Author: bugman
Date: Wed May 7 15:29:54 2008
New Revision: 6121
URL: http://svn.gna.org/viewcvs/relax?rev=6121&view=rev
Log:
Updated all the interfaces of the select user functions to the new relax
design.
Modified:
1.3/prompt/select.py
Modified: 1.3/prompt/select.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/select.py?rev=6121&r1=6120&r2=6121&view=diff
==============================================================================
--- 1.3/prompt/select.py (original)
+++ 1.3/prompt/select.py Wed May 7 15:29:54 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003, 2004, 2006 Edward d'Auvergne
#
+# Copyright (C) 2003, 2004, 2006, 2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -25,8 +25,8 @@
# relax module imports.
import help
+from generic_fns import selection
from relax_errors import RelaxBinError, RelaxError, RelaxIntError,
RelaxListStrError, RelaxNoneIntStrError, RelaxNoneStrError,
RelaxNoneStrListError, RelaxStrError
-from generic_fns.selection import reverse
class Select:
@@ -65,7 +65,7 @@
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class for selecting residues."""
+ """Class for selecting spins."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
@@ -74,111 +74,93 @@
self.__relax__ = relax
- def all(self, run=None):
- """Function for selecting all residues.
+ def all(self):
+ """Function for selecting all spins.
+
+ Examples
+ ~~~~~~~~
+
+ To select all spins, simply type:
+
+ relax> select.all()
+ """
+
+ # Function intro test.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "select.all()"
+ print text
+
+ # Execute the functional code.
+ selection.sel_all()
+
+
+ def read(self, file=None, dir=None, mol_name_col=None, res_num_col=0,
res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None,
boolean='OR', change_all=False):
+ """Function for selecting the spins contained in a file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run(s). By supplying a single string, array
of strings, or None, a
- single run, multiple runs, or all runs will be selected respectively.
+ file: The name of the file containing the list of spins to select.
+
+ dir: The directory where the file is located.
+
+ mol_name_col: The molecule name column (this defaults to no column).
+
+ res_num_col: The residue number column (the default is 0, i.e. the
first column).
+
+ res_name_col: The residue name column (this defaults to no column).
+
+ spin_num_col: The spin number column (this defaults to no column).
+
+ spin_name_col: The spin name column (this defaults to no column).
+
+ sep: The column separator (the default is white space).
+
+ boolean: The boolean operator specifying how spins should be
selected.
+
+ change_all: A flag specifying if all other spins should be changed.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ Empty lines and lines beginning with a hash are ignored.
+
+ The 'change_all' flag argument default is False meaning that all
spins currently either
+ selected or deselected will remain that way. Setting the argument
to True will cause all
+ spins not specified in the file to be deselected.
Examples
~~~~~~~~
- To select all residues for all runs type:
-
- relax> select.all()
-
-
- To select all residues for the run 'srls_m1', type:
-
- relax> select.all('srls_m1')
- relax> select.all(run='srls_m1')
- """
-
- # Function intro test.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "select.all("
- text = text + "run=" + `run` + ")"
- print text
-
- # The run argument.
- if run != None and type(run) != str and type(run) != list:
- raise RelaxNoneStrListError, ('run', run)
- if type(run) == list:
- for i in xrange(len(run)):
- if type(run[i]) != str:
- raise RelaxListStrError, ('run', run)
-
- # Execute the functional code.
- self.__relax__.generic.selection.sel_all(run=run)
-
-
- def read(self, run=None, file=None, dir=None, boolean='OR',
change_all=0, column=0):
- """Function for selecting the residues contained in a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run(s). By supplying a single string, array
of strings, or None, a
- single run, multiple runs, or all runs will be selected respectively.
-
- file: The name of the file containing the list of residues to
select.
-
- dir: The directory where the file is located.
-
- boolean: The boolean operator specifying how residues should be
selected.
-
- change_all: A flag specifying if all other residues should be
changed.
-
- column: The column containing the residue numbers (defaulting to 0,
the first column).
-
-
- Description
- ~~~~~~~~~~~
-
- Empty lines and lines beginning with a hash are ignored.
-
- The 'change_all' flag argument default is zero meaning that all
residues currently either
- selected or deselected will remain that way. Setting the argument
to 1 will cause all
- residues not specified in the file to be deselected.
