Author: bugman
Date: Mon Jun 18 18:19:51 2012
New Revision: 16939
URL: http://svn.gna.org/viewcvs/relax?rev=16939&view=rev
Log:
Refinement of the dipole_pair user function definitions.
Modified:
branches/interatomic/user_functions/dipole_pair.py
Modified: branches/interatomic/user_functions/dipole_pair.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/dipole_pair.py?rev=16939&r1=16938&r2=16939&view=diff
==============================================================================
--- branches/interatomic/user_functions/dipole_pair.py (original)
+++ branches/interatomic/user_functions/dipole_pair.py Mon Jun 18 18:19:51
2012
@@ -71,11 +71,11 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("To analyse relaxation or residual dipolar
coupling (RDC) data, pairs of spins which are coupled via the magnetic
dipole-dipole interaction need to be specified. This must proceed the use of
the other user functions in this class. An interatomic data object will be
created, if it is not already present, and this will be used to store all
subsequently loaded dipole-dipole data.")
-uf.desc[-1].add_paragraph("For analyses which use relaxation data,
specifying the dipole-dipole interaction will indicate that there is a
dipolar relaxation mechanism operating between the two spins. For RDC
dependent analyses, this indicates that a residual dipolar coupling is
expected between the two spins.")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To define the protein 15N heteronuclear
relaxation mechanism, type on of the following:")
+uf.desc[-1].add_paragraph("To analyse relaxation or residual dipolar
coupling (RDC) data, pairs of spins which are coupled via the magnetic
dipole-dipole interaction need to be specified. This must proceed the use of
the other user functions in this class. An interatomic data object will be
created, if not already present, and this will be used to store all
subsequently loaded dipole-dipole interaction information.")
+uf.desc[-1].add_paragraph("For analyses which use relaxation data,
specifying the dipole-dipole 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 a residual dipolar coupling is expected between the two
spins.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+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> dipole_pair.define('@N', '@H', True)")
uf.desc[-1].add_prompt("relax> dipole_pair.define(spin_id1='@N',
spin_id2='@H', direct_bond=True)")
uf.backend = dipole_pair.define
@@ -88,7 +88,7 @@
# The dipole_pair.read_dist user function.
uf = uf_info.add_uf('dipole_pair.read_dist')
-uf.title = "Load the r^-3 averaged distances for the magnetic dipole-dipole
interactions."
+uf.title = "Load the r^-3 averaged distances for the magnetic dipole-dipole
interactions from a file."
uf.title_short = "Magnetic dipole-dipole distance loading."
uf.add_keyarg(
name = "file",
@@ -143,7 +143,8 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This allows the r^-3 averaged interatomic
distances to be read from a file. This is useful in the case when the
dipole-dipole distances vary, replacing the need to call the
dipole_pair.set_dist user function many times. The format of the file should
be columnar, with the two spin ID strings in two separate columns and the
averaged distances in another.")
+uf.desc[-1].add_paragraph("As the magnetic dipole-dipole interaction is
averaged in NMR over the interatomic distance to the inverse third power, the
interatomic distances within a 3D structural file are of no use for defining
the interaction. Therefore these average distances must be explicitly
defined.")
+uf.desc[-1].add_paragraph("This user function allows these r^-3 averaged
interatomic distances to be read from a file. This is useful in the case
when the dipole-dipole distances vary, replacing the need to call the
dipole_pair.set_dist user function many times. The format of the file should
be columnar, with the two spin ID strings in two separate columns and the
averaged distances in any other.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To load the distances from the fifth column of
the 'distances' file, and where the spin IDs are in the first and second
columns, type one of the following:")
@@ -186,12 +187,10 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("To analyse relaxation data, the relaxation
mechanism and related parameters needs to be defined. This user function
allows pairs of spins which are coupled via the magnetic dipole-dipole
interaction to be defined. Hence the dipolar relaxation mechanism between
the two spins is to be considered active.")
-uf.desc[-1].add_paragraph("For an orientational dependent analysis, such as
model-free analysis with the spheroidal and ellipsoidal global diffusion
tensors, the two spins should already possess positional information. This
information will be used by this user function to calculate unit vectors
between the two spins. Without positional information, no vectors can be
calculated and an orientational dependent analysis will not be possible.")
