Author: bugman
Date: Wed Sep 24 18:33:07 2008
New Revision: 7256
URL: http://svn.gna.org/viewcvs/relax?rev=7256&view=rev
Log:
Shifted the focus of the Grace module from residues to spins.
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=7256&r1=7255&r2=7256&view=diff
==============================================================================
--- 1.3/generic_fns/grace.py (original)
+++ 1.3/generic_fns/grace.py Wed Sep 24 18:33:07 2008
@@ -57,11 +57,11 @@
# Loop over the data.
for i in xrange(len(data)):
# X-axis errors.
- if x_data_type != 'res' and data[i][3] != None:
+ if x_data_type != 'spin' and data[i][-3] != None:
x_errors = 1
# Y-axis errors.
- if data[i][5] != None:
+ if data[i][-1] != None:
y_errors = 1
# Plot of values.
@@ -84,8 +84,8 @@
# Plot of errors.
elif plot_data == 'error':
- # xy plot of residue number vs error.
- if x_data_type == 'res' and y_errors:
+ # xy plot of spin vs error.
+ if x_data_type == 'spin' and y_errors:
graph_type = 'xy'
# xy plot of error vs error.
@@ -128,17 +128,17 @@
x_return_conversion_factor = y_return_conversion_factor =
get_specific_fn('return_conversion_factor', ds[ds.current_pipe].pipe_type)
# Test if the X-axis data type is a minimisation statistic.
- if x_data_type != 'res' and
generic_fns.minimise.return_data_name(x_data_type):
+ if x_data_type != 'spin' and
generic_fns.minimise.return_data_name(x_data_type):
x_return_value = generic_fns.minimise.return_value
x_return_conversion_factor =
generic_fns.minimise.return_conversion_factor
# Test if the Y-axis data type is a minimisation statistic.
- if y_data_type != 'res' and
generic_fns.minimise.return_data_name(y_data_type):
+ if y_data_type != 'spin' and
generic_fns.minimise.return_data_name(y_data_type):
y_return_value = generic_fns.minimise.return_value
y_return_conversion_factor =
generic_fns.minimise.return_conversion_factor
- # Loop over the residues.
- for spin in spin_loop(spin_id):
+ # Loop over the spins.
+ for spin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True):
# Skip deselected spins.
if not spin.select:
continue
@@ -151,41 +151,41 @@
# Loop over the data points.
for j in xrange(points):
- # Initialise an empty array for the individual residue data.
- spin_data = [spin.num, spin.name, None, None, None, None]
-
- # Residue number on the x-axis.
- if x_data_type == 'res':
- spin_data[2] = spin.num
+ # Initialise an empty array for the individual spin data.
+ spin_data = [mol_name, res_num, res_name, spin.num, spin.name,
None, None, None, None]
+
+ # Spin ID string on the x-axis.
+ if x_data_type == 'spin':
+ spin_data[-4] = spin_id
# Parameter value for the x-axis.
else:
# Get the x-axis values and errors.
if plot_data == 'sim':
- spin_data[2], spin_data[3] = x_return_value(spin,
x_data_type, sim=j)
+ spin_data[-4], spin_data[-3] = x_return_value(spin,
x_data_type, sim=j)
else:
- spin_data[2], spin_data[3] = x_return_value(spin,
x_data_type)
+ spin_data[-4], spin_data[-3] = x_return_value(spin,
x_data_type)
# Get the y-axis values and errors.
if plot_data == 'sim':
- spin_data[4], spin_data[5] = y_return_value(spin,
y_data_type, sim=j)
+ spin_data[-2], spin_data[-1] = y_return_value(spin,
y_data_type, sim=j)
else:
- spin_data[4], spin_data[5] = y_return_value(spin,
y_data_type)
-
- # Go to the next residue if there is missing data.
- if spin_data[2] == None or spin_data[4] == None:
+ spin_data[-2], spin_data[-1] = y_return_value(spin,
y_data_type)
+
+ # Go to the next spin if there is missing data.
