Author: bugman
Date: Tue Jul 1 18:08:30 2014
New Revision: 24385
URL: http://svn.gna.org/viewcvs/relax?rev=24385&view=rev
Log:
Started to redesign the frame_order.pdb_model user function.
Instead of having the positive and negative representations in different PDB
models, and the Monte
Carlo simulations in different molecules, these will now all be shifted into
separate files.
For this to be possible, the file root rather than file names must now be
supplied to the
frame_order.pdb_model user function. To allow for different file
compression, the compress_type
argument is now used. The backend code correctly handles the file root
change, but the multiple
files are not created yet.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
branches/frame_order_cleanup/user_functions/frame_order.py
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=24385&r1=24384&r2=24385&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Tue Jul 1 18:08:30 2014
@@ -365,17 +365,19 @@
rotor(structure=structure, rotor_angle=rotor_angle[i], axis=axis[i],
axis_pt=pivot[i], label=label[i], centre=com[i], span=span[i],
blade_length=5e-10, staggered=staggered[i])
-def create_ave_pos(format='PDB', file=None, dir=None, force=False):
+def create_ave_pos(format='PDB', file=None, dir=None, compress_type=0,
force=False):
"""Create a PDB file of the molecule with the moving domains shifted to
the average position.
- @keyword format: The format for outputting the geometric
representation. Currently only the 'PDB' format is supported.
- @type format: str
- @keyword file: The name of the file for the average molecule
structure.
- @type file: str
- @keyword dir: The name of the directory to place the PDB file into.
- @type dir: str
- @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
- @type force: bool
+ @keyword format: The format for outputting the geometric
representation. Currently only the 'PDB' format is supported.
+ @type format: str
+ @keyword file: The name of the file for the average molecule
structure.
+ @type file: str
+ @keyword dir: The name of the directory to place the PDB file
into.
+ @type dir: str
+ @keyword compress_type: The compression type. The integer values
correspond to the compression type: 0, no compression; 1, Bzip2 compression;
2, Gzip compression.
+ @type compress_type: int
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
+ @type force: bool
"""
# Printout.
@@ -398,43 +400,47 @@
# Output to PDB format.
if format == 'PDB':
- file = open_write_file(file_name=file, dir=dir, force=force)
+ file = open_write_file(file_name=file+'.pdb', dir=dir,
compress_type=compress_type, force=force)
structure.write_pdb(file=file)
file.close()
-def create_distribution(format='PDB', file=None, dir=None, force=False):
+def create_distribution(format='PDB', file=None, dir=None, compress_type=0,
force=False):
"""Create a PDB file of a distribution of positions coving the full
dynamics of the moving domain.
- @keyword format: The format for outputting the geometric
representation. Currently only the 'PDB' format is supported.
- @type format: str
- @keyword file: The name of the file which will contain multiple
models spanning the full dynamics distribution of the frame order model.
- @type file: str
- @keyword dir: The name of the directory to place the PDB file into.
- @type dir: str
- @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
- @type force: bool
+ @keyword format: The format for outputting the geometric
representation. Currently only the 'PDB' format is supported.
+ @type format: str
+ @keyword file: The name of the file which will contain multiple
models spanning the full dynamics distribution of the frame order model.
+ @type file: str
+ @keyword dir: The name of the directory to place the PDB file
into.
+ @type dir: str
+ @keyword compress_type: The compression type. The integer values
correspond to the compression type: 0, no compression; 1, Bzip2 compression;
2, Gzip compression.
+ @type compress_type: int
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
+ @type force: bool
"""
# Printout.
subsection(file=sys.stdout, text="Creating a PDB file of a distribution
of positions coving the full dynamics of the moving domain.")
-def create_geometric_rep(format='PDB', file=None, dir=None, size=30.0,
inc=36, force=False):
+def create_geometric_rep(format='PDB', file=None, dir=None, compress_type=0,
size=30.0, inc=36, force=False):
"""Create a PDB file containing a geometric object representing the
frame order dynamics.
- @keyword format: The format for outputting the geometric
representation. Currently only the 'PDB' format is supported.
- @type format: str
- @keyword file: The name of the file of the PDB representation of
the frame order dynamics to create.
- @type file: str
- @keyword dir: The name of the directory to place the PDB file into.
- @type dir: str
- @keyword size: The size of the geometric object in Angstroms.
- @type size: float
- @keyword inc: The number of increments for the filling of the cone
objects.
