Author: bugman
Date: Sun Jan 6 12:03:56 2008
New Revision: 4391
URL: http://svn.gna.org/viewcvs/relax?rev=4391&view=rev
Log:
Converted all the 'structure' user functions to the new relax design.
Modified:
1.3/prompt/structure.py
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=4391&r1=4390&r2=4391&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Sun Jan 6 12:03:56 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003, 2004, 2006 Edward d'Auvergne
#
+# Copyright (C) 2003, 2004, 2006-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -20,8 +20,11 @@
#
#
###############################################################################
+# Python module imports.
import sys
+# relax module imports.
+from generic_fns import structure
import help
from relax_errors import RelaxBinError, RelaxFloatError, RelaxIntError,
RelaxNoneIntError, RelaxNoneStrError, RelaxStrError
@@ -39,13 +42,11 @@
self.__relax__ = relax
- def create_diff_tensor_pdb(self, run=None, scale=1.8e-6,
file='tensor.pdb', dir=None, force=0):
+ def create_diff_tensor_pdb(self, scale=1.8e-6, file='tensor.pdb',
dir=None, force=0):
"""Create a PDB file to represent the diffusion tensor.
Keyword Arguments
~~~~~~~~~~~~~~~~~
-
- run: The run to assign the structure to.
scale: Value for scaling the diffusion rates.
@@ -139,20 +140,15 @@
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "structure.create_diff_tensor_pdb("
- text = text + "run=" + `run`
- text = text + ", scale=" + `scale`
+ text = text + "scale=" + `scale`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
text = text + ", force=" + `force` + ")"
print text
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
# Scaling.
- #if type(scale) != float and type(scale) != int:
- # raise RelaxNumError, ('scaling factor', scale)
+ if type(scale) != float and type(scale) != int:
+ raise RelaxNumError, ('scaling factor', scale)
# File name.
if type(file) != str:
@@ -167,16 +163,14 @@
raise RelaxBinError, ('force flag', force)
# Execute the functional code.
- self.__relax__.generic.structure.create_diff_tensor_pdb(run=run,
scale=scale, file=file, dir=dir, force=force)
-
-
- def create_vector_dist(self, run=None, length=2e-9, symmetry=1,
file='XH_dist.pdb', dir=None, force=0):
+ structure.create_diff_tensor_pdb(scale=scale, file=file, dir=dir,
force=force)
+
+
+ def create_vector_dist(self, length=2e-9, symmetry=1,
file='XH_dist.pdb', dir=None, force=0):
"""Create a PDB file representation of the distribution of XH bond
vectors.
Keyword Arguments
~~~~~~~~~~~~~~~~~
-
- run: The run to assign the structure to.
length: The length of the vectors in the PDB representation
(meters).
@@ -207,18 +201,13 @@
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "structure.create_vector_dist("
- text = text + "run=" + `run`
- text = text + ", length=" + `length`
+ text = text + "length=" + `length`
text = text + ", symmetry=" + `symmetry`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
text = text + ", force=" + `force` + ")"
print text
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
# Vector length.
if type(length) != float:
raise RelaxFloatError, ('vector length', length)
@@ -240,16 +229,14 @@
raise RelaxBinError, ('force flag', force)
# Execute the functional code.
- self.__relax__.generic.structure.create_vector_dist(run=run,
length=length, symmetry=symmetry, file=file, dir=dir, force=force)
-
-
- def read_pdb(self, run=None, file=None, dir=None, model=None,
load_seq=1):
+ structure.create_vector_dist(length=length, symmetry=symmetry,
file=file, dir=dir, force=force)
+
+
+ def read_pdb(self, file=None, dir=None, model=None, load_seq=1):
"""The pdb loading function.
Keyword Arguments
~~~~~~~~~~~~~~~~~
-
- run: The run to assign the structure to.
file: The name of the PDB file.
