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List: relax-devel
Subject: Re: r5268 - /1.3/generic_fns/grace.py
From: Sébastien_Morin <sebastien.morin.1 () domain ! hid>
Date: 2008-04-03 20:17:43
Message-ID: 47F53B67.7010408 () domain ! hid
[Download RAW message or body]
Hi again...
I'll revert the change as you proposed and make the correct
modifications after... I'll also check if I introduced the same kind of
errors elsewhere.
Ciao
Séb
Edward d'Auvergne wrote:
> Hi,
>
> I've found a few more bugs that have been introduced, please see below.
>
>
> On Thu, Apr 3, 2008 at 7:04 PM, <sebastien.morin.1@domain.hid> wrote:
>
> > Author: semor
> > Date: Thu Apr 3 19:04:26 2008
> > New Revision: 5268
> >
> > URL: http://svn.gna.org/viewcvs/relax?rev=5268&view=rev
> > Log:
> > Changed "for i in xrange(len(cdp.res)):" to the spin_loop.
> >
> > This was proposed by Edward d'Auvergne in a post at :
> > https://mail.gna.org/public/relax-devel/2008-04/msg00012.html (Message-id:
> > <7f080ed10804030926p4be2e72apa2ccef85a9062e57@domain.hid>)
> >
> >
> > Modified:
> > 1.3/generic_fns/grace.py
> >
> > Modified: 1.3/generic_fns/grace.py
> > URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=5268&r1=5267&r2=5268&view=diff
> > ==============================================================================
> > --- 1.3/generic_fns/grace.py (original)
> > +++ 1.3/generic_fns/grace.py Thu Apr 3 19:04:26 2008
> > @@ -102,29 +102,29 @@
> > cdp = relax_data_store[relax_data_store.current_pipe]
> >
> > # Loop over the residues.
> > - for i in xrange(len(cdp.res)):
> > + for spin in spin_loop(spin_id):
> > # Remap the data structure 'cdp.res[i]'.
> > - data = cdp.res[i]
> > + spin = cdp.res[i]
> >
> > # Skip the residue if there is no match to 'self.res_num' (unless it is None).
> > if type(self.res_num) == int:
> > - if not data.num == self.res_num:
> > + if not spin.num == self.res_num:
> > continue
> > elif type(self.res_num) == str:
> > - if not match(self.res_num, `data.num`):
> > + if not match(self.res_num, `spin.num`):
> > continue
> >
> > # Skip the residue if there is no match to 'self.res_name' (unless it is None).
> > if self.res_name != None:
> > - if not match(self.res_name, data.name):
> > + if not match(self.res_name, spin.name):
> > continue
> >
> > # Skip deselected residues.
> > - if not data.select:
> > + if not spin.select:
> > continue
> >
> > # Number of data points per residue.
> > - if self.plot_data == 'sim':
> > + if self.plot_spin == 'sim':
> >
>
> This variable should not have changed. Maybe this was introduced by a
> global search and replace?
>
>
>
> > points = cdp.sim_number
> > else:
> > points = 1
> > @@ -132,43 +132,43 @@
> > # Loop over the data points.
> > for j in xrange(points):
> > # Initialise an empty array for the individual residue data.
> > - res_data = [data.num, data.name, None, None, None, None]
> > + res_spin = [spin.num, spin.name, None, None, None, None]
> >
>
> Again global replace? res_data should not be renamed.
>
>
>
>
> > # Residue number on the x-axis.
> > - if self.x_data_type == 'res':
> > - res_data[2] = data.num
> > + if self.x_spin_type == 'res':
> > + res_spin[2] = spin.num
> >
>
> Both self.x_data_type and res_data should not have changed names.
> Many of the changes below this have variables which shouldn't have had
> name changes, but I don't think I need to point out each one. They
> are quite numerous, so maybe it would be best to revert this revision,
> and start again?
>
> Cheers,
>
> Edward
>
>
>
>
> > # Parameter value for the x-axis.
> > else:
> > # Get the x-axis values and errors.
> > - if self.plot_data == 'sim':
> > - res_data[2], res_data[3] = self.x_return_value(self.run, \
> > i, self.x_data_type, sim=j) + if self.plot_spin == 'sim':
> > + res_spin[2], res_spin[3] = self.x_return_value(self.run, \
> > i, self.x_spin_type, sim=j) else:
> > - res_data[2], res_data[3] = self.x_return_value(self.run, \
> > i, self.x_data_type) + res_spin[2], res_spin[3] = \
> > self.x_return_value(self.run, i, self.x_spin_type)
> > # Get the y-axis values and errors.
> > - if self.plot_data == 'sim':
> > - res_data[4], res_data[5] = self.y_return_value(self.run, i, \
> > self.y_data_type, sim=j) + if self.plot_spin == 'sim':
> > + res_spin[4], res_spin[5] = self.y_return_value(self.run, i, \
> > self.y_spin_type, sim=j) else:
> > - res_data[4], res_data[5] = self.y_return_value(self.run, i, \
> > self.y_data_type) + res_spin[4], res_spin[5] = \
> > self.y_return_value(self.run, i, self.y_spin_type)
> > # Go to the next residue if there is missing data.
