Author: bugman
Date: Thu Jun 13 11:01:22 2013
New Revision: 20084
URL: http://svn.gna.org/viewcvs/relax?rev=20084&view=rev
Log:
Merged the interatom.create user function into interatom.define.
These user functions had overlapping functionality which would be confusing
for a user.
Modified:
trunk/pipe_control/interatomic.py
trunk/test_suite/system_tests/interatomic.py
trunk/user_functions/interatom.py
Modified: trunk/pipe_control/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/interatomic.py?rev=20084&r1=20083&r2=20084&view=diff
==============================================================================
--- trunk/pipe_control/interatomic.py (original)
+++ trunk/pipe_control/interatomic.py Thu Jun 13 11:01:22 2013
@@ -286,7 +286,7 @@
# Print out.
if verbose:
- print("Magnetic dipole-dipole interactions are now defined for the
following spins:\n")
+ print("Interatomic interactions are now defined for the following
spins:\n")
write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2"],
data=ids)
Modified: trunk/test_suite/system_tests/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/interatomic.py?rev=20084&r1=20083&r2=20084&view=diff
==============================================================================
--- trunk/test_suite/system_tests/interatomic.py (original)
+++ trunk/test_suite/system_tests/interatomic.py Thu Jun 13 11:01:22 2013
@@ -52,8 +52,8 @@
self.interpreter.spin.create(res_num=2, spin_name='H')
# Define the interatomic interaction.
- self.interpreter.interatom.create(spin_id1=':1@N', spin_id2=':1@H')
- self.interpreter.interatom.create(spin_id1=':2@N', spin_id2=':2@H')
+ self.interpreter.interatom.define(spin_id1=':1@N', spin_id2=':1@H',
direct_bond=False)
+ self.interpreter.interatom.define(spin_id1=':2@N', spin_id2=':2@H',
direct_bond=False)
# Add some test data.
cdp.interatomic[0].x = 1
@@ -95,11 +95,11 @@
self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'H')
# Check the interatomic data.
-
self.assertEqual(cdp.interatomic[interatom_index[i][0]].spin_id1, ':2@N')
-
self.assertEqual(cdp.interatomic[interatom_index[i][0]].spin_id2, ':2@H')
+
self.assertEqual(cdp.interatomic[interatom_index[i][0]].spin_id1, '#Test
mol:2@N')
+
self.assertEqual(cdp.interatomic[interatom_index[i][0]].spin_id2, '#Test
mol:2@H')
self.assertEqual(cdp.interatomic[interatom_index[i][0]].y, 2)
-
self.assertEqual(cdp.interatomic[interatom_index[i][1]].spin_id1, ':1@N')
-
self.assertEqual(cdp.interatomic[interatom_index[i][1]].spin_id2, ':1@H')
+
self.assertEqual(cdp.interatomic[interatom_index[i][1]].spin_id1, '#Test
mol:1@N')
+
self.assertEqual(cdp.interatomic[interatom_index[i][1]].spin_id2, '#Test
mol:1@H')
self.assertEqual(cdp.interatomic[interatom_index[i][1]].x, 1)
Modified: trunk/user_functions/interatom.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/interatom.py?rev=20084&r1=20083&r2=20084&view=diff
==============================================================================
--- trunk/user_functions/interatom.py (original)
+++ trunk/user_functions/interatom.py Thu Jun 13 11:01:22 2013
@@ -104,28 +104,36 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep +
'NH_dipole_pair.png'
-# The interatom.create user function.
-uf = uf_info.add_uf('interatom.create')
-uf.title = "Create a new spin."
-uf.title_short = "Spin creation."
-uf.display = True
+# The interatom.define user function.
+uf = uf_info.add_uf('interatom.define')
+uf.title = "Define interatomic interactions between pairs of spins."
