Author: bugman
Date: Wed May 7 14:40:19 2008
New Revision: 6110
URL: http://svn.gna.org/viewcvs/relax?rev=6110&view=rev
Log:
Updated all the deselect user functions to the new design (well, only the
interface).
Modified:
1.3/prompt/deselect.py
Modified: 1.3/prompt/deselect.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/deselect.py?rev=6110&r1=6109&r2=6110&view=diff
==============================================================================
--- 1.3/prompt/deselect.py (original)
+++ 1.3/prompt/deselect.py Wed May 7 14:40:19 2008
@@ -25,14 +25,15 @@
# relax module imports.
import help
-from relax_errors import RelaxBinError, RelaxError, RelaxIntError,
RelaxListStrError, RelaxNoneIntStrError, RelaxNoneStrError,
RelaxNoneStrListError, RelaxStrError
+from generic_fns import selection
+from relax_errors import RelaxBoolError, RelaxError, RelaxIntError,
RelaxListStrError, RelaxNoneIntStrError, RelaxNoneStrError,
RelaxNoneStrListError, RelaxStrError
class Deselect:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class for deselecting residues."""
+ """Class for deselecting spins."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
@@ -41,64 +42,49 @@
self.__relax__ = relax
- def all(self, run=None):
- """Function for deselecting all residues.
+ def all(self):
+ """Function for deselecting all spins.
+
+ Examples
+ ~~~~~~~~
+
+ To deselect all spins, simply type:
+
+ relax> deselect.all()
+ """
+
+ # Function intro test.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "deselect.all()"
+ print text
+
+ # Execute the functional code.
+ selection.desel_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,
change_all=False):
+ """Function for deselecting 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.
-
-
- Examples
- ~~~~~~~~
-
- To deselect all residues type:
-
- relax> deselect.all()
-
-
- To deselect 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 + "deselect.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.desel_all(run=run)
-
-
- def read(self, run=None, file=None, dir=None, change_all=0, column=0):
- """Function for deselecting 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
deselect.
+ file: The name of the file containing the list of spins to deselect.
dir: The directory where the file is located.
- 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).
+ 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).
+
+ change_all: A flag specifying if all other spins should be changed.
Description
@@ -106,43 +92,40 @@
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 selected.
-
-
- Examples
- ~~~~~~~~
-
- To deselect all overlapped residues in the file 'unresolved', type:
-
- relax> deselect.read('noe', 'unresolved')
- relax> deselect.read(run='noe', file='unresolved')
-
- To deselect the residues in the second column of the relaxation data
file 'r1.600' while
- selecting all other residues, type one of:
-
- relax> deselect.read('test', 'r1.600', change_all=1, column=1)
- relax> deselect.read(run='test', file='r1.600', change_all=1,
column=1)
+ 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 selected.
+
+
+ Examples
+ ~~~~~~~~
+
+ To deselect all overlapped residues listed with residue numbers in
the first column of the
+ file 'unresolved', type:
+
+ relax> deselect.read('unresolved')
+ relax> deselect.read(file='unresolved')
+
+ To deselect the spins in the second column of the relaxation data
file 'r1.600' while
+ selecting all other spins, for example type:
+
+ relax> deselect.read('r1.600', change_all=True, spin_num_col=1)
+ relax> deselect.read(file='r1.600', change_all=True, spin_num_col=1)
"""
# Function intro test.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "deselect.read("
- text = text + "run=" + `run`
- text = text + ", file=" + `file`
+ text = text + "file=" + `file`
text = text + ", dir=" + `dir`
- text = text + ", change_all=" + `change_all`
- text = text + ", column=" + `column` + ")"
- 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)
+ 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 + ", change_all=" + `change_all` + ")"
+ print text
# File name.
if type(file) != str:
@@ -152,133 +135,105 @@
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_name_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)
+
# 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)
-
- # Execute the functional code.
- self.__relax__.generic.selection.desel_read(run=run, file=file,
dir=dir, change_all=change_all, column=column)
-
-
- def res(self, run=None, num=None, name=None, change_all=0):
- """Function for deselecting specific residues.
+ if type(change_all) != bool:
+ raise RelaxBoolError, ('change_all', change_all)
+
+ # Execute the functional code.
+ selection.desel_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,
change_all=change_all)
+
+
+ def spin(self, spin_id=None, change_all=False):
+ """Function for deselecting specific 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.
-
- change_all: A flag specifying if all other residues should be
changed.
+ spin_id: The spin identification string.
+
+ change_all: A flag specifying if all other spins should be changed.
Description
~~~~~~~~~~~
- The residue number can be either an integer for deselecting a single
residue or a python
- regular expression, in string form, for deselecting 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 selected.
-
-
- Examples
- ~~~~~~~~
-
- To deselect all glycines for the run 'm5', type:
-
- relax> deselect.res(run='m5', name='GLY|ALA')
- relax> deselect.res(run='m5', name='[GA]L[YA]')
+ 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 deselect all glycines and alanines, type:
+
+ relax> deselect.spin(spin_id=':GLY|:ALA')
To deselect residue 12 MET type:
- relax> deselect.res('m5', 12)
- relax> deselect.res('m5', 12, 'MET')
- relax> deselect.res('m5', '12')
- relax> deselect.res('m5', '12', 'MET')
- relax> deselect.res(run='m5', num='12', name='MET')
- """
-
- # Function intro test.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "deselect.res("
- text = text + "run=" + `run`
- text = text + ", num=" + `num`
- text = text + ", name=" + `name`
+ relax> deselect.spin(':12')
+ relax> deselect.spin(spin_id=':12')
+ relax> deselect.spin(spin_id=':12&:MET')
+ """
+
+ # Function intro test.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "deselect.spin("
+ text = text + "spin_id=" + `spin_id`
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)
# Change all flag.
- if type(change_all) != int or (change_all != 0 and change_all != 1):
- raise RelaxBinError, ('change_all', change_all)
-
- # Execute the functional code.
- self.__relax__.generic.selection.desel_res(run=run, num=num,
name=name, change_all=change_all)
-
-
- def reverse(self, run=None):
- """Function for the reversal of the residue selection.
-
- 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.
-
-
- Examples
- ~~~~~~~~
-
- To deselect all currently selected residues and select those which
are deselected type:
+ if type(change_all) != bool:
+ raise RelaxBoolError, ('change_all', change_all)
+
+ # Execute the functional code.
+ selection.desel_spin(spin_id=spin_id, change_all=change_all)
+
+
+ def reverse(self):
+ """Function for the reversal of the spin selection.
+
+ Examples
+ ~~~~~~~~
+
+ To deselect all currently selected spins and select those which are
deselected type:
relax> deselect.reverse()
"""
# Function intro test.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "deselect.reverse("
- 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.reverse(run=run)
+ text = sys.ps3 + "deselect.reverse()"
+ print text
+
+ # Execute the functional code.
+ selection.reverse()
r6110 - /1.3/prompt/deselect.py