+ if spin_data[-4] == None or spin_data[-2] == None:
continue
# X-axis conversion factors.
- if x_data_type != 'res':
- spin_data[2] = array(spin_data[2]) /
x_return_conversion_factor(x_data_type)
- if spin_data[3]:
- spin_data[3] = array(spin_data[3]) /
x_return_conversion_factor(x_data_type)
+ if x_data_type != 'spin':
+ spin_data[-4] = array(spin_data[-4]) /
x_return_conversion_factor(x_data_type)
+ if spin_data[-3]:
+ spin_data[-3] = array(spin_data[-3]) /
x_return_conversion_factor(x_data_type)
# Y-axis conversion factors.
- spin_data[4] = array(spin_data[4]) /
y_return_conversion_factor(y_data_type)
- if spin_data[5]:
- spin_data[5] = array(spin_data[5]) /
y_return_conversion_factor(y_data_type)
+ spin_data[-2] = array(spin_data[-2]) /
y_return_conversion_factor(y_data_type)
+ if spin_data[-1]:
+ spin_data[-1] = array(spin_data[-1]) /
y_return_conversion_factor(y_data_type)
# Append the array to the full data structure.
data.append(spin_data)
@@ -216,7 +216,7 @@
system(grace_exe + " " + file_path + " &")
-def write(x_data_type='res', y_data_type=None, spin_id=None,
plot_data='value', file=None, dir=None, force=False, norm=True):
+def write(x_data_type='spin', y_data_type=None, spin_id=None,
plot_data='value', file=None, dir=None, force=False, norm=True):
"""Writing data to a file.
@keyword x_data_type: The category of the X-axis data.
@@ -263,7 +263,7 @@
x_return_grace_string = y_return_grace_string =
get_specific_fn('return_grace_string', ds[ds.current_pipe].pipe_type)
# Test if the X-axis data type is a minimisation statistic.
- if x_data_type != 'res' and
generic_fns.minimise.return_data_name(x_data_type):
+ if x_data_type != 'spin' and
generic_fns.minimise.return_data_name(x_data_type):
x_return_units = generic_fns.minimise.return_units
x_return_grace_string = generic_fns.minimise.return_grace_string
@@ -281,7 +281,7 @@
# Test for multiple data sets.
multi = True
try:
- len(data[0][2])
+ len(data[0][-4])
except TypeError:
multi = False
@@ -325,32 +325,32 @@
# Graph type xy.
if graph_type == 'xy':
# Write the data.
- file.write("%-30s%-30s\n" % (data[i][2], data[i][4]))
+ file.write("%-30s%-30s\n" % (data[i][-4], data[i][-2]))
# Graph type xydy.
elif graph_type == 'xydy':
# Catch y-axis errors of None.
- y_error = data[i][5]
+ y_error = data[i][-1]
if y_error == None:
y_error = 0.0
# Write the data.
- file.write("%-30s%-30s%-30s\n" % (data[i][2], data[i][4],
y_error))
+ file.write("%-30s%-30s%-30s\n" % (data[i][-4], data[i][-2],
y_error))
# Graph type xydxdy.
elif graph_type == 'xydxdy':
# Catch x-axis errors of None.
- x_error = data[i][3]
+ x_error = data[i][-3]
if x_error == None:
x_error = 0.0
# Catch y-axis errors of None.
- y_error = data[i][5]
+ y_error = data[i][-1]
if y_error == None:
y_error = 0.0
# Write the data.
- file.write("%-30s%-30s%-30s%-30s\n" % (data[i][2], data[i][4],
x_error, y_error))
+ file.write("%-30s%-30s%-30s%-30s\n" % (data[i][-4], data[i][-2],
x_error, y_error))
# End of graph and data set.
file.write("&\n")
@@ -382,15 +382,35 @@
# Graph G0.
file.write("@with g0\n")
- # X axis start and end.
- if x_data_type == 'res':
- file.write("@ world xmin " + `cdp.res[0].num - 1` + "\n")
- file.write("@ world xmax " + `cdp.res[-1].num + 1` + "\n")
-
- # X-axis label.
- if x_data_type == 'res':
- file.write("@ xaxis label \"Residue number\"\n")
- else:
+ # X-axis set up.
+ if x_data_type == 'spin':
+ # Determine the sequence data type.
+ seq_type = determine_seq_type(data)
+
+ # Residue only data.
+ if seq_type == 'res':
+ # Axis limits.
+ file.write("@ world xmin " +
`ds[ds.current_pipe].mol[0].res[0].num - 1` + "\n")
+ file.write("@ world xmax " +
`ds[ds.current_pipe].mol[0].res[-1].num + 1` + "\n")
+
+ # X-axis label.
+ file.write("@ xaxis label \"Residue number\"\n")
+
+ # Spin only data.
+ if seq_type == 'spin':
+ # Axis limits.
