Author: bugman
Date: Tue Jun 19 10:03:29 2012
New Revision: 16942
URL: http://svn.gna.org/viewcvs/relax?rev=16942&view=rev
Log:
Deletion of the structure.vectors user function as it has been superseded by
dipole_pair.unit_vectors.
Only the user function definition has deleted - the backend code will remain
so that it can be used
internally.
Modified:
branches/interatomic/user_functions/structure.py
Modified: branches/interatomic/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/structure.py?rev=16942&r1=16941&r2=16942&view=diff
==============================================================================
--- branches/interatomic/user_functions/structure.py (original)
+++ branches/interatomic/user_functions/structure.py Tue Jun 19 10:03:29 2012
@@ -775,86 +775,6 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
-# The structure.vectors user function.
-uf = uf_info.add_uf('structure.vectors')
-uf.title = "Extract and store the bond vectors from the loaded structures in
the corresponding interatomic data container."
-uf.title_short = "Bond vector extraction."
-uf.add_keyarg(
- name = "spin_id1",
- default = "@N",
- py_type = "str",
- arg_type = "spin ID",
- desc_short = "first spin ID string",
- desc = "The spin identification string for the first spin or atom of the
pair.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "spin_id2",
- default = "@H",
- py_type = "str",
- arg_type = "spin ID",
- desc_short = "second spin ID string",
- desc = "The spin identification string for the second spin or atom of
the pair.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "model",
- py_type = "int",
- desc_short = "model",
- desc = "The model to extract bond vectors from (which if not set will
cause the vectors of all models to be extracted).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "verbosity",
- default = 1,
- py_type = "int",
- desc_short = "verbosity level",
- desc = "The amount of information to print to screen. Zero corresponds
to minimal output while higher values increase the amount of output. The
default value is 1."
-)
-uf.add_keyarg(
- name = "ave",
- default = True,
- py_type = "bool",
- desc_short = "average vector flag",
- desc = "A flag which if True will cause the bond vectors from all models
to be averaged. If vectors from only one model is extracted, this will have
no effect."
-)
-uf.add_keyarg(
- name = "unit",
- default = True,
- py_type = "bool",
- desc_short = "unit vector flag",
- desc = "A flag which if True will cause the unit vector to calculated
rather than the full length bond vector."
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("For a number of types of analysis, bond vectors
or unit bond vectors are required for the calculations. This user function
allows these vectors to be extracted from the loaded structures. The bond
vector will be stored in a special interatomic data container associated with
two spin systems already loaded into the relax data store.")
-uf.desc[-1].add_paragraph("The extraction of vectors can occur in a number
of ways. For example if an NMR structure with N models is loaded or if
multiple molecules, from any source, of the same compound are loaded as
different models, there are three options for extracting the bond vector.
Firstly the bond vector of a single model can be extracted by setting the
model number. Secondly the bond vectors from all models can be extracted if
the model number is not set and the average vector flag is not set. Thirdly,
if the model number is not set and the average vector flag is set, then a
single vector which is the average for all models will be calculated.")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To extract the XH vectors of the backbone amide
nitrogens where in the PDB file the backbone nitrogen is called 'N' and the
attached proton is called 'H', assuming all H and N spins have already been
loaded, type one of:")
-uf.desc[-1].add_prompt("relax> structure.vectors('@N', '@H')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@N',
spin_id2='@H')")
-uf.desc[-1].add_paragraph("If the attached proton is called 'HN', type:")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@N',
spin_id2='@HN')")
-uf.desc[-1].add_paragraph("For the 'CA' spin bonded to the 'HA' proton,
type:")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@HA',
spin_id2='@CA')")
-uf.desc[-1].add_paragraph("If you are working with RNA, you can use the
residue name identifier to calculate the vectors for each residue separately.
For example to calculate the vectors for all possible spins in the bases,
type:")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H2',
spin_id2=':A')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H8',
spin_id2=':A')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H1',
spin_id2=':G')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H8',
spin_id2=':G')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H5',
spin_id2=':C')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H6',
spin_id2=':C')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H3',
spin_id2=':U')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H5',
spin_id2=':U')")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id1='@H6',
spin_id2=':U')")
-uf.backend = generic_fns.structure.main.vectors
-uf.menu_text = "&vectors"
-uf.wizard_height_desc = 400
-uf.wizard_size = (1000, 750)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
-
-
# The structure.write_pdb user function.
uf = uf_info.add_uf('structure.write_pdb')
uf.title = "Writing structures to a PDB file."
r16942 - /branches/interatomic/user_functions/structure.py