+uf.title_short = "Interatomic interaction setup."
uf.add_keyarg(
name = "spin_id1",
- py_type = "str",
- arg_type = "spin ID",
- desc_short = "first spin ID",
- desc = "The spin ID of the first spin.",
+ default = "@N",
+ py_type = "str",
+ arg_type = "spin ID",
+ desc_short = "first spin ID string",
+ desc = "The spin ID string for the first spin of the interatomic
interaction.",
wiz_combo_iter = get_spin_ids,
can_be_none = True
)
uf.add_keyarg(
name = "spin_id2",
- py_type = "str",
- arg_type = "spin ID",
- desc_short = "second spin ID",
- desc = "The spin ID of the first spin.",
+ default = "@H",
+ py_type = "str",
+ arg_type = "spin ID",
+ desc_short = "second spin ID string",
+ desc = "The spin ID string for the second spin of the interatomic
interaction.",
wiz_combo_iter = get_spin_ids,
can_be_none = True
+)
+uf.add_keyarg(
+ name = "direct_bond",
+ default = True,
+ py_type = "bool",
+ desc_short = "directly bonded atoms flag",
+ desc = "This is a flag which if True means that the two spins are
directly bonded. This flag is useful to simply the set up of the main
heteronuclear relaxation mechanism or one-bond residual dipolar couplings."
)
uf.add_keyarg(
name = "pipe",
@@ -139,52 +147,13 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This will add a new interatomic data container
connecting two existing spins to the relax data storage object.")
+uf.desc[-1].add_paragraph("To analyse relaxation or residual dipolar
coupling (RDC) data, for example, pairs of spins which are coupled via the
magnetic dipole-dipole interaction need to be defined. This function will
create an interatomic data object connecting two existing spins. This data
container will be used to store all all information about the interactomic
interaction including interatomic vectors and distances.")
+uf.desc[-1].add_paragraph("For analyses which use relaxation data, simply
defining the interatomic interaction will indicate that there is a dipolar
relaxation mechanism operating between the two spins. Note that for
model-free analyses or reduced spectral density mapping, only a single
relaxation mechanism can be handled. For RDC dependent analyses, the
presence of the interatomic interaction indicates that dipolar coupling is
expected between the two spins.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To connect the spins ':1@N' to ':1@H', type one
of:")
-uf.desc[-1].add_prompt("relax> interatom.create(':1@N', ':1@H')")
-uf.desc[-1].add_prompt("relax> interatom.create(spin_id1=':1@N',
spin_id2=':1@H')")
-uf.backend = interatomic.create_interatom
-uf.menu_text = "c&reate"
-uf.gui_icon = "oxygen.actions.list-add-relax-blue"
-uf.wizard_size = (700, 500)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep +
'NH_dipole_pair.png'
-
-
-# The interatom.define user function.
-uf = uf_info.add_uf('interatom.define')
-uf.title = "Define interatomic interactions between pairs of spins."
-uf.title_short = "Interatomic interaction setup."
-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 of the dipole
pair."
-)
-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 of the dipole
pair."
-)
-uf.add_keyarg(
- name = "direct_bond",
- default = True,
- py_type = "bool",
- desc_short = "directly bonded atoms flag",
- desc = "This is a flag which if True means that the two spins are
directly bonded. This flag is useful to simply the set up of the main
heteronuclear relaxation mechanism or one-bond residual dipolar couplings."
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("To analyse relaxation or residual dipolar
coupling (RDC) data, for example, pairs of spins which are coupled via the
magnetic dipole-dipole interaction need to be defined. This function will
create an interatomic data object which will be used to store all all
information about the interactomic interaction.")
-uf.desc[-1].add_paragraph("For analyses which use relaxation data, simply
defining the interatomic interaction will indicate that there is a dipolar
relaxation mechanism operating between the two spins. Note that for
model-free analyses or reduced spectral density mapping, only a single
relaxation mechanism can be handled. For RDC dependent analyses, this
indicates that dipolar coupling is expected between the two spins.")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_prompt("relax> interatom.define(':1@N', ':1@H')")
+uf.desc[-1].add_prompt("relax> interatom.define(spin_id1=':1@N',
spin_id2=':1@H')")
uf.desc[-1].add_paragraph("To define the protein 15N heteronuclear
relaxation mechanism for a model-free analysis, type one of the following:")
uf.desc[-1].add_prompt("relax> interatom.define('@N', '@H', True)")
uf.desc[-1].add_prompt("relax> interatom.define(spin_id1='@N',
spin_id2='@H', direct_bond=True)")
r20084 - in /trunk: pipe_control/interatomic.py test_suite/system_tests/interatomic.py user_functions/interatom.py