Author: bugman
Date: Fri Nov 23 18:15:48 2007
New Revision: 3871
URL: http://svn.gna.org/viewcvs/relax?rev=3871&view=rev
Log:
Merged revisions 3863-3869 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r3863 | bugman | 2007-11-23 17:08:49 +0100 (Fri, 23 Nov 2007) | 6 lines
Split the write() function in half.
The two new functions are write() and write_body(). The write() function
calls write_body(). This
write_body() is designed to be used by the display() function.
........
r3864 | bugman | 2007-11-23 17:11:39 +0100 (Fri, 23 Nov 2007) | 3 lines
Implemented the display() function.
........
r3865 | bugman | 2007-11-23 17:13:41 +0100 (Fri, 23 Nov 2007) | 3 lines
Implemented all the arg unit tests for the sequence.display() user function.
........
r3866 | bugman | 2007-11-23 17:15:00 +0100 (Fri, 23 Nov 2007) | 3 lines
Bug fix for all the arg unit tests for the sequence.display() user function.
........
r3867 | bugman | 2007-11-23 17:17:10 +0100 (Fri, 23 Nov 2007) | 3 lines
Implemented a unit test to test the display of an amino acid sequence.
........
r3868 | bugman | 2007-11-23 17:27:40 +0100 (Fri, 23 Nov 2007) | 3 lines
Implemented the sequence.display() user function.
........
r3869 | bugman | 2007-11-23 17:39:55 +0100 (Fri, 23 Nov 2007) | 3 lines
A few improvements to the unit test for the display of an amino acid
sequence.
........
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/sequence.py
branches/N_state_model/prompt/sequence.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py
branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
Propchange: branches/N_state_model/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Nov 23 18:15:48 2007
@@ -1,1 +1,1 @@
-/1.3:1-3692,3695,3697-3713,3715-3719,3721-3728,3730-3731,3733-3755,3757-3807,3809-3833,3836-3838,3840-3862
+/1.3:1-3692,3695,3697-3713,3715-3719,3721-3728,3730-3731,3733-3755,3757-3807,3809-3833,3836-3838,3840-3869
Modified: branches/N_state_model/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/sequence.py?rev=3871&r1=3870&r2=3871&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/sequence.py (original)
+++ branches/N_state_model/generic_fns/sequence.py Fri Nov 23 18:15:48 2007
@@ -25,22 +25,36 @@
from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxSequenceError
from relax_io import extract_data, open_write_file, strip
from generic_fns.selection import count_spins, spin_loop
-
-
-
-def display():
- """Function for displaying the molecule, residue, and spin sequence."""
+from sys import stdout
+
+
+
+def display(mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, sep=None):
+ """Function for displaying the molecule, residue, and/or spin sequence
data.
+
+ This calls the write_body() function to do most of the work.
+
+
+ @param mol_name_col: The column to contain the molecule name
information.
+ @type mol_name_col: int or None
+ @param res_name_col: The column to contain the residue name
information.
+ @type res_name_col: int or None
+ @param res_num_col: The column to contain the residue number
information.
+ @type res_num_col: int or None
+ @param spin_name_col: The column to contain the spin name information.
+ @type spin_name_col: int or None
+ @param spin_num_col: The column to contain the spin number
information.
+ @type spin_num_col: int or None
+ @param sep: The column seperator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ """
# Test if the sequence data is loaded.
if not count_spins():
raise RelaxNoSequenceError
- # Print a header.
- print "%-8s%-8s%-8s%-8s%-8s%-10s" % ("Mol name", "Res num", "Res name",
"Spin num", "Spin name", "Selected")
-
- # Print the data.
- for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
- print "%-8s%-8i%-8s%-8i%-8s%-10i" % (mol_name, res_num, res_name,
spin.num, spin.name, spin.select)
+ # Write the data.
+ write_body(file=stdout, 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)
def load_PDB_sequence():
@@ -275,6 +289,9 @@
def write(file=None, dir=None, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, force=0):
"""Function for writing molecule, residue, and/or sequence data.
+ This calls the write_body() function to do most of the work.
+
+
@param file: The name of the file to write the data to.
