Author: bugman
Date: Sat Jun 9 16:56:21 2012
New Revision: 16802
URL: http://svn.gna.org/viewcvs/relax?rev=16802&view=rev
Log:
The bmrb.display user function is now operational.
This user function never worked as pystarlib expects a file path as a string,
but a modification of
pystarlib fixes this. The bmrb.display simply now calls the write() function
with STDOUT as the
file. The write() function was modified to handle file handles.
Modified:
branches/uf_redesign/generic_fns/bmrb.py
Modified: branches/uf_redesign/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/generic_fns/bmrb.py?rev=16802&r1=16801&r2=16802&view=diff
==============================================================================
--- branches/uf_redesign/generic_fns/bmrb.py (original)
+++ branches/uf_redesign/generic_fns/bmrb.py Sat Jun 9 16:56:21 2012
@@ -33,6 +33,7 @@
import dep_check
from generic_fns import exp_info
from generic_fns.mol_res_spin import create_spin, generate_spin_id,
return_residue, return_spin
+from generic_fns.pipes import cdp_name
from info import Info_box
from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoModuleInstallError, RelaxNoPipeError
from relax_io import get_file_path, mkdir_nofail
@@ -42,21 +43,14 @@
def display(version='3.1'):
- """Display the results in the BMRB NMR-STAR format."""
-
- # Test if bmrblib is installed.
- if not dep_check.bmrblib_module:
- raise RelaxNoModuleInstallError('BMRB library', 'bmrblib')
-
- # Test if the current data pipe exists.
- if not ds.current_pipe:
- raise RelaxNoPipeError
-
- # Specific results writing function.
- write_function = specific_fns.setup.get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
-
- # Write the results.
- write_function(sys.stdout, version=version)
+ """Display the results in the BMRB NMR-STAR format.
+
+ @keyword version: The NMR-STAR version to create. This can be either
'2.1', '3.0', or '3.1'.
+ @type version: str
+ """
+
+ # Call the write() function with stdout.
+ write(file=sys.stdout, version=version)
def generate_sequence(N=0, spin_ids=None, spin_nums=None, spin_names=None,
res_nums=None, res_names=None, mol_names=None):
@@ -210,11 +204,12 @@
raise RelaxNoModuleInstallError('BMRB library', 'bmrblib')
# Test if the current data pipe exists.
- if not ds.current_pipe:
+ pipe_name = cdp_name()
+ if not pipe_name:
raise RelaxNoPipeError
# Make sure that the data pipe is empty.
- if not ds[ds.current_pipe].is_empty():
+ if not ds[pipe_name].is_empty():
raise RelaxError("The current data pipe is not empty.")
# Get the full file path.
@@ -225,46 +220,59 @@
raise RelaxFileError(file_path)
# Specific results reading function.
- read_function = specific_fns.setup.get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type)
+ read_function = specific_fns.setup.get_specific_fn('bmrb_read',
ds[pipe_name].pipe_type)
# Read the results.
read_function(file_path, version=version,
sample_conditions=sample_conditions)
def write(file=None, dir=None, version='3.1', force=False):
- """Create a BMRB NMR-STAR formatted file."""
+ """Create a BMRB NMR-STAR formatted file.
+
+ @keyword file: The name of the file to create or a file object.
+ @type file: str or file object
+ @keyword dir: The optional directory to place the file into. If
set to 'pipe_name', then it will be placed in a directory with the same name
as the current data pipe.
+ @type dir: str or None
+ @keyword version: The NMR-STAR version to create. This can be either
'2.1', '3.0', or '3.1'.
+ @type version: str
+ @keyword force: A flag which if True will allow a currently existing
file to be overwritten.
+ @type force: bool
+ """
# Test if bmrblib is installed.
if not dep_check.bmrblib_module:
raise RelaxNoModuleInstallError('BMRB library', 'bmrblib')
# Test if the current data pipe exists.
- if not ds.current_pipe:
+ pipe_name = cdp_name()
+ if not pipe_name:
raise RelaxNoPipeError
# Check the file name.
if file == None:
raise RelaxError("The file name must be specified.")
- # The special data pipe name directory.
- if dir == 'pipe_name':
- dir = ds.current_pipe
+ # A file object.
+ if isinstance(file, str):
+ # The special data pipe name directory.
+ if dir == 'pipe_name':
+ dir = pipe_name
+
+ # Get the full file path.
+ file = get_file_path(file, dir)
+
+ # Fail if the file already exists and the force flag is False.
+ if access(file, F_OK) and not force:
+ raise RelaxFileOverwriteError(file, 'force flag')
+
+ # Print out.
+ print("Opening the file '%s' for writing." % file)
+
+ # Create the directories.
+ mkdir_nofail(dir, verbosity=0)
# Specific results writing function.
- write_function = specific_fns.setup.get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
-
- # Get the full file path.
- file_path = get_file_path(file, dir)
-
- # Fail if the file already exists and the force flag is False.
- if access(file_path, F_OK) and not force:
- raise RelaxFileOverwriteError(file_path, 'force flag')
-
- # Print out.
- print("Opening the file '%s' for writing." % file_path)
-
- # Create the directories.
- mkdir_nofail(dir, verbosity=0)
+ write_function = specific_fns.setup.get_specific_fn('bmrb_write',
ds[pipe_name].pipe_type)
# Get the info box.
info = Info_box()
@@ -281,10 +289,11 @@
cdp.exp_info.software_setup(name=exp_info.SOFTWARE['relax'].name,
version=version_full(), vendor_name=exp_info.SOFTWARE['relax'].authors,
url=exp_info.SOFTWARE['relax'].url, cite_ids=['relax_ref1', 'relax_ref2'],
tasks=exp_info.SOFTWARE['relax'].tasks)
# Execute the specific BMRB writing code.
- write_function(file_path, version=version)
+ write_function(file, version=version)
# Add the file to the results file list.
- if not hasattr(cdp, 'result_files'):
- cdp.result_files = []
- cdp.result_files.append(['text', 'BMRB', file_path])
- status.observers.result_file.notify()
+ if isinstance(file, str):
+ if not hasattr(cdp, 'result_files'):
+ cdp.result_files = []
+ cdp.result_files.append(['text', 'BMRB', file])
+ status.observers.result_file.notify()
r16802 - /branches/uf_redesign/generic_fns/bmrb.py