe_from=" + `pipe_from`
text = text + ", pipe_to=" + `pipe_to`
- text = text + ", id=" + `id`
- text = text + ", frq_label=" + `frq_label` + ")"
+ text = text + ", id=" + `id` + ")"
print text
# The pipe_from argument.
@@ -141,103 +124,85 @@
if pipe_from == None and pipe_to == None:
raise RelaxError, "The pipe_from and pipe_to arguments cannot
both be set to None."
- # Relaxation data type.
+ # Id string.
if id != None and type(id) != str:
- raise RelaxNoneStrError, ('relaxation label', id)
-
- # Frequency label.
- if frq_label != None and type(frq_label) != str:
- raise RelaxNoneStrError, ('frequency label', frq_label)
-
- # Execute the functional code.
- rdc.copy(pipe_from=pipe_from, pipe_to=pipe_to, id=id,
frq_label=frq_label)
-
-
- def delete(self, id=None, frq_label=None):
- """Function for deleting the relaxation data corresponding to id and
frq_label.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
-
- frq_label: The field strength label.
+ raise RelaxNoneStrError, ('identification string', id)
+
+ # Execute the functional code.
+ rdc.copy(pipe_from=pipe_from, pipe_to=pipe_to, id=id)
+
+
+ def delete(self, id=None):
+ """Delete the RDC data corresponding to id.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The RDC identification string.
Examples
~~~~~~~~
- To delete the relaxation data corresponding to id='NOE',
frq_label='600', type:
-
- relax> rdc.delete('NOE', '600')
+ To delete the RDC data corresponding to id='PH_gel', type:
+
+ relax> rdc.delete('PH_gel')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "rdc.delete("
- text = text + "id=" + `id`
- text = text + ", frq_label=" + `frq_label` + ")"
- print text
-
- # Relaxation data type.
- if type(id) != str:
- raise RelaxStrError, ('relaxation label', id)
-
- # Frequency label.
- if type(frq_label) != str:
- raise RelaxStrError, ('frequency label', frq_label)
-
- # Execute the functional code.
- rdc.delete(id=id, frq_label=frq_label)
-
-
- def display(self, id=None, frq_label=None):
- """Function for displaying the relaxation data corresponding to id
and frq_label.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
-
- frq_label: The field strength label.
+ text = text + "id=" + `id` + ")"
+ print text
+
+ # Id string.
+ if type(id) != str:
+ raise RelaxStrError, ('identification string', id)
+
+ # Execute the functional code.
+ rdc.delete(id=id)
+
+
+ def display(self, id=None):
+ """Display the RDC data corresponding to id.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The RDC identification string.
Examples
~~~~~~~~
- To display the NOE relaxation data at 600 MHz, type:
-
- relax> rdc.display('NOE', '600')
+ To display the 'phage' RDC data, type:
+
+ relax> rdc.display('phage')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "rdc.display("
- text = text + "id=" + `id`
- text = text + ", frq_label=" + `frq_label` + ")"
- print text
-
- # Relaxation data type.
- if type(id) != str:
- raise RelaxStrError, ('relaxation label', id)
-
- # Frequency label.
- if type(frq_label) != str:
- raise RelaxStrError, ('frequency label', frq_label)
-
- # Execute the functional code.
- rdc.display(id=id, frq_label=frq_label)
+ text = text + "id=" + `id` + ")"
+ print text
+
+ # Id string.
+ if type(id) != str:
+ raise RelaxStrError, ('identification string', id)
+
+ # Execute the functional code.
+ rdc.display(id=id)
def read(self, id=None, file=None, dir=None, mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None,
data_col=2, error_col=3, sep=None):
- """Function for reading R1, R2, or NOE relaxation data from a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The RDC identification string.
-
- file: The name of the file containing the relaxation data.
+ """Read the RDC data from file.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The RDC identification string.
+
+ file: The name of the file containing the RDC data.
dir: The directory where the file is located.
@@ -251,7 +216,7 @@
spin_name_col: The spin name column (this defaults to no column).
- data_col: The relaxation data column (the default is 2).
+ data_col: The RDC data column (the default is 2).
error_col: The experimental error column (the default is 3).
@@ -331,15 +296,13 @@
rdc.read(id=id, file=file, dir=dir, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, data_col=data_col,
error_col=error_col, sep=sep)
- def write(self, id=None, frq_label=None, file=None, dir=None,
force=False):
- """Function for writing R1, R2, or NOE relaxation data to a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
-
- frq_label: The field strength label.
+ def write(self, id=None, file=None, dir=None, force=False):
+ """Write the RDC data to file.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The RDC identification string.
file: The name of the file.
@@ -352,27 +315,21 @@
~~~~~~~~~~~
If no directory name is given, the file will be placed in the
current working directory.
- The 'id' and 'frq_label' arguments are required for selecting which
relaxation data
- to write to file.
+ The 'id' argument are required for selecting which RDC data set will
be written to file.
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "rdc.write("
text = text + "id=" + `id`
- text = text + ", frq_label=" + `frq_label`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
text = text + ", force=" + `force` + ")"
print text
- # Relaxation data type.
- if type(id) != str:
- raise RelaxStrError, ('relaxation label', id)
-
- # Frequency label.
- if type(frq_label) != str:
- raise RelaxStrError, ('frequency label', frq_label)
+ # Id string.
+ if type(id) != str:
+ raise RelaxStrError, ('identification string', id)
# File.
if type(file) != str:
@@ -387,4 +344,4 @@
raise RelaxBoolError, ('force flag', force)
# Execute the functional code.
- rdc.write(id=id, frq_label=frq_label, file=file, dir=dir,
force=force)
+ rdc.write(id=id, file=file, dir=dir, force=force)
r6848 - /branches/rdc_analysis/prompt/rdc.py