@type file: str
@param dir: The directory to contain the file (defaults to
the current directory if
@@ -303,36 +320,60 @@
# Open the file for writing.
seq_file = open_write_file(file, dir, force)
+ # Write the data.
+ write_body(file=seq_file, 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)
+
+ # Close the results file.
+ seq_file.close()
+
+
+
+def write_body(file=None, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None):
+ """Function for writing to the given file object the molecule, residue,
and/or sequence data.
+
+ @param file: The file object to write the data to.
+ @type file: file object
+ @param mol_name_col: The column to contain the molecule name
information.
+ @type mol_name_col: int or None
+ @param res_name_col: The column to contain the residue name
information.
+ @type res_name_col: int or None
+ @param res_num_col: The column to contain the residue number
information.
+ @type res_num_col: int or None
+ @param spin_name_col: The column to contain the spin name information.
+ @type spin_name_col: int or None
+ @param spin_num_col: The column to contain the spin number
information.
+ @type spin_num_col: int or None
+ @param sep: The column seperator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ """
+
# No special seperator character.
if sep == None:
sep = ''
# Write a header.
if mol_name_col != None:
- seq_file.write("%-10s " % ("Mol_name"+sep))
+ file.write("%-10s " % ("Mol_name"+sep))
if res_num_col != None:
- seq_file.write("%-10s " % ("Res_num"+sep))
+ file.write("%-10s " % ("Res_num"+sep))
if res_name_col != None:
- seq_file.write("%-10s " % ("Res_name"+sep))
+ file.write("%-10s " % ("Res_name"+sep))
if spin_num_col != None:
- seq_file.write("%-10s " % ("Spin_num"+sep))
+ file.write("%-10s " % ("Spin_num"+sep))
if spin_name_col != None:
- seq_file.write("%-10s " % ("Spin_name"+sep))
- seq_file.write('\n')
+ file.write("%-10s " % ("Spin_name"+sep))
+ file.write('\n')
# Loop over the spins.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
if mol_name_col != None:
- seq_file.write("%-10s " % (str(mol_name)+sep))
+ file.write("%-10s " % (str(mol_name)+sep))
if res_num_col != None:
- seq_file.write("%-10s " % (str(res_num)+sep))
+ file.write("%-10s " % (str(res_num)+sep))
if res_name_col != None:
- seq_file.write("%-10s " % (str(res_name)+sep))
+ file.write("%-10s " % (str(res_name)+sep))
if spin_num_col != None:
- seq_file.write("%-10s " % (str(spin.num)+sep))
+ file.write("%-10s " % (str(spin.num)+sep))
if spin_name_col != None:
- seq_file.write("%-10s " % (str(spin.name)+sep))
- seq_file.write('\n')
-
- # Close the results file.
- seq_file.close()
+ file.write("%-10s " % (str(spin.name)+sep))
+ file.write('\n')
Modified: branches/N_state_model/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/sequence.py?rev=3871&r1=3870&r2=3871&view=diff
==============================================================================
--- branches/N_state_model/prompt/sequence.py (original)
+++ branches/N_state_model/prompt/sequence.py Fri Nov 23 18:15:48 2007
@@ -42,27 +42,63 @@
self.__relax__ = relax
- def display(self, run=None):
- """Function for displaying the sequence.
+ def display(self, mol_name_col=0, res_num_col=1, res_name_col=2,
spin_num_col=3, spin_name_col=4, sep=None):
+ """Function for displaying sequences of molecules, residues, and/or
spins.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
+ mol_name_col: The molecule name column (the default is 0, i.e. the
first column).
+
+ res_num_col: The residue number column (the default is 1, i.e. the
second column).
+
+ res_name_col: The residue name column (the default is 2, i.e. the
third column).
+
+ spin_num_col: The spin number column (the default is 3, i.e. the
forth column).
+
+ spin_name_col: The spin name column (the default is 4, i.e. the
fifth column).
+
+ sep: The column separator (the default is white space).
