Author: bugman
Date: Thu Dec 7 07:17:29 2006
New Revision: 2924
URL: http://svn.gna.org/viewcvs/relax?rev=2924&view=rev
Log:
You can now specify a different column for residue numbers in the selection
user functions.
This affects both the 'select.read()' and 'unselect.read()' user functions.
Modified:
1.3/generic_fns/selection.py
1.3/prompt/select.py
1.3/prompt/unselect.py
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=2924&r1=2923&r2=2924&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Thu Dec 7 07:17:29 2006
@@ -93,7 +93,7 @@
select = []
for i in xrange(len(file_data)):
try:
- select.append(int(file_data[i][0]))
+ select.append(int(file_data[i][column]))
except:
raise RelaxError, "Improperly formatted file."
@@ -217,7 +217,7 @@
self.relax.data.res[self.run][i].select = 0
- def unsel_read(self, run=None, file=None, dir=None, change_all=None):
+ def unsel_read(self, run=None, file=None, dir=None, change_all=None,
column=None):
"""Function for unselecting the residues contained in a file."""
# Extract the data from the file.
@@ -230,7 +230,7 @@
unselect = []
for i in xrange(len(file_data)):
try:
- unselect.append(int(file_data[i][0]))
+ unselect.append(int(file_data[i][column]))
except:
raise RelaxError, "Improperly formatted file."
Modified: 1.3/prompt/select.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/select.py?rev=2924&r1=2923&r2=2924&view=diff
==============================================================================
--- 1.3/prompt/select.py (original)
+++ 1.3/prompt/select.py Thu Dec 7 07:17:29 2006
@@ -80,7 +80,7 @@
self.__relax__.generic.selection.sel_all(run=run)
- def read(self, run=None, file=None, dir=None, change_all=0):
+ def read(self, run=None, file=None, dir=None, change_all=0, column=0):
"""Function for selecting the residues contained in a file.
Keyword Arguments
@@ -94,14 +94,14 @@
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).
Description
~~~~~~~~~~~
- The file must contain one residue number per line. The number is
taken as the first column
- of the file and all other columns are ignored. Empty lines and
lines beginning with a hash
- are ignored.
+ 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 unselected will remain that way. Setting the argument
to 1 will cause all
@@ -111,10 +111,16 @@
Examples
~~~~~~~~
- To select all residues in the file 'isolated_peaks', type:
+ 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)
"""
# Function intro test.
@@ -123,7 +129,8 @@
text = text + "run=" + `run`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
- text = text + ", change_all=" + `change_all` + ")"
+ text = text + ", change_all=" + `change_all`
+ text = text + ", column=" + `column` + ")"
print text
# The run argument.
@@ -146,8 +153,12 @@
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.sel_read(run=run, file=file,
dir=dir, 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.sel_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):
Modified: 1.3/prompt/unselect.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/unselect.py?rev=2924&r1=2923&r2=2924&view=diff
==============================================================================
--- 1.3/prompt/unselect.py (original)
+++ 1.3/prompt/unselect.py Thu Dec 7 07:17:29 2006
@@ -80,7 +80,7 @@
self.__relax__.generic.selection.unsel_all(run=run)
- def read(self, run=None, file=None, dir=None, change_all=0):
+ def read(self, run=None, file=None, dir=None, change_all=0, column=0):
"""Function for unselecting the residues contained in a file.
Keyword Arguments
@@ -94,14 +94,14 @@
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).
Description
~~~~~~~~~~~
- The file must contain one residue number per line. The number is
taken as the first column
- of the file and all other columns are ignored. Empty lines and
lines beginning with a hash
- are ignored.
+ 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 unselected will remain that way. Setting the argument
to 1 will cause all
@@ -115,6 +115,12 @@
relax> unselect.read('noe', 'unresolved')
relax> unselect.read(run='noe', file='unresolved')
+
+ To unselect the residues in the second column of the relaxation data
file 'r1.600' while
+ selecting all other residues, type one of:
+
+ relax> unselect.read('test', 'r1.600', change_all=1, column=1)
+ relax> unselect.read(run='test', file='r1.600', change_all=1,
column=1)
"""
# Function intro test.
@@ -123,7 +129,8 @@
text = text + "run=" + `run`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
- text = text + ", change_all=" + `change_all` + ")"
+ text = text + ", change_all=" + `change_all`
+ text = text + ", column=" + `column` + ")"
print text
# The run argument.
@@ -146,8 +153,12 @@
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.unsel_read(run=run, file=file,
dir=dir, 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.unsel_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):
r2924 - in /1.3: generic_fns/selection.py prompt/select.py prompt/unselect.py