Author: bugman
Date: Mon Jun 11 20:08:22 2012
New Revision: 16849
URL: http://svn.gna.org/viewcvs/relax?rev=16849&view=rev
Log:
Converted the rdc.read user function definition to use the interatomic data
objects.
This is currently only for the front ends of the user function.
Modified:
branches/interatomic/user_functions/rdc.py
Modified: branches/interatomic/user_functions/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/rdc.py?rev=16849&r1=16848&r2=16849&view=diff
==============================================================================
--- branches/interatomic/user_functions/rdc.py (original)
+++ branches/interatomic/user_functions/rdc.py Mon Jun 11 20:08:22 2012
@@ -295,63 +295,30 @@
default = "D",
py_type = "str",
desc_short = "data type",
- desc = "Whether the RDC data is in the D or 2D format.",
+ desc = "Specify if the RDC data is in the D or 2D format.",
wiz_element_type = "combo",
wiz_combo_choices = ["D", "2D"],
wiz_read_only = True
)
uf.add_keyarg(
- name = "spin_id_col",
+ name = "spin_id1_col",
+ default = 1,
py_type = "int",
- arg_type = "free format",
- desc_short = "spin ID column",
- desc = "The spin ID string column (an alternative to the mol, res, and
spin name and number columns).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "mol_name_col",
+ min = 1,
+ desc_short = "first spin ID column",
+ desc = "The spin ID string column for the first spin."
+)
+uf.add_keyarg(
+ name = "spin_id2_col",
+ default = 2,
py_type = "int",
- arg_type = "free format",
- desc_short = "molecule name column",
- desc = "The molecule name column (alternative to the spin_id_col).",
- 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 (alternative to the spin_id_col).",
- 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 (alternative to the spin_id_col).",
- 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 (alternative to the spin_id_col).",
- 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 (alternative to the spin_id_col).",
- can_be_none = True
+ min = 1,
+ desc_short = "second spin ID column",
+ desc = "The spin ID string column for the second spin."
)
uf.add_keyarg(
name = "data_col",
py_type = "int",
- arg_type = "free format",
desc_short = "data column",
desc = "The RDC data column.",
can_be_none = True
@@ -359,7 +326,6 @@
uf.add_keyarg(
name = "error_col",
py_type = "int",
- arg_type = "free format",
desc_short = "error column",
desc = "The experimental error column.",
can_be_none = True
@@ -367,16 +333,12 @@
uf.add_keyarg(
name = "sep",
py_type = "str",
- arg_type = "free format",
desc_short = "column separator",
desc = "The column separator (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 to restrict the loading of data to certain
spin subsets.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = ["white space", ",", ";", ":"],
+ wiz_combo_data = [None, ",", ";", ":"],
+ wiz_read_only = False,
can_be_none = True
)
uf.add_keyarg(
@@ -393,7 +355,7 @@
uf.desc[-1].add_list_element("'D' means that the splitting in the aligned
sample was taken as J + D.")
uf.desc[-1].add_list_element("'2D' means that the splitting in the aligned
sample was assumed to be J + 2D.")
uf.desc[-1].add_paragraph("Internally, relax uses the D notation. Therefore
if set to '2D', the values will be doubled when read in.")
-uf.desc[-1].add_paragraph("If neg_g_corr is set to True, a sign inversion
will be applied to all RDC values to be loaded. This is sometimes needed for
15N if the data is not compensated for the negative gyromagnetic ratio.")
+uf.desc[-1].add_paragraph("If the negative gyromagnetic ratio correction
flag is set, a sign inversion will be applied to all RDC values to be loaded.
This is sometimes needed for 15N if the data is not compensated for the
negative gyromagnetic ratio.")
uf.desc[-1].add_paragraph("The spin system can be identified in the file
using two different formats. The first is the spin ID string column which
can include the molecule name, the residue name and number, and the spin name
and number. Alternatively the molecule name, residue number and name, and
spin number and name columns can be supplied allowing this information to be
in separate columns. Note that the numbering of columns starts at one. The
spin ID can be used to restrict the reading to certain spin types, for
example only 15N spins when only residue information is in the file.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
@@ -407,7 +369,7 @@
uf.backend = rdc.read
uf.menu_text = "&read"
uf.gui_icon = "oxygen.actions.document-open"
-uf.wizard_height_desc = 180
+uf.wizard_height_desc = 300
uf.wizard_size = (1000, 750)
uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
r16849 - /branches/interatomic/user_functions/rdc.py