Author: bugman
Date: Thu Feb 11 14:29:25 2010
New Revision: 10690
URL: http://svn.gna.org/viewcvs/relax?rev=10690&view=rev
Log:
Merged revisions 10688-10689 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r10688 | bugman | 2010-02-09 11:36:44 +0100 (Tue, 09 Feb 2010) | 5 lines
Added support for using Me pseudo-atom RDCs.
This follows the method of Verdier, et al., JMR, 2003, 163, 353-359.
........
r10689 | bugman | 2010-02-11 14:26:13 +0100 (Thu, 11 Feb 2010) | 3 lines
Added the cite_html() method to the citation base class to produce a HTML
formatted citation.
........
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/info.py
branches/bieri_gui/specific_fns/n_state_model.py
Propchange: branches/bieri_gui/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Feb 11 14:29:25 2010
@@ -1,1 +1,1 @@
-/1.3:1-10686
+/1.3:1-10689
Modified: branches/bieri_gui/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/info.py?rev=10690&r1=10689&r2=10690&view=diff
==============================================================================
--- branches/bieri_gui/info.py (original)
+++ branches/bieri_gui/info.py Thu Feb 11 14:29:25 2010
@@ -171,6 +171,58 @@
return cite
+ def cite_html(self, author=True, title=True, journal=True, volume=True,
number=True, pages=True, year=True, doi=True, url=True):
+ """Compile a citation for HTML display.
+
+ @keyword author: The author flag.
+ @type author: bool
+ @keyword title: The title flag.
+ @type title: bool
+ @keyword journal: The journal flag.
+ @type journal: bool
+ @keyword volume: The volume flag.
+ @type volume: bool
+ @keyword number: The number flag.
+ @type number: bool
+ @keyword pages: The pages flag.
+ @type pages: bool
+ @keyword year: The year flag.
+ @type year: bool
+ @keyword doi: The doi flag.
+ @type doi: bool
+ @return: The full citation.
+ @rtype: str
+ """
+
+ # Build the citation.
+ cite = ''
+ if author and hasattr(self, 'author'):
+ cite = cite + self.author
+ if year and hasattr(self, 'year'):
+ cite = cite + ' (' + repr(self.year) + ').'
+ if title and hasattr(self, 'title'):
+ cite = cite + ' ' + self.title
+ if journal and hasattr(self, 'journal'):
+ cite = cite + ' <em>' + self.journal + '<em>,'
+ if volume and hasattr(self, 'volume'):
+ cite = cite + ' <strong>' + self.volume + '</strong>'
+ if number and hasattr(self, 'number'):
+ cite = cite + '(' + self.number + '),'
+ if pages and hasattr(self, 'pages'):
+ cite = cite + ' ' + self.pages
+ if doi and hasattr(self, 'doi'):
+ cite = cite + ' (<a href="http://dx.doi.org/%s>abstract</a>)' %
self.doi
+ if url and hasattr(self, 'url'):
+ cite = cite + ' ('+self.url + ')'
+
+ # End.
+ if cite[-1] != '.':
+ cite = cite + '.'
+
+ # Return the citation.
+ return cite
+
+
class Clore90(Ref):
"""Bibliography container."""
Modified: branches/bieri_gui/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/n_state_model.py?rev=10690&r1=10689&r2=10690&view=diff
==============================================================================
--- branches/bieri_gui/specific_fns/n_state_model.py (original)
+++ branches/bieri_gui/specific_fns/n_state_model.py Thu Feb 11 14:29:25 2010
@@ -803,7 +803,7 @@
if not spin.select:
continue
- # Skip spins without RDC data or unit XH bond vectors.
+ # Skip spins without RDC data.
if not hasattr(spin, 'rdc'):
# Add rows of None if other data exists.
if hasattr(spin, 'pcs'):
@@ -816,9 +816,9 @@
continue
# RDC data exists but the XH bond vectors are missing?
- if not hasattr(spin, 'xh_vect') and not hasattr(spin,
'bond_vect'):
+ if not hasattr(spin, 'members') and not hasattr(spin, 'xh_vect')
and not hasattr(spin, 'bond_vect'):
# Throw a warning.
- warn(RelaxWarning("RDC data exists but the XH bond vectors
are missing, skipping spin " + spin_id))
+ warn(RelaxWarning("RDC data exists but the XH bond vectors
are missing, skipping spin %s." % spin_id))
# Add rows of None if other data exists.
if hasattr(spin, 'pcs'):
@@ -830,16 +830,53 @@
# Jump to the next spin.
continue
- # Append the RDC and XH vectors to the lists.
- if hasattr(spin, 'xh_vect'):
- obj = getattr(spin, 'xh_vect')
+ # Pseudo-atom set up.
+ if hasattr(spin, 'members'):
+ # Skip non-Me groups.
+ if len(spin.members) != 3:
+ warn(RelaxWarning("Only methyl group pseudo atoms are
supported due to their fast rotation, skipping spin %s." % spin_id))
+ continue
+
+ # The summed vector.
+ vect = zeros(3, float64)
+ for i in range(3):
+ # Get the spin.
+ spin_i = return_spin(spin.members[i])
+
+ # Add the bond vector.
+ if hasattr(spin_i, 'xh_vect'):
+ obj = getattr(spin_i, 'xh_vect')
+ else:
+ obj = getattr(spin_i, 'bond_vect')
+ vect = vect + obj
+
+ # Normalise.
+ vect = vect / norm(vect)
+
+ # The RDC for the Me-pseudo spin where:
+ # <D> = -1/3 Dpar.
+ # See Verdier, et al., JMR, 2003, 163, 353-359.
+ rdc = -3.0 * array(spin.rdc)
+
+ # Normal spin set up.
else:
- obj = getattr(spin, 'bond_vect')
- rdcs.append(spin.rdc)
- if isinstance(obj[0], float):
- vectors.append([obj])
+ # Append the RDC and XH vectors to the lists.
+ if hasattr(spin, 'xh_vect'):
+ vect = getattr(spin, 'xh_vect')
+ else:
+ vect = getattr(spin, 'bond_vect')
+
+ # The RDC.
+ rdc = array(spin.rdc)
+
+ # Add the RDC.
+ rdcs.append(rdc)
+
+ # Add the bond vectors.
+ if isinstance(vect[0], float):
+ vectors.append([vect])
else:
- vectors.append(obj)
+ vectors.append(vect)
# Append the PCS errors (or a list of None).
if hasattr(spin, 'rdc_err'):
r10690 - in /branches/bieri_gui: ./ info.py specific_fns/n_state_model.py