Author: bugman
Date: Thu Jul 7 18:55:27 2011
New Revision: 13506
URL: http://svn.gna.org/viewcvs/relax?rev=13506&view=rev
Log:
Converted all the sequence user functions to use the new documentation design.
Modified:
branches/gui_testing/prompt/sequence.py
Modified: branches/gui_testing/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/prompt/sequence.py?rev=13506&r1=13505&r2=13506&view=diff
==============================================================================
--- branches/gui_testing/prompt/sequence.py (original)
+++ branches/gui_testing/prompt/sequence.py Thu Jul 7 18:55:27 2011
@@ -25,7 +25,7 @@
__docformat__ = 'plaintext'
# relax module imports.
-from base_class import User_fn_class
+from base_class import User_fn_class, _build_doc
import arg_check
from generic_fns import sequence
from relax_errors import RelaxError
@@ -35,45 +35,6 @@
"""Class for manipulating sequence data."""
def copy(self, pipe_from=None, pipe_to=None):
- """Copy the molecule, residue, and spin sequence data from one data
pipe to another.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- pipe_from: The name of the data pipe to copy the sequence data from.
-
- pipe_to: The name of the data pipe to copy the sequence data to.
-
-
- Description
- ~~~~~~~~~~~
-
- This function will copy the sequence data between data pipes. The
destination data pipe
- must not contain any sequence data. If the pipe_from or pipe_to
arguments are not
- supplied, then both will default to the current data pipe (hence
giving one argument is
- essential).
-
-
- Examples
- ~~~~~~~~
-
- To copy the sequence from the data pipe 'm1' to the current data
pipe, type:
-
- relax> sequence.copy('m1')
- relax> sequence.copy(pipe_from='m1')
-
-
- To copy the sequence from the current data pipe to the data pipe
'm9', type:
-
- relax> sequence.copy(pipe_to='m9')
-
-
- To copy the sequence from the data pipe 'm1' to 'm2', type:
-
- relax> sequence.copy('m1', 'm2')
- relax> sequence.copy(pipe_from='m1', pipe_to='m2')
- """
-
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "sequence.copy("
@@ -92,27 +53,37 @@
# Execute the functional code.
sequence.copy(pipe_from=pipe_from, pipe_to=pipe_to)
+ # The function doc info.
+ copy._doc_title = "Copy the molecule, residue, and spin sequence data
from one data pipe to another."
+ copy._doc_title_short = "Sequence data copying."
+ copy._doc_args = [
+ ["pipe_from", "The name of the data pipe to copy the sequence data
from."],
+ ["pipe_to", "The name of the data pipe to copy the sequence data
to."]
+ ]
+ copy._doc_desc = """
+ This will copy the sequence data between data pipes. The
destination data pipe must not contain any sequence data. If the source and
destination pipes are not specified, then both will default to the current
data pipe (hence providing one is essential).
+ """
+ copy._doc_examples = """
+ To copy the sequence from the data pipe 'm1' to the current data
pipe, type:
+
+ relax> sequence.copy('m1')
+ relax> sequence.copy(pipe_from='m1')
+
+
+ To copy the sequence from the current data pipe to the data pipe
'm9', type:
+
+ relax> sequence.copy(pipe_to='m9')
+
+
+ To copy the sequence from the data pipe 'm1' to 'm2', type:
+
+ relax> sequence.copy('m1', 'm2')
+ relax> sequence.copy(pipe_from='m1', pipe_to='m2')
+ """
+ _build_doc(copy)
+
def display(self, sep=None, mol_name_flag=True, res_num_flag=True,
res_name_flag=True, spin_num_flag=True, spin_name_flag=True):
- """Function for displaying sequences of molecules, residues, and/or
spins.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- sep: The column separator (the default of None corresponds to white
space).
-
- mol_name_flag: A flag whic if True will cause the molecule name
column to be shown.
-
- res_num_flag: A flag whic if True will cause the residue number
column to be shown.
-
- res_name_flag: A flag whic if True will cause the residue name
column to be shown.
-
- spin_num_flag: A flag whic if True will cause the spin number
column to be shown.
-
- spin_name_flag: A flag whic if True will cause the spin name column
to be shown.
-
- """
-
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "sequence.display("
@@ -135,84 +106,21 @@
# Execute the functional code.
sequence.display(sep=sep, mol_name_flag=mol_name_flag,
res_num_flag=res_num_flag, res_name_flag=res_name_flag,
spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
+ # The function doc info.
+ display._doc_title = "Display sequences of molecules, residues, and/or
spins."
+ display._doc_title_short = "Sequence display."