-
-
- Examples
- ~~~~~~~~
-
- To select all residues in the file 'isolated_peaks', type one of:
-
- relax> select.read('noe', 'isolated_peaks')
- relax> select.read(run='noe', file='isolated_peaks')
-
- To select the residues in the second column of the relaxation data
file 'r1.600' while
- deselecting all other residues, type one of:
-
- relax> select.read('test', 'r1.600', change_all=1, column=1)
- relax> select.read(run='test', file='r1.600', change_all=1, column=1)
+ To select all residues listed with residue numbers in the first
column of the file
+ 'isolated_peaks', type one of:
+
+ relax> select.read('isolated_peaks')
+ relax> select.read(file='isolated_peaks')
+
+ To select the spins in the second column of the relaxation data file
'r1.600' while
+ deselecting all other spins, for example type:
+
+ relax> select.read('r1.600', res_num_col=None, spin_num_col=1,
change_all=True)
+ relax> select.read(file='r1.600', res_num_col=None, spin_num_col=1,
change_all=True)
"""
# Function intro test.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "select.read("
- text = text + "run=" + `run`
- text = text + ", file=" + `file`
+ text = text + "file=" + `file`
text = text + ", dir=" + `dir`
+ text = text + ", mol_name_col=" + `mol_name_col`
+ text = text + ", res_num_col=" + `res_num_col`
+ text = text + ", res_name_col=" + `res_name_col`
+ text = text + ", spin_num_col=" + `spin_num_col`
+ text = text + ", spin_name_col=" + `spin_name_col`
+ text = text + ", sep=" + `sep`
text = text + ", boolean=" + `boolean`
- text = text + ", change_all=" + `change_all`
- text = text + ", column=" + `column` + ")"
+ text = text + ", change_all=" + `change_all` + ")"
print text
-
- # The run argument.
- if run != None and type(run) != str and type(run) != list:
- raise RelaxNoneStrListError, ('run', run)
- if type(run) == list:
- for i in xrange(len(run)):
- if type(run[i]) != str:
- raise RelaxListStrError, ('run', run)
# File name.
if type(file) != str:
@@ -188,151 +170,138 @@
if dir != None and type(dir) != str:
raise RelaxNoneStrError, ('directory name', dir)
+ # Molecule name column.
+ if mol_name_col != None and type(mol_name_col) != int:
+ raise RelaxNoneIntError, ('molecule name column', mol_name_col)
+
+ # Residue number column.
+ if res_num_col != None and type(res_num_col) != int:
+ raise RelaxNoneIntError, ('residue number column', res_num_col)
+
+ # Residue name column.
+ if res_name_col != None and type(res_name_col) != int:
+ raise RelaxNoneIntError, ('residue name column', res_name_col)
+
+ # Spin number column.
+ if spin_num_col != None and type(spin_num_col) != int:
+ raise RelaxNoneIntError, ('spin number column', spin_num_col)
+
+ # Spin name column.
+ if spin_name_col != None and type(spin_name_col) != int:
+ raise RelaxNoneIntError, ('spin name column', spin_name_col)
+
+ # Column separator.
+ if sep != None and type(sep) != str:
+ raise RelaxNoneStrError, ('column separator', sep)
+
# Boolean operator.
if type(boolean) != str:
raise RelaxStrError, ('boolean operator', boolean)
# Change all flag.
- if type(change_all) != int or (change_all != 0 and change_all != 1):
- raise RelaxBinError, ('change_all', change_all)
-
- # The residue column.
- if type(column) != int:
- raise RelaxIntError, ('residue number column', column)
+ if type(change_all) != bool:
+ raise RelaxBoolError, ('change_all', change_all)
# Execute the functional code.
- self.__relax__.generic.selection.sel_read(run=run, file=file,
dir=dir, boolean=boolean, change_all=change_all, column=column)
-
-
- def res(self, run=None, num=None, name=None, boolean='OR', change_all=0):
- """Function for selecting specific residues.
+ selection.sel_read(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, sep=sep,
boolean=boolean, change_all=change_all)
+
+
+ def reverse(self, spin_id=None):
+ """Function for the reversal of the spin selection for the given
spins.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run(s). By supplying a single string, array
of strings, or None, a
- single run, multiple runs, or all runs will be selected respectively.
-
- num: The residue number.
-
- name: The residue name.
-
- boolean: The boolean operator specifying how residues should be
selected.
-
- change_all: A flag specifying if all other residues should be
changed.
+ spin_id: The spin identification string.
Description
~~~~~~~~~~~
- The residue number can be either an integer for selecting a single
residue or a python
- regular expression, in string form, for selecting multiple residues.
For details about
- using regular expression, see the python documentation for the
module 're'.
-
- The residue name argument must be a string. Regular expression is
also allowed.
-
- The 'change_all' flag argument default is zero meaning that all
residues currently either
- selected or deselected will remain that way. Setting the argument
to 1 will cause all
- residues not specified by 'num' or 'name' to become deselected.
+ By supplying the spin_id argument, a subset of spin can have their
selection status
+ reversed.