+
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "sequence.display("
- text = text + "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` + ")"
print text
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
+ # 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)
# Execute the functional code.
- self.__relax__.generic.sequence.display(run=run)
+ sequence.display(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)
def read(self, file=None, dir=None, mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None):
Modified:
branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py?rev=3871&r1=3870&r2=3871&view=diff
==============================================================================
--- branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py
(original)
+++ branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py Fri
Nov 23 18:15:48 2007
@@ -52,6 +52,84 @@
sequence_fns = Sequence(relax)
+ def test_display_argfail_mol_name_col(self):
+ """The proper failure of the sequence.display() user function for
the mol_name_col argument."""
+
+ # Loop over the data types.
+ for data in DATA_TYPES:
+ # Catch the None, int, and bin arguments, and skip them.
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
+ continue
+
+ # The argument test.
+ self.assertRaises(RelaxNoneIntError, self.sequence_fns.display,
mol_name_col=data[1])
+
+
+ def test_display_argfail_res_num_col(self):
+ """The proper failure of the sequence.display() user function for
the res_num_col argument."""
+
+ # Loop over the data types.
+ for data in DATA_TYPES:
+ # Catch the None, int, and bin arguments, and skip them.
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
+ continue
+
+ # The argument test.
+ self.assertRaises(RelaxNoneIntError, self.sequence_fns.display,
res_num_col=data[1])
+
+
+ def test_display_argfail_res_name_col(self):
+ """The proper failure of the sequence.display() user function for
the res_name_col argument."""
+
+ # Loop over the data types.
+ for data in DATA_TYPES:
+ # Catch the None, int, and bin arguments, and skip them.
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
+ continue
+
+ # The argument test.
+ self.assertRaises(RelaxNoneIntError, self.sequence_fns.display,
res_name_col=data[1])
+
+
+ def test_display_argfail_spin_num_col(self):
+ """The proper failure of the sequence.display() user function for
the spin_num_col argument."""
+
+ # Loop over the data types.
+ for data in DATA_TYPES:
+ # Catch the None, int, and bin arguments, and skip them.
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
+ continue
+
+ # The argument test.
+ self.assertRaises(RelaxNoneIntError, self.sequence_fns.display,
spin_num_col=data[1])
+
+
+ def test_display_argfail_spin_name_col(self):
+ """The proper failure of the sequence.display() user function for
the spin_name_col argument."""
+
+ # Loop over the data types.
+ for data in DATA_TYPES:
+ # Catch the None, int, and bin arguments, and skip them.
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
+ continue
+
+ # The argument test.
+ self.assertRaises(RelaxNoneIntError, self.sequence_fns.display,
spin_name_col=data[1])
+
+
+ def test_display_argfail_sep(self):
+ """The proper failure of the sequence.display() user function for
the sep argument."""
+
+ # Loop over the data types.
+ for data in DATA_TYPES:
+ # Catch the None and str arguments, and skip them.
+ if data[0] == 'None' or data[0] == 'str':
+ continue
+
+ # The argument test.
+ self.assertRaises(RelaxNoneStrError, self.sequence_fns.display,
sep=data[1])
+
+
def test_read_argfail_file(self):
"""Test the proper failure of the sequence.read() user function for
the file argument."""
Modified:
branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py?rev=3871&r1=3870&r2=3871&view=diff
==============================================================================
--- branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
(original)
+++ branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py Fri
Nov 23 18:15:48 2007
@@ -63,6 +63,27 @@
remove(self.tmpfile)
except OSError:
pass
+
+
+ def test_display_protein_sequence(self):
+ """Test the display of an amino acid sequence.
+
+ The functions tested are generic_fns.sequence.display() and
prompt.sequence.display().
+ """
+
+ # Alias the 'orig' relax data store.
+ cdp = relax_data_store['orig']
+
+ # Create a simple animo acid sequence.
+ cdp.mol[0].res[0].num = 1
+ cdp.mol[0].res[0].name = 'GLY'
+ cdp.mol[0].res.add_item('PRO', 2)
+ cdp.mol[0].res.add_item('LEU', 3)
+ cdp.mol[0].res.add_item('GLY', 4)
+ cdp.mol[0].res.add_item('SER', 5)
+
+ # Try displaying the residue sequence.
+ self.sequence_fns.display(mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None)
def test_read_protein_noe_data(self):
r3871 - in /branches/N_state_model: ./ generic_fns/ prompt/ test_suite/unit_tests/ test_suite/unit_tests/_prompt/