Author: bugman
Date: Tue Aug 13 14:45:51 2013
New Revision: 20581
URL: http://svn.gna.org/viewcvs/relax?rev=20581&view=rev
Log:
Merged revisions 20571-20576,20580 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20571 | bugman | 2013-08-09 10:02:09 +0200 (Fri, 09 Aug 2013) | 5 lines
A number of updates and improvements to the document explaining how to
setup a Mac OS X framework.
This Framework Python setup is used to build the binary distribution files.
........
r20572 | bugman | 2013-08-09 11:20:53 +0200 (Fri, 09 Aug 2013) | 3 lines
Updated the Mac Framework testing script to handled 4-way binaries (ppc74
included).
........
r20573 | bugman | 2013-08-09 11:33:39 +0200 (Fri, 09 Aug 2013) | 3 lines
Better support for 4-way binaries in the Mac OS X Framework detection
script.
........
r20574 | bugman | 2013-08-09 11:44:14 +0200 (Fri, 09 Aug 2013) | 3 lines
Added support for the 'current ar archive random library' file type in the
Mac OS X Framework testing script.
........
r20575 | bugman | 2013-08-09 12:36:08 +0200 (Fri, 09 Aug 2013) | 3 lines
Added py2app to the Mac OS X Framework setup instructions.
........
r20576 | bugman | 2013-08-09 14:58:32 +0200 (Fri, 09 Aug 2013) | 5 lines
Shifted code from pipe_control.spectrum to the new lib.spectrum.peak_list
relax library module.
This follows from
http://thread.gmane.org/gmane.science.nmr.relax.devel/3972/focus=4347.
........
r20580 | bugman | 2013-08-13 14:42:28 +0200 (Tue, 13 Aug 2013) | 3 lines
Added a special script for locating all Python versions and printing out
the installed modules.
........
Added:
branches/relax_disp/devel_scripts/python_seek.py
- copied unchanged from r20580, trunk/devel_scripts/python_seek.py
branches/relax_disp/lib/spectrum/
- copied from r20580, trunk/lib/spectrum/
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/devel_scripts/framework_bin_test
branches/relax_disp/docs/Mac_framework_build_3way
branches/relax_disp/lib/__init__.py
branches/relax_disp/pipe_control/spectrum.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Aug 13 14:45:51 2013
@@ -1,1 +1,1 @@
-/trunk:1-20569
+/trunk:1-20580
Modified: branches/relax_disp/devel_scripts/framework_bin_test
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/devel_scripts/framework_bin_test?rev=20581&r1=20580&r2=20581&view=diff
==============================================================================
--- branches/relax_disp/devel_scripts/framework_bin_test (original)
+++ branches/relax_disp/devel_scripts/framework_bin_test Tue Aug 13 14:45:51
2013
@@ -78,7 +78,37 @@
# The type.
file_type = None
- if data[0][:-1] == 'Mach-O universal binary with 3 architectures':
+ if data[0][:-1] == 'Mach-O universal binary with 4 architectures':
+ file_type = '4-way'
+
+ # Arch.
+ arch = [None, None, None, None]
+ for i in range(4):
+ row = data[i+1].split('\t')
+ arch[i] = row[1][:-1]
+ arch.sort()
+
+ # The full file type printout.
+ if arch == ['Mach-O 64-bit executable ppc64', 'Mach-O 64-bit
executable x86_64', 'Mach-O executable i386', 'Mach-O executable ppc']:
+ part_type = '%s [i386, ppc, x86_64, ppc64]' % file_type
+ full_type = '%s exec [i386, ppc, x86_64, ppc64]' % file_type
+ elif arch == ['Mach-O 64-bit bundle ppc64', 'Mach-O 64-bit
bundle x86_64', 'Mach-O bundle i386', 'Mach-O bundle ppc']:
+ part_type = '%s [i386, ppc, x86_64, ppc64]' % file_type
+ full_type = '%s bundle [i386, ppc, x86_64, ppc64]' %
file_type
+ elif arch == ['Mach-O 64-bit dynamically linked shared library
ppc64', 'Mach-O 64-bit dynamically linked shared library x86_64', 'Mach-O
dynamically linked shared library i386', 'Mach-O dynamically linked shared
library ppc']:
+ part_type = '%s [i386, ppc, x86_64, ppc64]' % file_type
+ full_type = '%s lib [i386, ppc, x86_64, ppc64]' % file_type
+ elif arch == ['Mach-O 64-bit object ppc64', 'Mach-O 64-bit
object x86_64', 'Mach-O object i386', 'Mach-O object ppc']:
+ part_type = '%s [i386, ppc, x86_64, ppc64]' % file_type
+ full_type = '%s obj [i386, ppc, x86_64, ppc64]' % file_type
+ elif arch == ['current ar archive random library', 'current ar
archive random library', 'current ar archive random library', 'current ar
archive random library']:
+ part_type = '%s ar' % file_type
+ full_type = '%s current ar archive random library' %
file_type
+ else:
+ full_type = '%s %s' % (file_type, arch)
+ part_type = full_type
+
+ elif data[0][:-1] == 'Mach-O universal binary with 3 architectures':
file_type = '3-way'
