Author: bugman
Date: Mon Jun 11 23:09:37 2012
New Revision: 16878
URL: http://svn.gna.org/viewcvs/relax?rev=16878&view=rev
Log:
Converted the structure.vectors user function definition to the new
interatomic data design.
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=16878&r1=16877&r2=16878&view=diff
==============================================================================
--- branches/interatomic/user_functions/structure.py (original)
+++ branches/interatomic/user_functions/structure.py Mon Jun 11 23:09:37 2012
@@ -777,22 +777,24 @@
# 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 spin container."
+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 = "attached",
- default = "H",
- py_type = "str",
- desc_short = "attached atom",
- desc = "The name of the second atom which attached to the spin of
interest. Regular expression is allowed, for example 'H*'."
-)
-uf.add_keyarg(
- name = "spin_id",
+ name = "spin_id1",
default = "@N",
py_type = "str",
arg_type = "spin ID",
- desc_short = "spin ID string",
- desc = "The spin identification string for restricting the loading of
vectors to certain spins.",
+ 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(
@@ -825,30 +827,27 @@
)
# 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 that from the atom associated with the spin system loaded in
relax to the specified attached atom. For example if the attached atom is
set to 'H' and the protein backbone amide spins 'N' are loaded, the all 'N-H'
vectors will be extracted. But if set to 'CA', all atoms named 'CA' in the
structures will be searched for and all 'N-Ca' bond vectors will be
extracted.")
+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 atom is called 'H', assuming multiple types of spin have already
been loaded, type one of:")
-uf.desc[-1].add_prompt("relax> structure.vectors(spin_id='@N')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H', spin_id='@N')")
-uf.desc[-1].add_prompt("relax> structure.vectors(attached='H',
spin_id='@N')")
-uf.desc[-1].add_paragraph("If the attached atom is called 'HN', type:")
-uf.desc[-1].add_prompt("relax> structure.vectors(attached='HN',
spin_id='@N')")
+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(attached='HA',
spin_id='@CA')")
+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('H2', spin_id=':A')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H8', spin_id=':A')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H1', spin_id=':G')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H8', spin_id=':G')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H5', spin_id=':C')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H6', spin_id=':C')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H3', spin_id=':U')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H5', spin_id=':U')")
-uf.desc[-1].add_prompt("relax> structure.vectors('H6', spin_id=':U')")
-uf.desc[-1].add_paragraph("Alternatively, assuming the desired spins have
been loaded, regular expression can be used:")
-uf.desc[-1].add_prompt("relax> structure.vectors('H*')")
+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
r16878 - /branches/interatomic/user_functions/structure.py