+ file.write("@ world xmin " +
`ds[ds.current_pipe].mol[0].res[0].spin[0].num - 1` + "\n")
+ file.write("@ world xmax " +
`ds[ds.current_pipe].mol[0].res[0].spin[-1].num + 1` + "\n")
+
+ # X-axis label.
+ file.write("@ xaxis label \"Spin number\"\n")
+
+ # Mixed data.
+ if seq_type == 'mixed':
+ # X-axis label.
+ file.write("@ xaxis label \"Spin identification string\"\n")
+
+ else:
# Get the units.
units = x_return_units(x_data_type)
@@ -462,39 +482,39 @@
# Normalisation.
norm_fact = 1.0
if norm:
- norm_fact = data[i][4][0]
+ norm_fact = data[i][-2][0]
# Loop over the data of the set.
- for j in xrange(len(data[i][2])):
+ for j in xrange(len(data[i][-4])):
# Graph type xy.
if graph_type == 'xy':
# Write the data.
- file.write("%-30s%-30s\n" % (data[i][2][j],
data[i][4][j]/norm_fact))
+ file.write("%-30s%-30s\n" % (data[i][-4][j],
data[i][-2][j]/norm_fact))
# Graph type xydy.
elif graph_type == 'xydy':
# Catch y-axis errors of None.
- y_error = data[i][5][j]
+ y_error = data[i][-1][j]
if y_error == None:
y_error = 0.0
# Write the data.
- file.write("%-30s%-30s%-30s\n" % (data[i][2][j],
data[i][4][j]/norm_fact, y_error/norm_fact))
+ file.write("%-30s%-30s%-30s\n" % (data[i][-4][j],
data[i][-2][j]/norm_fact, y_error/norm_fact))
# Graph type xydxdy.
elif graph_type == 'xydxdy':
# Catch x-axis errors of None.
- x_error = data[i][3][j]
+ x_error = data[i][-3][j]
if x_error == None:
x_error = 0.0
# Catch y-axis errors of None.
- y_error = data[i][5][j]
+ y_error = data[i][-1][j]
if y_error == None:
y_error = 0.0
# Write the data.
- file.write("%-30s%-30s%-30s%-30s\n" % (data[i][2][j],
data[i][4][j]/norm_fact, x_error, y_error/norm_fact))
+ file.write("%-30s%-30s%-30s%-30s\n" % (data[i][-4][j],
data[i][-2][j]/norm_fact, x_error, y_error/norm_fact))
# End of the data set i.
file.write("&\n")
@@ -531,14 +551,34 @@
# Graph G0.
file.write("@with g0\n")
- # X axis start and end.
- if x_data_type == 'res':
- file.write("@ world xmin " + `cdp.res[0].num - 1` + "\n")
- file.write("@ world xmax " + `cdp.res[-1].num + 1` + "\n")
-
- # X-axis label.
- if x_data_type == 'res':
- file.write("@ xaxis label \"Residue number\"\n")
+ # X-axis set up.
+ if x_data_type == 'spin':
+ # Determine the sequence data type.
+ seq_type = determine_seq_type(data)
+
+ # Residue only data.
+ if seq_type == 'res':
+ # Axis limits.
+ file.write("@ world xmin " +
`ds[ds.current_pipe].mol[0].res[0].num - 1` + "\n")
+ file.write("@ world xmax " +
`ds[ds.current_pipe].mol[0].res[-1].num + 1` + "\n")
+
+ # X-axis label.
+ file.write("@ xaxis label \"Residue number\"\n")
+
+ # Spin only data.
+ if seq_type == 'spin':
+ # Axis limits.
+ file.write("@ world xmin " +
`ds[ds.current_pipe].mol[0].res[0].spin[0].num - 1` + "\n")
+ file.write("@ world xmax " +
`ds[ds.current_pipe].mol[0].res[0].spin[-1].num + 1` + "\n")
+
+ # X-axis label.
+ file.write("@ xaxis label \"Spin number\"\n")
+
+ # Mixed data.
+ if seq_type == 'mixed':
+ # X-axis label.
+ file.write("@ xaxis label \"Spin identification string\"\n")
+
else:
# Get the units.
units = x_return_units(x_data_type)
@@ -588,4 +628,4 @@
file.write("@ s%i errorbar riser linewidth 0.5\n" % i)
# Legend.
- file.write("@ s%i legend \"Residue %s\"\n" % (i, data[i][1] + " "
+ `data[i][0]`))
+ file.write("@ s%i legend \"Spin %s\"\n" % (i, data[i][5]))
r7256 - /1.3/generic_fns/grace.py