+ display._doc_args = [
+ ["sep", "The column separator (the default of None corresponds to
white space)."],
+ ["mol_name_flag", "A flag whic if True will cause the molecule name
column to be shown."],
+ ["res_num_flag", "A flag whic if True will cause the residue number
column to be shown."],
+ ["res_name_flag", "A flag whic if True will cause the residue name
column to be shown."],
+ ["spin_num_flag", "A flag whic if True will cause the spin number
column to be shown."],
+ ["spin_name_flag", "A flag whic if True will cause the spin name
column to be shown."]
+ ]
+ _build_doc(display)
+
def read(self, file=None, dir=None, spin_id_col=None, mol_name_col=None,
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, spin_id=None):
- """Read the molecule, residue, and spin sequence from a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- file: The name of the file containing the sequence data.
-
- dir: The directory where the file is located.
-
- spin_id_col: The spin ID string column (an alternative to the mol,
res, and spin name and
- number columns).
-
- mol_name_col: The molecule name column (alternative to the
spin_id_col).
-
- res_num_col: The residue number column (alternative to the
spin_id_col).
-
- res_name_col: The residue name column (alternative to the
spin_id_col).
-
- spin_num_col: The spin number column (alternative to the
spin_id_col).
-
- spin_name_col: The spin name column (alternative to the
spin_id_col).
-
- sep: The column separator (the default is white space).
-
- spin_id: The spin ID string to restrict the loading of data to
certain spin subsets.
-
-
- Description
- ~~~~~~~~~~~
-
- The spin system can be identified in the file using two different
formats. The first is the
- spin ID string column which can include the molecule name, the
residue name and number, and
- the spin name and number. Alternatively the mol_name_col,
res_num_col, res_name_col,
- spin_num_col, and/or spin_name_col arguments can be supplied
allowing this information to be
- in separate columns. Note that the numbering of columns starts at
one. The spin_id
- argument can be used to restrict the reading to certain spin types,
for example only 15N
- spins when only residue information is in the file.
-
-
- Examples
- ~~~~~~~~
-
- The following commands will read protein backbone 15N sequence data
out of a file called
- 'seq' where the residue numbers and names are in the first and
second columns respectively:
-
- relax> sequence.read('seq')
- relax> sequence.read('seq', res_num_col=1, res_name_col=2)
- relax> sequence.read(file='seq', res_num_col=1, res_name_col=2,
sep=None)
-
-
- The following commands will read the residue sequence out of the
file 'noe.out' which also
- contains the NOE values:
-
- relax> sequence.read('noe.out')
- relax> sequence.read('noe.out', res_num_col=1, res_name_col=2)
- relax> sequence.read(file='noe.out', res_num_col=1, res_name_col=2)
-
-
- The following commands will read the sequence out of the file
'noe.600.out' where the
- residue numbers are in the second column, the names are in the sixth
column and the columns
- are separated by commas:
-
- relax> sequence.read('noe.600.out', res_num_col=2, res_name_col=6,
sep=',')
- relax> sequence.read(file='noe.600.out', res_num_col=2,
res_name_col=6, sep=',')
-
-
- The following commands will read the RNA residues and atoms
(including C2, C5, C6, C8, N1,
- and N3) from the file '500.NOE', where the residue number, residue
name, spin number, and
- spin name are in the first to fourth columns respectively:
-
- relax> sequence.read('500.NOE', res_num_col=1, res_name_col=2,
spin_num_col=3,
- spin_name_col=4)
- relax> sequence.read(file='500.NOE', res_num_col=1, res_name_col=2,
spin_num_col=3,
- spin_name_col=4)
- """
-
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "sequence.read("
@@ -243,38 +151,62 @@
# Execute the functional code.
sequence.read(file=file, dir=dir, spin_id_col=spin_id_col,
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, spin_id=spin_id)
+ # The function doc info.
+ read._doc_title = "Read the molecule, residue, and spin sequence from a
file."
+ read._doc_title_short = "Read sequence from file."
+ read._doc_args = [
+ ["file", "The name of the file containing the sequence data."],
+ ["dir", "The directory where the file is located."],
+ ["spin_id_col", "The spin ID string column (an alternative to the
mol, res, and spin name and number columns)."],
+ ["mol_name_col", "The molecule name column (alternative to the
spin_id_col)."],
+ ["res_num_col", "The residue number column (alternative to the
spin_id_col)."],
+ ["res_name_col", "The residue name column (alternative to the
spin_id_col)."],
+ ["spin_num_col", "The spin number column (alternative to the
spin_id_col)."],
+ ["spin_name_col", "The spin name column (alternative to the
spin_id_col)."],
+ ["sep", "The column separator (the default is white space)."],
+ ["spin_id", "The spin ID string to restrict the loading of data to
certain spin subsets."]