- @type inc: int
- @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
- @type force: bool
+ @keyword format: The format for outputting the geometric
representation. Currently only the 'PDB' format is supported.
+ @type format: str
+ @keyword file: The name of the file of the PDB representation
of the frame order dynamics to create.
+ @type file: str
+ @keyword dir: The name of the directory to place the PDB file
into.
+ @type dir: str
+ @keyword compress_type: The compression type. The integer values
correspond to the compression type: 0, no compression; 1, Bzip2 compression;
2, Gzip compression.
+ @type compress_type: int
+ @keyword size: The size of the geometric object in Angstroms.
+ @type size: float
+ @keyword inc: The number of increments for the filling of the
cone objects.
+ @type inc: int
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
+ @type force: bool
"""
# Printout.
@@ -463,6 +469,6 @@
# Create the PDB file.
if format == 'PDB':
- pdb_file = open_write_file(file, dir, force=force)
+ pdb_file = open_write_file(file+'.pdb', dir,
compress_type=compress_type, force=force)
structure.write_pdb(pdb_file)
pdb_file.close()
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=24385&r1=24384&r2=24385&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Tue
Jul 1 18:08:30 2014
@@ -53,17 +53,19 @@
cdp.num_int_pts = num
-def pdb_model(ave_pos_file="ave_pos.pdb", rep_file="frame_order.pdb",
dist_file="domain_distribution.pdb", dir=None, size=30.0, inc=36,
force=False):
+def pdb_model(ave_pos="ave_pos", rep="frame_order",
dist="domain_distribution", dir=None, compress_type=0, size=30.0, inc=36,
force=False):
"""Create 3 different PDB files for representing the frame order
dynamics of the system.
- @keyword ave_pos_file: The name of the file for the average molecule
structure.
- @type ave_pos_file: str or None
- @keyword rep_file: The name of the file of the PDB representation
of the frame order dynamics to create.
- @type rep_file: str or None
- @keyword dist_file: The name of the file which will contain multiple
models spanning the full dynamics distribution of the frame order model.
- @type dist_file: str or None
+ @keyword ave_pos: The file root for the average molecule structure.
+ @type ave_pos: str or None
+ @keyword rep: The file root of the PDB representation of the
frame order dynamics to create.
+ @type rep: str or None
+ @keyword dist: The file root which will contain multiple models
spanning the full dynamics distribution of the frame order model.
+ @type dist: str or None
@keyword dir: The name of the directory to place the PDB file
into.
@type dir: str
+ @keyword compress_type: The compression type. The integer values
correspond to the compression type: 0, no compression; 1, Bzip2 compression;
2, Gzip compression.
+ @type compress_type: int
@keyword size: The size of the geometric object in Angstroms.
@type size: float
@keyword inc: The number of increments for the filling of the
cone objects.
@@ -73,27 +75,27 @@
"""
# Check that at least one PDB file name is given.
- if not ave_pos_file and not rep_file and not dist_file:
+ if not ave_pos and not rep and not dist:
raise RelaxError("Minimally one PDB file name must be supplied.")
# Test if the current data pipe exists.
pipes.test()
# Create the average position structure.
- if ave_pos_file:
- create_ave_pos(file=ave_pos_file, dir=dir, force=force)
+ if ave_pos:
+ create_ave_pos(file=ave_pos, dir=dir, compress_type=compress_type,
force=force)
# Nothing more to do for the rigid model.
if cdp.model == 'rigid':
return
# Create the geometric representation.
- if rep_file:
- create_geometric_rep(file=rep_file, dir=dir, size=size, inc=inc,
force=force)
+ if rep:
+ create_geometric_rep(file=rep, dir=dir, compress_type=compress_type,
size=size, inc=inc, force=force)
# Create the distribution.
- if dist_file:
- create_distribution(file=dist_file, dir=dir, force=force)
+ if dist:
+ create_distribution(file=dist, dir=dir, compress_type=compress_type,
force=force)
def pivot(pivot=None, order=1, fix=False):
Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=24385&r1=24384&r2=24385&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py Tue Jul 1
18:08:30 2014
@@ -49,34 +49,34 @@
uf.title = "Create a PDB file representation of the frame order dynamics."
uf.title_short = "Frame order dynamics PDB representation."