> > - if res_data[2] == None or res_data[4] == None:
> > + if res_spin[2] == None or res_spin[4] == None:
> > continue
> >
> > # X-axis conversion factors.
> > - if self.x_data_type != 'res':
> > - res_data[2] = array(res_data[2]) / \
> > self.x_return_conversion_factor(self.x_data_type)
> > - if res_data[3]:
> > - res_data[3] = array(res_data[3]) / \
> > self.x_return_conversion_factor(self.x_data_type) + if \
> > self.x_spin_type != 'res': + res_spin[2] = array(res_spin[2]) \
> > / self.x_return_conversion_factor(self.x_spin_type) + if \
> > res_spin[3]: + res_spin[3] = array(res_spin[3]) / \
> > self.x_return_conversion_factor(self.x_spin_type)
> > # Y-axis conversion factors.
> > - res_data[4] = array(res_data[4]) / \
> > self.y_return_conversion_factor(self.y_data_type)
> > - if res_data[5]:
> > - res_data[5] = array(res_data[5]) / \
> > self.y_return_conversion_factor(self.y_data_type) + res_spin[4] = \
> > array(res_spin[4]) / self.y_return_conversion_factor(self.y_spin_type) + \
> > if res_spin[5]: + res_spin[5] = array(res_spin[5]) / \
> > self.y_return_conversion_factor(self.y_spin_type)
> > # Append the array to the full data structure.
> > - self.data.append(res_data)
> > + self.spin.append(res_spin)
> >
> >
> > def view(self, file=None, dir=None, grace_exe='xmgrace'):
> >
> >
> > _______________________________________________
> > relax (http://nmr-relax.com)
> >
> > This is the relax-commits mailing list
> > relax-commits@domain.hid
> >
> > To unsubscribe from this list, get a password
> > reminder, or change your subscription options,
> > visit the list information page at
> > https://mail.gna.org/listinfo/relax-commits
> >
> >
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
> This is the relax-devel mailing list
> relax-devel@domain.hid
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
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>
>
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Hi again...<br>
<br>
I'll revert the change as you proposed and make the correct
modifications after... I'll also check if I introduced the same kind of
errors elsewhere.<br>
<br>
Ciao<br>
<br>
<br>
Séb<br>
<br>
<br>
Edward d'Auvergne wrote:
<blockquote
cite="mid:7f080ed10804031148r75a295a2u99569bb13b99ffc5@domain.hid"
type="cite">
<pre wrap="">Hi,
I've found a few more bugs that have been introduced, please see below.
On Thu, Apr 3, 2008 at 7:04 PM, <a class="moz-txt-link-rfc2396E" \
href="mailto:sebastien.morin.1@domain.hid"><sebastien.morin.1@domain.hid></a> \
wrote: </pre>
<blockquote type="cite">
<pre wrap="">Author: semor
Date: Thu Apr 3 19:04:26 2008
New Revision: 5268
URL: <a class="moz-txt-link-freetext" \
href="http://svn.gna.org/viewcvs/relax?rev=5268&view=rev">http://svn.gna.org/viewcvs/relax?rev=5268&view=rev</a>
Log:
Changed "for i in xrange(len(cdp.res)):" to the spin_loop.
This was proposed by Edward d'Auvergne in a post at :
<a class="moz-txt-link-freetext" \
href="https://mail.gna.org/public/relax-devel/2008-04/msg00012.html">https://mail.gna.org/public/relax-devel/2008-04/msg00012.html</a> \
(Message-id: <a class="moz-txt-link-rfc2396E" \
href="mailto:7f080ed10804030926p4be2e72apa2ccef85a9062e57@domain.hid"><7f080ed10804030926p4be2e72apa2ccef85a9062e57@domain.hid></a>)
Modified:
1.3/generic_fns/grace.py
Modified: 1.3/generic_fns/grace.py
URL: <a class="moz-txt-link-freetext" \
href="http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=5268&r1=5267&r2=52 \
68&view=diff">http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=5268&r1=5267&r2=5268&view=diff</a>
==============================================================================
--- 1.3/generic_fns/grace.py (original)
+++ 1.3/generic_fns/grace.py Thu Apr 3 19:04:26 2008
@@ -102,29 +102,29 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Loop over the residues.
- for i in xrange(len(cdp.res)):
+ for spin in spin_loop(spin_id):
# Remap the data structure 'cdp.res[i]'.
- data = cdp.res[i]
+ spin = cdp.res[i]
# Skip the residue if there is no match to 'self.res_num' (unless it is \
None). if type(self.res_num) == int:
- if not data.num == self.res_num:
+ if not spin.num == self.res_num:
continue
elif type(self.res_num) == str:
- if not match(self.res_num, `data.num`):
+ if not match(self.res_num, `spin.num`):
continue
# Skip the residue if there is no match to 'self.res_name' (unless it is \
None). if self.res_name != None:
- if not match(self.res_name, data.name):
+ if not match(self.res_name, spin.name):
continue
# Skip deselected residues.
- if not data.select:
+ if not spin.select:
continue
# Number of data points per residue.
- if self.plot_data == 'sim':
+ if self.plot_spin == 'sim':
</pre>
</blockquote>
<pre wrap=""><!---->
This variable should not have changed. Maybe this was introduced by a
global search and replace?
