Author: bugman
Date: Thu Sep 25 09:39:41 2014
New Revision: 26025
URL: http://svn.gna.org/viewcvs/relax?rev=26025&view=rev
Log:
Incorporated the contents of the summarise.py script into the frame order
auto-analysis module.
This has been converted into the summarise() function which will generate a
results summary table as
the analysis is still running.
Modified:
branches/frame_order_cleanup/auto_analyses/frame_order.py
Modified: branches/frame_order_cleanup/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/frame_order.py?rev=26025&r1=26024&r2=26025&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Thu Sep 25
09:39:41 2014
@@ -43,6 +43,7 @@
# Python module imports.
+from math import pi
from numpy import float64, zeros
from os import F_OK, access, getcwd, sep
import sys
@@ -57,12 +58,166 @@
from lib.io import open_write_file
from lib.order.order_parameters import iso_cone_theta_to_S
from lib.text.sectioning import section, subsection, title
+from lib.text.table import MULTI_COL, format_table
+from pipe_control import pipes, results
from pipe_control.mol_res_spin import return_spin, spin_loop
-from pipe_control.pipes import get_pipe
from pipe_control.structure.mass import pipe_centre_of_mass
from prompt.interpreter import Interpreter
from specific_analyses.frame_order.data import generate_pivot
from status import Status; status = Status()
+
+
+
+def summarise(file_name='summary', dir=None, force=True):
+ """Summarise the frame order auto-analysis results.
+
+ This function can be used while a frame order analysis is running to
summarise the results. It will create a table of the statistics and model
parameters for all of the optimised frame order models for which results files
currently exist.
+
+
+ @keyword file_name: The file to save the table into.
+ @type file_name: str
+ @keyword dir: The optional directory to place the file into.
+ @type dir: None or str
+ @keyword force: A flag which if True will cause any preexisting
file to be overwritten.
+ @type force: bool
+ """
+
+ # The model names and directories.
+ model_names = [
+ 'Rigid',
+ 'Free rotor',
+ 'Rotor',
+ 'Iso cone, free rotor',
+ 'Iso cone, torsionless',
+ 'Iso cone, torsionless (perm A)',
+ 'Iso cone',
+ 'Iso cone (perm A)',
+ 'Pseudo ellipse, torsionless',
+ 'Pseudo ellipse, torsionless (perm A)',
+ 'Pseudo ellipse, torsionless (perm B)',
+ 'Pseudo ellipse',
+ 'Pseudo ellipse (perm A)',
+ 'Pseudo ellipse (perm B)',
+ 'Double rotor'
+ ]
+ model_dirs = {
+ 'Rigid': 'rigid',
+ 'Free rotor': 'free_rotor',
+ 'Rotor': 'rotor',
+ 'Iso cone, free rotor': 'iso_cone, free_rotor',
+ 'Iso cone, torsionless': 'iso_cone_torsionless',
+ 'Iso cone, torsionless (perm A)': 'iso_cone_torsionless_permutation_A',
+ 'Iso cone': 'iso_cone',
+ 'Iso cone (perm A)': 'iso_cone_permutation_A',
+ 'Pseudo ellipse, torsionless': 'pseudo-ellipse_torsionless',
+ 'Pseudo ellipse, torsionless (perm A)':
'pseudo-ellipse_torsionless_permutation_A',
+ 'Pseudo ellipse, torsionless (perm B)':
'pseudo-ellipse_torsionless_permutation_B',
+ 'Pseudo ellipse': 'pseudo-ellipse',
+ 'Pseudo ellipse (perm A)': 'pseudo-ellipse_permutation_A',
+ 'Pseudo ellipse (perm B)': 'pseudo-ellipse_permutation_B',
+ 'Double rotor': 'double_rotor'
+ }
+
+ # The analysis directory and structures.
+ contents = []
+ contents.append(["Analysis directory", getcwd()])
+ string = format_table(contents=contents)
+
+ # Table header.