+ ]
+ read._doc_desc = """
+ The spin system can be identified in the file using two different
formats. The first is the spin ID string column which can include the
molecule name, the residue name and number, and the spin name and number.
Alternatively the molecule name, residue number, residue name, spin number
and/or spin name columns can be supplied allowing this information to be in
separate columns. Note that the numbering of columns starts at one. The
spin ID string can be used to restrict the reading to certain spin types, for
example only 15N spins when only residue information is in the file.
+ """
+ read._doc_examples = """
+ The following commands will read protein backbone 15N sequence data
out of a file called
+ 'seq' where the residue numbers and names are in the first and
second columns respectively:
+
+ relax> sequence.read('seq')
+ relax> sequence.read('seq', res_num_col=1, res_name_col=2)
+ relax> sequence.read(file='seq', res_num_col=1, res_name_col=2,
sep=None)
+
+
+ The following commands will read the residue sequence out of the
file 'noe.out' which also
+ contains the NOE values:
+
+ relax> sequence.read('noe.out')
+ relax> sequence.read('noe.out', res_num_col=1, res_name_col=2)
+ relax> sequence.read(file='noe.out', res_num_col=1, res_name_col=2)
+
+
+ The following commands will read the sequence out of the file
'noe.600.out' where the
+ residue numbers are in the second column, the names are in the sixth
column and the columns
+ are separated by commas:
+
+ relax> sequence.read('noe.600.out', res_num_col=2, res_name_col=6,
sep=',')
+ relax> sequence.read(file='noe.600.out', res_num_col=2,
res_name_col=6, sep=',')
+
+
+ The following commands will read the RNA residues and atoms
(including C2, C5, C6, C8, N1,
+ and N3) from the file '500.NOE', where the residue number, residue
name, spin number, and
+ spin name are in the first to fourth columns respectively:
+
+ relax> sequence.read('500.NOE', res_num_col=1, res_name_col=2,
spin_num_col=3,
+ spin_name_col=4)
+ relax> sequence.read(file='500.NOE', res_num_col=1, res_name_col=2,
spin_num_col=3,
+ spin_name_col=4)
+ """
+ _build_doc(read)
+
def write(self, file, dir=None, sep=None, mol_name_flag=False,
res_num_flag=False, res_name_flag=False, spin_num_flag=False,
spin_name_flag=False, force=False):
- """Write the molecule, residue, and spin sequence to a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- file: The name of the file.
-
- dir: The directory name.
-
- sep: The column separator (the default of None corresponds to white
space).
-
- mol_name_flag: A flag whic if True will cause the molecule name
column to be shown.
-
- res_num_flag: A flag whic if True will cause the residue number
column to be shown.
-
- res_name_flag: A flag whic if True will cause the residue name
column to be shown.
-
- spin_num_flag: A flag whic if True will cause the spin number
column to be shown.
-
- spin_name_flag: A flag whic if True will cause the spin name column
to be shown.
-
- force: A flag which if True will cause the file to be overwritten.
-
-
- Description
- ~~~~~~~~~~~
-
- If no directory name is given, the file will be placed in the
current working directory.
- """
-
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "sequence.write("
@@ -302,3 +234,22 @@
# Execute the functional code.
sequence.write(file=file, dir=dir, sep=sep,
mol_name_flag=mol_name_flag, res_num_flag=res_num_flag,
res_name_flag=res_name_flag, spin_num_flag=spin_num_flag,
spin_name_flag=spin_name_flag, force=force)
+
+ # The function doc info.
+ write._doc_title = "Write the molecule, residue, and spin sequence to a
file."
+ write._doc_title_short = "Write sequence to file."
+ write._doc_args = [
+ ["file", "The name of the file."],
+ ["dir", "The directory name."],
+ ["sep", "The column separator (the default of None corresponds to
white space)."],
+ ["mol_name_flag", "A flag which if True will cause the molecule name
column to be shown."],
+ ["res_num_flag", "A flag which if True will cause the residue number
column to be shown."],
+ ["res_name_flag", "A flag which if True will cause the residue name
column to be shown."],
+ ["spin_num_flag", "A flag which if True will cause the spin number
column to be shown."],
+ ["spin_name_flag", "A flag which if True will cause the spin name
column to be shown."],
+ ["force", "A flag which if True will cause the file to be
overwritten."]
+ ]
+ write._doc_desc = """
+ Write the sequence data to file. If no directory name is given, the
file will be placed in the current working directory.
+ """
+ _build_doc(write)
r13506 - /branches/gui_testing/prompt/sequence.py