Author: tlinnet
Date: Thu Dec 5 22:48:11 2013
New Revision: 21797
URL: http://svn.gna.org/viewcvs/relax?rev=21797&view=rev
Log:
Added interpreter.spectrum.read_spins function.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/user_functions/spectrum.py
Modified: trunk/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/spectrum.py?rev=21797&r1=21796&r2=21797&view=diff
==============================================================================
--- trunk/user_functions/spectrum.py (original)
+++ trunk/user_functions/spectrum.py Thu Dec 5 22:48:11 2013
@@ -363,6 +363,113 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'
+# The spectrum.read_spins user function.
+uf = uf_info.add_uf('spectrum.read_spins')
+uf.title = "Read peak assignments from a file and create spins."
+uf.title_short = "Peak assignments reading."
+uf.add_keyarg(
+ name = "file",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "file name",
+ desc = "The name of the file containing the intensity data.",
+ wiz_filesel_style = FD_OPEN
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory where the file is located.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_id_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin ID string column",
+ desc = "The spin ID string column used by the generic intensity file
format (an alternative to the mol, res, and spin name and number columns).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "mol_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "molecule name column",
+ desc = "The molecule name column used by the generic intensity file
format (alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "res_num_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "residue number column",
+ desc = "The residue number column used by the generic intensity file
format (alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "res_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "residue name column",
+ desc = "The residue name column used by the generic intensity file
format (alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_num_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin number column",
+ desc = "The spin number column used by the generic intensity file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin name column",
+ desc = "The spin name column used by the generic intensity file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "sep",
+ py_type = "str",
+ arg_type = "free format",
+ desc_short = "column separator",
+ desc = "The column separator used by the generic intensity format (the
default is white space).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_id",
+ py_type = "str",
+ desc_short = "spin ID string",
+ desc = "The spin ID string used to restrict the loading of data to
certain spin subsets.",
+ can_be_none = True
+)
+# File formats.
+uf.desc.append(Desc_container("File formats"))
+uf.desc[-1].add_paragraph("The peak list or intensity file will be
automatically determined.")
+uf.desc[-1].add_paragraph("Sparky peak list: The file should be a Sparky
peak list saved after typing the command 'lt'. The default is to assume that
columns 0, 1, 2, and 3 (1st, 2nd, 3rd, and 4th) contain the Sparky
assignment, w1, w2, and peak intensity data respectively. The frequency data
w1 and w2 are ignored while the peak intensity data can either be the peak
height or volume displayed by changing the window options. If the peak
intensity data is not within column 3, set the integration column to the
appropriate number (column numbering starts from 0 rather than 1).")
+uf.desc[-1].add_paragraph("XEasy peak list: The file should be the saved
XEasy text window output of the list peak entries command, 'tw' followed by
'le'. As the columns are fixed, the peak intensity column is hardwired to
number 10 (the 11th column) which contains either the peak height or peak
volume data. Because the columns are fixed, the integration column number
will be ignored.")
+uf.desc[-1].add_paragraph("NMRView: The file should be a NMRView peak list.
The default is to use column 16 (which contains peak heights) for peak
intensities. To use use peak volumes (or evolumes), int_col must be set to
15.")
+uf.desc[-1].add_paragraph("NMRPipe seriesTab: The file should be a
NMRPipe-format Spectral Series list. If the spectrum_id='auto', the IDs are
auto generated in form of Z_A{i}.")
+uf.desc[-1].add_paragraph("Generic intensity file: This is a generic format
which can be created by scripting to support non-supported peak lists. It
should contain in the first few columns enough information to identify the
spin. This can include columns for the molecule name, residue number,
residue name, spin number, and spin name. Alternatively a spin ID string
column can be used. The peak intensities can be placed in another column
specified by the integration column number. Intensities from multiple
spectra can be placed into different columns, and these can then be specified
simultaneously by setting the integration column value to a list of columns.
This list must be matched by setting the spectrum ID to a list of the same
length. If columns are delimited by a character other than whitespace, this
can be specified with the column separator. The spin ID can be used to
restrict the loading to specific spin subsets.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To read the spin assignments from the Sparky
formatted files 'ref.list' and 'sat.list', type:")
+uf.desc[-1].add_prompt("relax> spectrum.read_spins(file='ref.list')")
+uf.desc[-1].add_prompt("relax> spectrum.read_spins(file='sat.list')")
+uf.desc[-1].add_paragraph("To read the spin assignments from the XEasy
formatted files 'ref.text' and 'sat.text', type:")
+uf.desc[-1].add_prompt("relax> spectrum.read_spins(file='ref.text')")
+uf.desc[-1].add_prompt("relax> spectrum.read_spins(file='sat.text')")
+uf.backend = spectrum.read_spins
+uf.menu_text = "&read_spins"
+uf.gui_icon = "oxygen.actions.document-open"
+uf.wizard_height_desc = 300
+uf.wizard_size = (1000, 750)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'
+
+
# The spectrum.replicated user function.
uf = uf_info.add_uf('spectrum.replicated')
uf.title = "Specify which spectra are replicates of each other."
r21797 - /trunk/user_functions/spectrum.py