-uf.desc[-1].add_paragraph("As the magnetic dipole-dipole interaction is
averaged in NMR over the interatomic distance to the inverse third power, the
interatomic distances within a 3D structural file are of no use for defining
the interaction. Therefore these average distances must be explicitly
defined.")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To set the N-H distance for protein the 15N
heteronuclear relaxation mechanism, type on of the following:")
+uf.desc[-1].add_paragraph("As the magnetic dipole-dipole interaction is
averaged in NMR over the interatomic distance to the inverse third power, the
interatomic distances within a 3D structural file are of no use for defining
the interaction. Therefore these average distances must be explicitly
supplied. This user function allows these distances to be set up.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To set the N-H distance for protein the 15N
heteronuclear relaxation mechanism to 1.02 Angstrom, type one of the
following:")
uf.desc[-1].add_prompt("relax> dipole_pair.set_dist('@N', '@H', 1.02 *
1e-10)")
uf.desc[-1].add_prompt("relax> dipole_pair.set_dist(spin_id1='@N',
spin_id2='@H', ave_dist=1.02 * 1e-10)")
uf.backend = dipole_pair.set_dist
@@ -215,16 +214,15 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("For an orientational dependent analysis, such as
model-free analysis with the spheroidal and ellipsoidal global diffusion
tensors or any analysis using RDCs, the unit vectors between the two dipoles
must be calculated prior to starting the analysis. For the unit vector
extraction, the two interacting spins should already possess positional
information, and the interaction defined via the dipole_pair.define user
function. This information will be used to calculate unit vectors between
the two spins. Without positional information, no vectors can be calculated
and an orientational dependent analysis will not be possible.")
-uf.desc[-1].add_paragraph("The number of unit vectors per interaction will
be defined by the number of positions each spin possesses together with the
averaging flag. If both spins have N positions loaded, the number of
positions N for both must match. In this case, as well as when one spin has
N positions and the other a single position, then N unit vectors will be
calculated. This is unless the averaging flag is set, in which case an
averaged unit vector of unit length will be calculated.")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To calculate the the N-H distance for protein
the 15N heteronuclear relaxation mechanism, type on of the following:")
-uf.desc[-1].add_prompt("relax> dipole_pair.unit_vectors('@N', '@H', 1.02 *
1e-10)")
-uf.desc[-1].add_prompt("relax> dipole_pair.unit_vectors(spin_id1='@N',
spin_id2='@H', ave_dist=1.02 * 1e-10)")
+uf.desc[-1].add_paragraph("For an orientational dependent analysis, such as
model-free analysis with the spheroidal and ellipsoidal global diffusion
tensors or any analysis using RDCs, the unit vectors between the two dipoles
must be calculated prior to starting the analysis. For the unit vector
extraction, the two interacting spins should already possess positional
information and the dipole-dipole interaction should already be defined via
the dipole_pair.define user function. This information will be used to
calculate unit vectors between the two spins. Without positional
information, no vectors can be calculated and an orientational dependent
analysis will not be possible.")
+uf.desc[-1].add_paragraph("The number of unit vectors per interaction will
be defined by the number of positions each spin possesses together with the
averaging flag. If both spins have N and M positions loaded, the number of
positions for both must match (N=M). In this case, as well as when one spin
has N positions and the other a single position, then N unit vectors will be
calculated. This is unless the averaging flag is set in which case an
averaged vector of unit length will be calculated.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To calculate the unit vectors prior to a
model-free analysis, type one of the following:")
+uf.desc[-1].add_prompt("relax> dipole_pair.unit_vectors(True)")
+uf.desc[-1].add_prompt("relax> dipole_pair.unit_vectors(ave=True)")
uf.backend = dipole_pair.unit_vectors
uf.menu_text = "&unit_vectors"
-uf.gui_icon = "oxygen.actions.edit-rename"
-uf.wizard_height_desc = 350
-uf.wizard_size = (900, 700)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep +
'NH_dipole_pair.png'
+uf.wizard_height_desc = 400
+uf.wizard_size = (900, 600)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep +
'NH_dipole_pair.png'
r16939 - /branches/interatomic/user_functions/dipole_pair.py