+ headings1 = []
+ headings1.append(["Model", "k", "chi2", "AIC", "Motional eigenframe",
MULTI_COL, MULTI_COL, "Order parameters (deg)", MULTI_COL, MULTI_COL,
MULTI_COL])
+ headings1.append([None, None, None, None, "a", "b/th", "g/ph", "thx",
"thy", "smax", "smax2"])
+
+ # 2nd table header.
+ headings2 = []
+ headings2.append(["Model", "Average position", MULTI_COL, MULTI_COL,
MULTI_COL, MULTI_COL, MULTI_COL, "Pivot point", MULTI_COL, MULTI_COL])
+ headings2.append([None, "x", "y", "z", "a", "b", "g", "x", "y", "z"])
+
+ # Loop over the models.
+ contents1 = []
+ contents2 = []
+ for i in range(len(model_names)):
+ # No file.
+ if not access(model_dirs[model_names[i]]+'/results.bz2', F_OK):
+ continue
+
+ # Create a data pipe.
+ pipes.create(model_names[i], 'frame order')
+
+ # Load the data.
+ results.read(file='results', dir=model_dirs[model_names[i]])
+
+ # Number of params.
+ k = len(cdp.params)
+
+ # Format the model information.
+ contents1.append([model_names[i], k, cdp.chi2, cdp.chi2 + 2*k, None,
None, None, None, None, None, None])
+ contents2.append([model_names[i], 0.0, 0.0, 0.0, None, None, None,
None, None, None])
+
+ # Eigen alpha.
+ if hasattr(cdp, 'eigen_alpha') and cdp.eigen_alpha != None:
+ contents1[-1][4] = cdp.eigen_alpha
+
+ # Eigen beta.
+ if hasattr(cdp, 'eigen_beta') and cdp.eigen_beta != None:
+ contents1[-1][5] = cdp.eigen_beta
+ elif hasattr(cdp, 'axis_theta') and cdp.axis_theta != None:
+ contents1[-1][5] = cdp.axis_theta
+
+ # Eigen gamma.
+ if hasattr(cdp, 'eigen_gamma') and cdp.eigen_gamma != None:
+ contents1[-1][6] = cdp.eigen_gamma
+ elif hasattr(cdp, 'axis_phi') and cdp.axis_phi != None:
+ contents1[-1][6] = cdp.axis_phi
+
+ # Order x.
+ if hasattr(cdp, 'cone_theta_x') and cdp.cone_theta_x != None:
+ contents1[-1][7] = cdp.cone_theta_x / 2.0 / pi * 360.0
+ elif hasattr(cdp, 'cone_theta') and cdp.cone_theta != None:
+ contents1[-1][7] = cdp.cone_theta / 2.0 / pi * 360.0
+
+ # Order y.
+ if hasattr(cdp, 'cone_theta_y') and cdp.cone_theta_y != None:
+ contents1[-1][8] = cdp.cone_theta_y / 2.0 / pi * 360.0
+
+ # Order torsion.
+ if hasattr(cdp, 'cone_sigma_max') and cdp.cone_sigma_max != None:
+ contents1[-1][9] = cdp.cone_sigma_max / 2.0 / pi * 360.0
+
+ # Order torsion 2.
+ if hasattr(cdp, 'cone_sigma_max_2') and cdp.cone_sigma_max_2 != None:
+ contents1[-1][10] = cdp.cone_sigma_max_2 / 2.0 / pi * 360.0
+
+ # The average position parameters.
+ if hasattr(cdp, 'ave_pos_x') and cdp.ave_pos_x != None:
+ contents2[-1][1] = cdp.ave_pos_x
+ if hasattr(cdp, 'ave_pos_y') and cdp.ave_pos_y != None:
+ contents2[-1][2] = cdp.ave_pos_y
+ if hasattr(cdp, 'ave_pos_z') and cdp.ave_pos_z != None:
+ contents2[-1][3] = cdp.ave_pos_z
+ if hasattr(cdp, 'ave_pos_alpha') and cdp.ave_pos_alpha != None:
+ contents2[-1][4] = cdp.ave_pos_alpha
+ if hasattr(cdp, 'ave_pos_beta') and cdp.ave_pos_beta != None:
+ contents2[-1][5] = cdp.ave_pos_beta
+ if hasattr(cdp, 'ave_pos_gamma') and cdp.ave_pos_gamma != None:
+ contents2[-1][6] = cdp.ave_pos_gamma
+
+ # The pivot point.