</pre>
<blockquote type="cite">
<pre wrap=""> points = cdp.sim_number
else:
points = 1
@@ -132,43 +132,43 @@
# Loop over the data points.
for j in xrange(points):
# Initialise an empty array for the individual residue data.
- res_data = [data.num, data.name, None, None, None, None]
+ res_spin = [spin.num, spin.name, None, None, None, None]
</pre>
</blockquote>
<pre wrap=""><!---->
Again global replace? res_data should not be renamed.
</pre>
<blockquote type="cite">
<pre wrap=""> # Residue number on the x-axis.
- if self.x_data_type == 'res':
- res_data[2] = data.num
+ if self.x_spin_type == 'res':
+ res_spin[2] = spin.num
</pre>
</blockquote>
<pre wrap=""><!---->
Both self.x_data_type and res_data should not have changed names.
Many of the changes below this have variables which shouldn't have had
name changes, but I don't think I need to point out each one. They
are quite numerous, so maybe it would be best to revert this revision,
and start again?
Cheers,
Edward
</pre>
<blockquote type="cite">
<pre wrap=""> # Parameter value for the x-axis.
else:
# Get the x-axis values and errors.
- if self.plot_data == 'sim':
- res_data[2], res_data[3] = self.x_return_value(self.run, i, \
self.x_data_type, sim=j) + if self.plot_spin == 'sim':
+ res_spin[2], res_spin[3] = self.x_return_value(self.run, i, \
self.x_spin_type, sim=j) else:
- res_data[2], res_data[3] = self.x_return_value(self.run, i, \
self.x_data_type) + res_spin[2], res_spin[3] = \
self.x_return_value(self.run, i, self.x_spin_type)
# Get the y-axis values and errors.
- if self.plot_data == 'sim':
- res_data[4], res_data[5] = self.y_return_value(self.run, i, \
self.y_data_type, sim=j) + if self.plot_spin == 'sim':
+ res_spin[4], res_spin[5] = self.y_return_value(self.run, i, \
self.y_spin_type, sim=j) else:
- res_data[4], res_data[5] = self.y_return_value(self.run, i, \
self.y_data_type) + res_spin[4], res_spin[5] = \
self.y_return_value(self.run, i, self.y_spin_type)
# Go to the next residue if there is missing data.
- if res_data[2] == None or res_data[4] == None:
+ if res_spin[2] == None or res_spin[4] == None:
continue
# X-axis conversion factors.
- if self.x_data_type != 'res':
- res_data[2] = array(res_data[2]) / \
self.x_return_conversion_factor(self.x_data_type)
- if res_data[3]:
- res_data[3] = array(res_data[3]) / \
self.x_return_conversion_factor(self.x_data_type) + if \
self.x_spin_type != 'res': + res_spin[2] = array(res_spin[2]) / \
self.x_return_conversion_factor(self.x_spin_type) + if \
res_spin[3]: + res_spin[3] = array(res_spin[3]) / \
self.x_return_conversion_factor(self.x_spin_type)
# Y-axis conversion factors.
- res_data[4] = array(res_data[4]) / \
self.y_return_conversion_factor(self.y_data_type)
- if res_data[5]:
- res_data[5] = array(res_data[5]) / \
self.y_return_conversion_factor(self.y_data_type) + res_spin[4] = \
array(res_spin[4]) / self.y_return_conversion_factor(self.y_spin_type) + \
if res_spin[5]: + res_spin[5] = array(res_spin[5]) / \
self.y_return_conversion_factor(self.y_spin_type)
# Append the array to the full data structure.
- self.data.append(res_data)
+ self.spin.append(res_spin)
def view(self, file=None, dir=None, grace_exe='xmgrace'):
_______________________________________________
relax (<a class="moz-txt-link-freetext" \
href="http://nmr-relax.com">http://nmr-relax.com</a>)
This is the relax-commits mailing list
<a class="moz-txt-link-abbreviated" \
href="mailto:relax-commits@domain.hid">relax-commits@domain.hid</a>
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
<a class="moz-txt-link-freetext" \
href="https://mail.gna.org/listinfo/relax-commits">https://mail.gna.org/listinfo/relax-commits</a>
</pre>
</blockquote>
<pre wrap=""><!---->
_______________________________________________
relax (<a class="moz-txt-link-freetext" \
href="http://nmr-relax.com">http://nmr-relax.com</a>)
This is the relax-devel mailing list
<a class="moz-txt-link-abbreviated" \
href="mailto:relax-devel@domain.hid">relax-devel@domain.hid</a>
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
<a class="moz-txt-link-freetext" \
href="https://mail.gna.org/listinfo/relax-devel">https://mail.gna.org/listinfo/relax-devel</a>
</pre>
</blockquote>
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