# Arch.
@@ -101,6 +131,9 @@
elif arch == ['Mach-O 64-bit object x86_64', 'Mach-O object
i386', 'Mach-O object ppc']:
part_type = '%s [i386, ppc, x86_64]' % file_type
full_type = '%s obj [i386, ppc, x86_64]' % file_type
+ elif arch == ['current ar archive random library', 'current ar
archive random library', 'current ar archive random library']:
+ part_type = '%s ar' % file_type
+ full_type = '%s current ar archive random library' %
file_type
else:
full_type = '%s %s' % (file_type, arch)
part_type = full_type
@@ -128,6 +161,9 @@
elif arch == ['Mach-O object i386', 'Mach-O object ppc']:
part_type = '%s [i386, ppc]' % file_type
full_type = '%s obj [i386, ppc]' % file_type
+ elif arch == ['current ar archive random library', 'current ar
archive random library']:
+ part_type = '%s ar' % file_type
+ full_type = '%s current ar archive random library' %
file_type
else:
full_type = '%s %s' % (file_type, arch)
part_type = full_type
Modified: branches/relax_disp/docs/Mac_framework_build_3way
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/Mac_framework_build_3way?rev=20581&r1=20580&r2=20581&view=diff
==============================================================================
--- branches/relax_disp/docs/Mac_framework_build_3way (original)
+++ branches/relax_disp/docs/Mac_framework_build_3way Tue Aug 13 14:45:51 2013
@@ -14,7 +14,7 @@
PATH=$PATH:$HOME/bin
export PATH
-Check the Python Framework 3-way architecture using the
scripts/framework_bin_test script. The Tk module might fail as the 10.5 Mac
SDK could be only i386 and ppc build. Then a custom Tcl/Tk build will be
required (e.g. at http://cran.r-project.org/bin/macosx/tools/) and the
tkinter module build by hand, changing the -isysroot flag to / at the last
step.
+Check the Python Framework 3-way architecture using the
devel_scripts/framework_bin_test script. The Tk module might fail as the
10.5 Mac SDK could be only i386 and ppc build. Then a custom Tcl/Tk build
will be required (e.g. at http://cran.r-project.org/bin/macosx/tools/) and
the tkinter module build by hand, changing the -isysroot flag to / at the
last step.
@@ -32,9 +32,9 @@
Install the appropriate GNU fortran version to add to Xcode (for example
gfortran-42-5664.pkg from http://r.research.att.com/tools/). Xcode does not
come with a Fortran compiler and the fink version will not be able to create
Universal 3-way binaries.
-$ PATH=/usr/local/bin/:$PATH ~/bin/python2.7 setup.py install
+$ PATH=/usr/local/bin/:$PATH C_INCLUDE_PATH=/sw/include/suitesparse/
~/bin/python2.7 setup.py install
-The PATH option is needed if gfortran is located in both /usr/local/bin/ and
/sw/bin/.
+The PATH option is needed if gfortran is located in both /usr/local/bin/ and
/sw/bin/. The C_INCLUDE_PATH may be needed if the suitesparse header files
cannot be found.
@@ -98,4 +98,35 @@
Download and unpack the latest source release. In the base directory, type:
$ cd wxPython
-$ ~/bin/python2.7 build-wxpython.py --build_dir=../bld --osx_cocoa
--mac-universal-binary --prefix=$HOME --unicode --install
+$ ~/bin/python2.7 build-wxpython.py --build_dir=../bld --osx_cocoa
--mac_universal_binary --prefix=$HOME --unicode --install
+
+
+
+# SCons.
+
+Download and unpack the latest 2.x.x release, then type:
+
+$ ~/bin/python2.7 setup.py install
+$ cd ~/bin
+$ ln -s
/Users/edward/Library/Frameworks/Python.framework/Versions/2.7/bin/scons-2.x.x
scons
+
+Then edit the scons file and change the top of the file from:
+
+#! /usr/bin/env python
+#
+# SCons - a Software Constructor
+#
+
+To:
+
+#! /Users/edward/bin/python
+#
+# SCons - a Software Constructor
+#
+
+
+# Py2app.
+
+This is needed to create the universal binary DMG distribution file.
