Author: bugman
Date: Fri Mar 15 17:30:55 2013
New Revision: 18836
URL: http://svn.gna.org/viewcvs/relax?rev=18836&view=rev
Log:
Deletion of the frame_order.domain_to_pdb user function.
The redesign of the frame_order.pdb_model user function will make
frame_order.domain_to_pdb
obsolete. The user function is ugly anyway as it forces a user to create a
separate PDB file for
each domain.
Modified:
branches/frame_order_testing/specific_fns/frame_order.py
branches/frame_order_testing/user_functions/frame_order.py
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=18836&r1=18835&r2=18836&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Fri Mar 15
17:30:55 2013
@@ -381,35 +381,6 @@
# Return the ID.
return cdp.domain[id]
-
-
- def _domain_to_pdb(self, domain=None, pdb=None):
- """Match domains to PDB files.
-
- @keyword domain: The domain to associate the PDB file to.
- @type domain: str
- @keyword pdb: The PDB file to associate the domain to.
- @type pdb: str
- """
-
- # Check that the domain exists.
- exists = False
- for i in range(len(cdp.align_tensors)):
- if hasattr(cdp.align_tensors[i], 'domain') and domain ==
cdp.align_tensors[i].domain:
- exists = True
- if not exists:
- raise RelaxError("The domain '%s' cannot be found" % domain)
-
- # Init if needed.
- if not hasattr(cdp, 'domain_to_pdb'):
- cdp.domain_to_pdb = []
-
- # Strip the file ending if given.
- if search('.pdb$', pdb):
- pdb = pdb[:-4]
-
- # Add the data.
- cdp.domain_to_pdb.append([domain, pdb])
def _grid_row(self, incs, lower, upper, dist_type=None, end_point=True):
Modified: branches/frame_order_testing/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/frame_order.py?rev=18836&r1=18835&r2=18836&view=diff
==============================================================================
--- branches/frame_order_testing/user_functions/frame_order.py (original)
+++ branches/frame_order_testing/user_functions/frame_order.py Fri Mar 15
17:30:55 2013
@@ -90,35 +90,6 @@
uf.menu_text = "&average_position"
uf.wizard_height_desc = 450
uf.wizard_size = (1000, 750)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
-
-
-# The frame_order.domain_to_pdb user function.
-uf = uf_info.add_uf('frame_order.domain_to_pdb')
-uf.title = "Match the domains to PDB files."
-uf.title_short = "Domains to PDB matching."
-uf.add_keyarg(
- name = "domain",
- py_type = "str",
- desc_short = "domain",
- desc = "The domain to associate the PDB file to."
-)
-uf.add_keyarg(
- name = "pdb",
- py_type = "str",
- desc_short = "PDB file",
- desc = "The PDB file to associate the domain to."
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("To display the frame order cone models within
Pymol, the two domains need to be associated with PDB files. Then the
reference domain will be fixed in the PDB frame, and the moving domain will
be rotated to its average position.")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To set the 'N' domain to the PDB file
'bax_N_1J7O_1st.pdb', type one of:")
-uf.desc[-1].add_prompt("relax> frame_order.domain_to_pdb('N',
'bax_N_1J7O_1st.pdb')")
-uf.desc[-1].add_prompt("relax> frame_order.domain_to_pdb(domain='N',
pdb='bax_N_1J7O_1st.pdb')")
-uf.backend = frame_order_obj._domain_to_pdb
-uf.menu_text = "&domain_to_pdb"
uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
r18836 - in /branches/frame_order_testing: specific_fns/frame_order.py user_functions/frame_order.py