+ contents2[-1][7] = cdp.pivot_x
+ contents2[-1][8] = cdp.pivot_y
+ contents2[-1][9] = cdp.pivot_z
+
+ # Add the tables.
+ string += format_table(headings=headings1, contents=contents1,
custom_format=[None, None, "%.2f", "%.2f", "%.3f", "%.3f", "%.3f", "%.2f",
"%.2f", "%.2f", "%.2f"])
+ string += format_table(headings=headings2, contents=contents2,
custom_format=[None, "%.3f", "%.3f", "%.3f", "%.3f", "%.3f", "%.3f", "%.3f",
"%.3f", "%.3f"])
+
+ # Write out.
+ sys.stdout.write("\n\n\n")
+ sys.stdout.write(string)
+ file = open_write_file(file_name=file_name, dir=dir, force=force)
+ file.write(string)
+ file.close()
+
class Frame_order_analysis:
@@ -402,7 +557,7 @@
print("Obtaining the average position from the rigid model.")
# Get the rigid data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_RIGID])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_RIGID])
# Copy the average position parameters from the rigid model.
cdp.ave_pos_x = pipe.ave_pos_x
@@ -418,7 +573,7 @@
print("Obtaining the average position from the free rotor model.")
# Get the free rotor data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_FREE_ROTOR])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_FREE_ROTOR])
# Copy the average position parameters from the free rotor model.
cdp.ave_pos_x = pipe.ave_pos_x
@@ -449,7 +604,7 @@
print("Obtaining the cone axis from the rotor model.")
# Get the rotor data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_ROTOR])
# The cone axis as the axis alpha angle.
if model == MODEL_FREE_ROTOR:
@@ -465,7 +620,7 @@
print("Obtaining the cone axis from the isotropic cone model.")
# Get the iso cone data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_ISO_CONE])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_ISO_CONE])
# Copy the cone axis parameters.
cdp.axis_theta = pipe.axis_theta
@@ -477,7 +632,7 @@
print("Obtaining the full eigenframe from the pseudo-ellipse
model.")
# Get the pseudo-ellipse data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_PSEUDO_ELLIPSE])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_PSEUDO_ELLIPSE])
# Copy the three Euler angles.
cdp.eigen_alpha = pipe.eigen_alpha
@@ -503,7 +658,7 @@
# The cone angle from the isotropic cone model.
if model in [MODEL_ISO_CONE_TORSIONLESS, MODEL_PSEUDO_ELLIPSE,
MODEL_ISO_CONE_FREE_ROTOR]:
# Get the iso cone data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_ISO_CONE])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_ISO_CONE])
# Copy the cone angle directly.
if model == MODEL_ISO_CONE_TORSIONLESS:
@@ -526,7 +681,7 @@
print("Obtaining the cone X and Y angles from the pseudo-ellipse
model.")
# Get the pseudo-ellipse data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_PSEUDO_ELLIPSE])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_PSEUDO_ELLIPSE])
# Copy the cone axis.
cdp.cone_theta_x = pipe.cone_theta_x
@@ -539,7 +694,7 @@
print("Obtaining the torsion angle from the rotor model.")
# Get the rotor data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_ROTOR])
# Copy the cone axis.
cdp.cone_sigma_max = pipe.cone_sigma_max
@@ -564,7 +719,7 @@
print("Obtaining the pivot point from the rotor model.")
# Get the iso cone data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
+ pipe = pipes.get_pipe(self.pipe_name_dict[MODEL_ROTOR])
# Copy the pivot parameters.
cdp.pivot_x = pipe.pivot_x
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