Download the latest version from https://pypi.python.org/pypi/py2app/. Then
open it and:
+
+$ ~/bin/python2.7 setup.py install
Modified: branches/relax_disp/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/__init__.py?rev=20581&r1=20580&r2=20581&view=diff
==============================================================================
--- branches/relax_disp/lib/__init__.py (original)
+++ branches/relax_disp/lib/__init__.py Tue Aug 13 14:45:51 2013
@@ -47,6 +47,7 @@
'selection',
'software',
'spectral_densities',
+ 'spectrum',
'statistics',
'structure',
'text',
Modified: branches/relax_disp/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/spectrum.py?rev=20581&r1=20580&r2=20581&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/spectrum.py (original)
+++ branches/relax_disp/pipe_control/spectrum.py Tue Aug 13 14:45:51 2013
@@ -32,8 +32,9 @@
# relax module imports.
from lib.errors import RelaxError, RelaxImplementError,
RelaxNoSequenceError, RelaxNoSpectraError
-from lib.io import extract_data, read_spin_data, strip, write_data
+from lib.io import extract_data, write_data
from lib.software import nmrpipe, nmrview, sparky, xeasy
+from lib.spectrum.peak_list import autodetect_format, intensity_generic
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_loop
@@ -250,38 +251,6 @@
# Set the error to the RMSD multiplied by the square root of the
total number of points.
for key in spin.intensity.keys():
spin.intensity_err[key] = spin.baseplane_rmsd[key] * sqrt(spin.N)
-
-
-def autodetect_format(file_data):
- """Automatically detect the format of the peak list.
-
- @param file_data: The processed results file data.
- @type file_data: list of lists of str
- """
-
- # The first header line.
- for line in file_data:
- if line != []:
- break
-
- # Sparky format.
- if line[0] == 'Assignment':
- return 'sparky'
-
- # NMRView format.
- if line == ['label', 'dataset', 'sw', 'sf']:
- return 'nmrview'
-
- # NMRPipe SeriesTab.
- if line[0] == 'REMARK' and line[1] == 'SeriesTab':
- return 'seriestab'
-
- # XEasy format.
- if line == ['No.', 'Color', 'w1', 'w2', 'ass.', 'in', 'w1', 'ass.',
'in', 'w2', 'Volume', 'Vol.', 'Err.', 'Method', 'Comment']:
- return 'xeasy'
-
- # Assume a generic format.
- return 'generic'
def baseplane_rmsd(error=0.0, spectrum_id=None, spin_id=None):
@@ -481,79 +450,6 @@
"""
raise RelaxImplementError
-
-
-def intensity_generic(file_data=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,
data_col=None, sep=None, spin_id=None):
- """Return the process data from the generic peak intensity file.
-
- The residue number, heteronucleus and proton names, and peak intensity
will be returned.
-
-
- @keyword file_data: The data extracted from the file converted into
a list of lists.
- @type file_data: list of lists of str
- @keyword spin_id_col: The column containing the spin ID strings (used
by the generic intensity file format). If supplied, the mol_name_col,
res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be
none. @type spin_id_col: int or None @keyword mol_name_col: The column
containing the molecule name information (used by the generic intensity file
format). If supplied, spin_id_col must be None.
- @type mol_name_col: int or None
- @keyword res_name_col: The column containing the residue name
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
- @type res_name_col: int or None
- @keyword res_num_col: The column containing the residue number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
- @type res_num_col: int or None
- @keyword spin_name_col: The column containing the spin name information
(used by the generic intensity file format). If supplied, spin_id_col must
be None.
- @type spin_name_col: int or None
- @keyword spin_num_col: The column containing the spin number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
- @type spin_num_col: int or None
- @keyword data_col: The column containing the peak intensities.
- @type data_col: int or list of int
- @keyword sep: The column separator which, if None, defaults to
whitespace.
- @type sep: str or None
- @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins.
- @type spin_id: None or str
- @raises RelaxError: When the expected peak intensity is not a float.
- @return: The extracted data as a list of lists. The
first dimension corresponds to the spin. The second dimension consists of
the proton name, heteronucleus name, spin ID string, and the intensity value.
- @rtype: list of lists of str, str, str, float
- """
-
- # Check the intensity column argument.
- if data_col == None:
- raise RelaxError("The data column argument has not been supplied.")
-
- # Strip the data.
- file_data = strip(file_data)
-
- # Convert the the data_col argument to a list if needed.
- if not isinstance(data_col, list):
- data_col = [data_col]
-
- # Loop over the data columns.
- data = []
- for i in range(len(data_col)):
- # Loop over the data.
- row_index = 0
- for values in read_spin_data(file_data=file_data,
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, data_col=data_col[i], sep=sep, spin_id=spin_id):
- # Check the values.
- if len(values) != 6:
- raise RelaxError("The molecule name, residue number and
name, spin number and name, and value columns could not be found in the data
%s." % repr(values))
-
- # Unpack.
- mol_name, res_num, res_name, spin_num, spin_name, value = values
-
- # Create the unique spin ID.
- id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
-
- # Store the necessary data.
- if i == 0:
- # Convert the value to a list if multiple columns are
present.
- if len(data_col) > 1:
- data.append([None, None, id, [value], id])
- else:
- data.append([None, None, id, value, id])
- else:
- data[row_index][3].append(value)
-
- # Go to the next row.
- row_index += 1
-
- # Return the data.
- return data
def read(file=None, dir=None, spectrum_id=None, heteronuc=None, proton=None,
int_col=None, int_method=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, ncproc=None, verbose=True):
r20581 - in /branches/relax_disp: ./ devel_scripts/ docs/ lib/ lib/spectrum/ pipe_control/