Author: bugman
Date: Thu Aug 7 19:21:09 2008
New Revision: 7088
URL: http://svn.gna.org/viewcvs/relax?rev=7088&view=rev
Log:
Created the interfaces for the PCS user functions.
Added:
branches/rdc_analysis/prompt/pcs.py
- copied, changed from r7075, branches/rdc_analysis/prompt/rdc.py
Copied: branches/rdc_analysis/prompt/pcs.py (from r7075,
branches/rdc_analysis/prompt/rdc.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/prompt/pcs.py?p2=branches/rdc_analysis/prompt/pcs.py&p1=branches/rdc_analysis/prompt/rdc.py&r1=7075&r2=7088&rev=7088&view=diff
==============================================================================
--- branches/rdc_analysis/prompt/rdc.py (original)
+++ branches/rdc_analysis/prompt/pcs.py Thu Aug 7 19:21:09 2008
@@ -21,18 +21,18 @@
###############################################################################
# Module docstring.
-"""User functions involved with RDCs."""
+"""User functions involved with pseudocontact shifts."""
# Python module imports.
import sys
# relax module imports.
import help
-from generic_fns import rdc
+from generic_fns import pcs
from relax_errors import RelaxError, RelaxBoolError, RelaxBinError,
RelaxFloatError, RelaxIntError, RelaxNoneIntError, RelaxNoneStrError,
RelaxStrError
-class RDC:
+class PCS:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
@@ -46,17 +46,17 @@
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("
+ """Back calculate the pseudocontact shifts.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The alignment identification string.
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pcs.back_calc("
text = text + "id=" + `id` + ")"
print text
@@ -65,48 +65,48 @@
raise RelaxStrError, ('identification string', id)
# Execute the functional code.
- rdc.back_calc(id=id)
+ pcs.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.
+ """Copy PCS data from pipe_from to pipe_to.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ pipe_from: The name of the pipe to copy the PCS data from.
+
+ pipe_to: The name of the pipe to copy the PCS data to.
+
+ id: The alignment identification string.
Description
~~~~~~~~~~~
- 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.
+ This function will copy PCS data from 'pipe_from' to 'pipe_to'. If
id is not given then all
+ PCS data will be copied, otherwise only a specific data set will be.
Examples
~~~~~~~~
- 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)
- 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.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "rdc.copy("
+ To copy all PCS data from pipe 'm1' to pipe 'm9', type one of:
+
+ relax> pcs.copy('m1', 'm9')
+ relax> pcs.copy(pipe_from='m1', pipe_to='m9')
+ relax> pcs.copy('m1', 'm9', None)
+ relax> pcs.copy(pipe_from='m1', pipe_to='m9', id=None)
+
+ To copy only the 'Th' PCS data from 'm3' to 'm6', type one of:
+
+ relax> pcs.copy('m3', 'm6', 'Th')
+ relax> pcs.copy(pipe_from='m3', pipe_to='m6', id='Th')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pcs.copy("
text = text + "pipe_from=" + `pipe_from`
text = text + ", pipe_to=" + `pipe_to`
text = text + ", id=" + `id` + ")"
@@ -126,63 +126,63 @@
# Id string.
if id != None and type(id) != str:
- raise RelaxNoneStrError, ('identification string', id)
-
- # Execute the functional code.
- rdc.copy(pipe_from=pipe_from, pipe_to=pipe_to, id=id)
+ raise RelaxNoneStrError, ('alignment identification string', id)
+
+ # Execute the functional code.
+ pcs.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.
+ """Delete the PCS data corresponding to the alignment id.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The alignment identification string.
Examples
~~~~~~~~
- 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("
+ To delete the PCS data corresponding to id='PH_gel', type:
+
+ relax> pcs.delete('PH_gel')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pcs.delete("
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)
+ raise RelaxStrError, ('alignment identification string', id)
+
+ # Execute the functional code.
+ pcs.delete(id=id)
def display(self, id=None):
- """Display the RDC data corresponding to id.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The RDC identification string.
+ """Display the PCS data corresponding to the alignment id.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The alignment identification string.
Examples
~~~~~~~~
- To display the 'phage' RDC data, type:
-
- relax> rdc.display('phage')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "rdc.display("
+ To display the 'phage' PCS data, type:
+
+ relax> pcs.display('phage')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pcs.display("
text = text + "id=" + `id` + ")"
print text
@@ -191,18 +191,18 @@
raise RelaxStrError, ('identification string', id)
# Execute the functional code.
- rdc.display(id=id)
+ pcs.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):
- """Read the RDC data from file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The RDC identification string.
-
- file: The name of the file containing the RDC data.
+ """Read the PCS data from file.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The PCS identification string.
+
+ file: The name of the file containing the PCS data.
dir: The directory where the file is located.
@@ -216,7 +216,7 @@
spin_name_col: The spin name column (this defaults to no column).
- data_col: The RDC data column (the default is 2).
+ data_col: The PCS data column (the default is 2).
error_col: The experimental error column (the default is 3).
@@ -226,15 +226,15 @@
Examples
~~~~~~~~
- The following commands will read the RDC data out of the file
'Tb.txt' where the columns are
- separated by the symbol ',', and store the RDCs under the identifier
'Tb'.
-
- relax> rdc.read('Tb', 'Tb.txt', sep=',')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "rdc.read("
+ The following commands will read the PCS data out of the file
'Tb.txt' where the columns are
+ separated by the symbol ',', and store the PCSs under the identifier
'Tb'.
+
+ relax> pcs.read('Tb', 'Tb.txt', sep=',')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pcs.read("
text = text + "id=" + `id`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
@@ -293,16 +293,16 @@
raise RelaxNoneStrError, ('column separator', sep)
# Execute the functional code.
- 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)
+ pcs.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, file=None, dir=None, force=False):
- """Write the RDC data to file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- id: The RDC identification string.
+ """Write the PCS data to file.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ id: The PCS identification string.
file: The name of the file.
@@ -315,12 +315,12 @@
~~~~~~~~~~~
If no directory name is given, the file will be placed in the
current working directory.
- 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("
+ The 'id' argument are required for selecting which PCS data set will
be written to file.
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "pcs.write("
text = text + "id=" + `id`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
@@ -344,4 +344,4 @@
raise RelaxBoolError, ('force flag', force)
# Execute the functional code.
- rdc.write(id=id, file=file, dir=dir, force=force)
+ pcs.write(id=id, file=file, dir=dir, force=force)
r7088 - /branches/rdc_analysis/prompt/pcs.py