@@ -274,34 +261,28 @@
Example
~~~~~~~
- To load all structures from the PDB file 'test.pdb' in the directory
'~/pdb' for use in the
- model-free analysis run 'm8', type:
-
- relax> structure.read_pdb('m8', 'test.pdb', '~/pdb', 1)
- relax> structure.read_pdb(run='m8', file='test.pdb', dir='pdb',
model=1)
+ To load all structures from the PDB file 'test.pdb' in the directory
'~/pdb', type:
+
+ relax> structure.read_pdb('test.pdb', '~/pdb', 1)
+ relax> structure.read_pdb(file='test.pdb', dir='pdb', model=1)
To load the 10th model from the file 'test.pdb', use:
- relax> structure.read_pdb('m1', 'test.pdb', model=10)
- relax> structure.read_pdb(run='m1', file='test.pdb', model=10)
+ relax> structure.read_pdb('test.pdb', model=10)
+ relax> structure.read_pdb(file='test.pdb', model=10)
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "structure.read_pdb("
- text = text + "run=" + `run`
- text = text + ", file=" + `file`
+ text = text + "file=" + `file`
text = text + ", dir=" + `dir`
text = text + ", model=" + `model`
text = text + ", load_seq=" + `load_seq` + ")"
print text
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
# File name.
if type(file) != str:
raise RelaxStrError, ('file name', file)
@@ -319,16 +300,14 @@
raise RelaxBinError, ('load sequence flag', load_seq)
# Execute the functional code.
- self.__relax__.generic.structure.read_pdb(run=run, file=file,
dir=dir, model=model, load_seq=load_seq)
-
-
- def vectors(self, run=None, heteronuc='N', proton='H', res_num=None,
res_name=None):
+ structure.read_pdb(file=file, dir=dir, model=model,
load_seq=load_seq)
+
+
+ def vectors(self, heteronuc='N', proton='H', res_num=None,
res_name=None):
"""Function for calculating/extracting XH vectors from the structure.
Keyword arguments
~~~~~~~~~~~~~~~~~
-
- run: The run to assign the vectors to.
heteronuc: The heteronucleus name as specified in the PDB file.
@@ -353,40 +332,34 @@
~~~~~~~
To calculate the XH vectors of the backbone amide nitrogens where in
the PDB file the
- backbone nitrogen is called 'N' and the attached proton is called
'H', assuming the run
- 'test', type:
-
- relax> structure.vectors('test')
- relax> structure.vectors('test', 'N')
- relax> structure.vectors('test', 'N', 'H')
- relax> structure.vectors('test', heteronuc='N', proton='H')
+ backbone nitrogen is called 'N' and the attached proton is called
'H', type:
+
+ relax> structure.vectors()
+ relax> structure.vectors('N')
+ relax> structure.vectors('N', 'H')
+ relax> structure.vectors(heteronuc='N', proton='H')
If the attached proton is called 'HN', type:
- relax> structure.vectors('test', proton='HN')
+ relax> structure.vectors(proton='HN')
If you are working with RNA, you can use the residue name identifier
to calculate the
vectors for each residue separately. For example:
- relax> structure.vectors('m1', 'N1', 'H1', res_name='G')
- relax> structure.vectors('m1', 'N3', 'H3', res_name='U')
+ relax> structure.vectors('N1', 'H1', res_name='G')
+ relax> structure.vectors('N3', 'H3', res_name='U')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "structure.vectors("
- text = text + "run=" + `run`
- text = text + ", heteronuc=" + `heteronuc`
+ text = text + "heteronuc=" + `heteronuc`
text = text + ", proton=" + `proton`
text = text + ", res_num=" + `res_num`
text = text + ", res_name=" + `res_name` + ")"
print text
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
# The heteronucleus argument.
if type(heteronuc) != str:
raise RelaxStrError, ('heteronucleus', heteronuc)
@@ -404,4 +377,4 @@
raise RelaxNoneStrError, ('residue name', res_name)
# Execute the functional code.
- self.__relax__.generic.structure.vectors(run=run,
heteronuc=heteronuc, proton=proton, res_num=res_num, res_name=res_name)
+ structure.vectors(heteronuc=heteronuc, proton=proton,
res_num=res_num, res_name=res_name)
r4391 - /1.3/prompt/structure.py