uf.add_keyarg(
- name = "ave_pos_file",
- default = "ave_pos.pdb",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "average structure file name",
- desc = "The name of the 3D structure PDB file for the molecular
structure with the moving domains shifted to the average position.",
+ name = "ave_pos",
+ default = "ave_pos",
+ py_type = "str",
+ arg_type = "str",
+ desc_short = "average structure file root",
+ desc = "The file root of the 3D structure PDB file for the molecular
structure with the moving domains shifted to the average position.",
wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
wiz_filesel_style = FD_SAVE,
can_be_none = True
)
uf.add_keyarg(
- name = "rep_file",
- default = "frame_order.pdb",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "PDB representation file name",
- desc = "The name of the PDB file for the geometric object representation
of the frame order dynamics.",
+ name = "rep",
+ default = "frame_order",
+ py_type = "str",
+ arg_type = "str",
+ desc_short = "PDB representation file root",
+ desc = "The file root of the PDB file for the geometric object
representation of the frame order dynamics.",
wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
wiz_filesel_style = FD_SAVE,
can_be_none = True
)
uf.add_keyarg(
- name = "dist_file",
- default = "domain_distribution.pdb",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "distribution file name",
- desc = "The name of the file which will contain multiple models spanning
the full dynamics distribution of the frame order model.",
+ name = "dist",
+ default = "domain_distribution",
+ py_type = "str",
+ arg_type = "str",
+ desc_short = "distribution file root",
+ desc = "The file root of the file which will contain multiple models
spanning the full dynamics distribution of the frame order model.",
wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
wiz_filesel_style = FD_SAVE,
can_be_none = True
@@ -88,6 +88,25 @@
desc_short = "directory name",
desc = "The directory where the file is to be located.",
can_be_none = True
+)
+uf.add_keyarg(
+ name = "compress_type",
+ default = 0,
+ py_type = "int",
+ desc_short = "file compression",
+ desc = "The type of compression to use when creating the files.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = [
+ "No compression",
+ "bzip2 compression",
+ "gzip compression"
+ ],
+ wiz_combo_data = [
+ 0,
+ 1,
+ 2
+ ],
+ wiz_read_only = True
)
uf.add_keyarg(
name = "size",
@@ -113,7 +132,8 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This function creates a PDB file containing an
artificial geometric structure representing the Frame Order cone models.")
+uf.desc[-1].add_paragraph("This function creates a set of PDB files for
representing the frame order cone models. This includes a file for the
average position of the molecule, a file containing a geometric
representation of the frame order motions, and a file containing a
distribution of structures which sample the motional modes.")
+uf.desc[-1].add_paragraph("The three files are specified via the file root
whereby the extensions '.pdb', '.pdb.gz', etc. should not be provided. This
is important for the geometric representation whereby different files are
created for the positive and negative representations (due to symmetry in the
NMR data, these cannot be differentiated), and for the Monte Carlo
simulations. For example if the file root is 'frame_order', the positive and
negative representations will be placed in the 'frame_order_pos.pdb.gz' and
'frame_order_neg.pdb.gz' files and the Monte Carlo simulations in the
'frame_order_sim_pos.pdb.gz' and 'frame_order_sim_neg.pdb.gz' files. For
models where there is no difference in representation between the positive
and negative directions, the files 'frame_order.pdb.gz' and
'frame_order_sim.pdb.gz' will be produced.")
uf.desc[-1].add_paragraph("There are four different types of residue within
the PDB. The pivot point is represented as as a single carbon atom of the
residue 'PIV'. The cone consists of numerous H atoms of the residue 'CON'.
The cone axis vector is presented as the residue 'AXE' with one carbon atom
positioned at the pivot and the other x Angstroms away on the cone axis (set
by the geometric object size). Finally, if Monte Carlo have been performed,
there will be multiple 'MCC' residues representing the cone for each
simulation, and multiple 'MCA' residues representing the multiple cone axes.")
uf.desc[-1].add_paragraph("To create the diffusion in a cone PDB
representation, a uniform distribution of vectors on a sphere is generated
using spherical coordinates with the polar angle defined by the cone axis.
By incrementing the polar angle using an arccos distribution, a radial array
of vectors representing latitude are created while incrementing the azimuthal
angle evenly creates the longitudinal vectors. These are all placed into the
PDB file as H atoms and are all connected using PDB CONECT records. Each H
atom is connected to its two neighbours on the both the longitude and
latitude. This creates a geometric PDB object with longitudinal and
latitudinal lines representing the filled cone.")
uf.backend = pdb_model
r24385 - in /branches/frame_order_cleanup: specific_analyses/frame_order/ user_functions/