Examples
~~~~~~~~
- To select only glycines and alanines for the run 'm3', assuming they
have been loaded with
- the names GLY and ALA, type:
-
- relax> select.res(run='m3', name='GLY|ALA', change_all=1)
- relax> select.res(run='m3', name='[GA]L[YA]', change_all=1)
-
- To select residue 5 CYS in addition to the currently selected
residues, type:
-
- relax> select.res('m3', 5)
- relax> select.res('m3', 5, 'CYS')
- relax> select.res('m3', '5')
- relax> select.res('m3', '5', 'CYS')
- relax> select.res(run='m3', num='5', name='CYS')
+ To select all currently deselected spins and deselect those which
are selected type:
+
+ relax> select.reverse()
"""
# Function intro test.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "select.res("
- text = text + "run=" + `run`
- text = text + ", num=" + `num`
- text = text + ", name=" + `name`
+ text = sys.ps3 + "select.reverse("
+ text = text + "spin_id=" + `spin_id` + ")"
+ print text
+
+ # Spin identification string.
+ if spin_id != None and type(spin_id) != str:
+ raise RelaxNoneStrError, ('Spin identification string', spin_id)
+
+ # Execute the functional code.
+ reverse(selection=selection)
+
+
+ def spin(self, spin_id=None, boolean='OR', change_all=False):
+ """Function for selecting specific spins.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ spin_id: The spin identification string.
+
+ boolean: The boolean operator specifying how spins should be
selected.
+
+ change_all: A flag specifying if all other spins should be changed.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ The 'change_all' flag argument default is False meaning that all
spins currently either
+ selected or deselected will remain that way. Setting the argument
to True will cause all
+ spins not specified by 'spin_id' to be selected.
+
+
+ Examples
+ ~~~~~~~~
+
+ To select only glycines and alanines, assuming they have been loaded
with the names GLY and
+ ALA, type one of:
+
+ relax> select.spin(spin_id=':GLY|:ALA')
+
+ To select residue 5 CYS in addition to the currently selected
residues, type one of:
+
+ relax> select.spin(':5')
+ relax> select.spin(':5&:CYS')
+ relax> select.spin(spin_id=':5&:CYS')
+ """
+
+ # Function intro test.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "select.spin("
+ text = text + "spin_id=" + `spin_id`
text = text + ", boolean=" + `boolean`
text = text + ", change_all=" + `change_all` + ")"
print text
- # The run argument.
- if run != None and type(run) != str and type(run) != list:
- raise RelaxNoneStrListError, ('run', run)
- if type(run) == list:
- for i in xrange(len(run)):
- if type(run[i]) != str:
- raise RelaxListStrError, ('run', run)
-
- # Residue number.
- if num != None and type(num) != int and type(num) != str:
- raise RelaxNoneIntStrError, ('residue number', num)
-
- # Residue name.
- if name != None and type(name) != str:
- raise RelaxNoneStrError, ('residue name', name)
-
- # Neither are given.
- if num == None and name == None:
- raise RelaxError, "At least one of the number or name arguments
is required."
+ # Spin identification string.
+ if spin_id != None and type(spin_id) != str:
+ raise RelaxNoneStrError, ('Spin identification string', spin_id)
# Boolean operator.
if type(boolean) != str:
raise RelaxStrError, ('boolean operator', boolean)
# Change all flag.
- if type(change_all) != int or (change_all != 0 and change_all != 1):
- raise RelaxBinError, ('change_all', change_all)
+ if type(change_all) != bool:
+ raise RelaxBoolError, ('change_all', change_all)
# Execute the functional code.
- self.__relax__.generic.selection.sel_res(run=run, num=num,
name=name, boolean=boolean, change_all=change_all)
-
-
- def reverse(self, selection=None):
- """Function for the reversal of the spin system selection for the
given spins.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- selection: The selection string identifying the molecules,
residues, and spins to reverse
- the selection of.
-
-
- Description
- ~~~~~~~~~~~
-
- If the selection argument is left on the default of None, then the
selection status of all
- spin systems of the current data pipe will be reversed.
-
-
- Examples
- ~~~~~~~~
-
- To deselect all currently selected residues and select those which
are deselected type:
-
- relax> select.reverse()
- """
-
- # Function intro test.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "select.reverse("
- text = text + "selection=" + `selection` + ")"
- print text
-
- # The selection argument.
- if selection != None and type(selection) != str:
- raise RelaxNoneStrError, ('selection', selection)
-
- # Execute the functional code.
- reverse(selection=selection)
+ selection.sel_res(spin_id=spin_id, boolean=boolean,
change_all=change_all)
r6121 - /1.3/prompt/select.py