Author: bugman
Date: Wed Feb 20 09:55:12 2008
New Revision: 5039
URL: http://svn.gna.org/viewcvs/relax?rev=5039&view=rev
Log:
Merged revisions 5033-5037 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r5033 | bugman | 2008-02-20 09:23:23 +0100 (Wed, 20 Feb 2008) | 5 lines
Fixes for the generic_fns.structure.atom_add() function.
The atomic_data dictionary is now expected to be passed into the function.
........
r5034 | bugman | 2008-02-20 09:24:01 +0100 (Wed, 20 Feb 2008) | 5 lines
Fixes for the generic_fns.structure.atom_connect() function.
The atomic_data dictionary is now expected to be passed into the function.
........
r5035 | bugman | 2008-02-20 09:31:00 +0100 (Wed, 20 Feb 2008) | 3 lines
Shifted all the relative atomic mass values into the physical_constants
module.
........
r5036 | bugman | 2008-02-20 09:32:44 +0100 (Wed, 20 Feb 2008) | 3 lines
Updated the docstring of the generic_fns.structure.atomic_mass() function
to epydoc format.
........
r5037 | bugman | 2008-02-20 09:36:10 +0100 (Wed, 20 Feb 2008) | 6 lines
Updated the generic_fns.structure.autoscale_tensor() function.
The docstring was changed to epydoc format, the default method changed from
None to 'mass', and a
few comments were added.
........
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/structure.py
branches/N_state_model/physical_constants.py
Propchange: branches/N_state_model/
------------------------------------------------------------------------------
Binary property 'svnmerge-integrated' - no diff available.
Modified: branches/N_state_model/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/structure.py?rev=5039&r1=5038&r2=5039&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/structure.py (original)
+++ branches/N_state_model/generic_fns/structure.py Wed Feb 20 09:55:12 2008
@@ -34,13 +34,14 @@
from generic_fns import molmol
from generic_fns.sequence import load_PDB_sequence
from generic_fns.selection import exists_mol_res_spin_data, return_molecule,
return_residue, return_spin, spin_loop
+from physical_constants import ArH, ArC, ArN, ArO, ArS
from relax_errors import RelaxError, RelaxFileError, RelaxNoPdbChainError,
RelaxNoPdbError, RelaxNoResError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxNoTensorError, RelaxNoVectorsError, RelaxPdbError, RelaxPdbLoadError,
RelaxRegExpError
from relax_io import get_file_path
from relax_warnings import RelaxNoAtomWarning, RelaxNoPDBFileWarning,
RelaxWarning, RelaxZeroVectorWarning
-def atom_add(atom_id=None, record_name='', atom_name='', res_name='',
chain_id='', res_num=None, pos=[None, None, None], segment_id='', element=''):
+def atom_add(atomic_data=None, atom_id=None, record_name='', atom_name='',
res_name='', chain_id='', res_num=None, pos=[None, None, None],
segment_id='', element=''):
"""Function for adding an atom to the atomic_data structure.
The atomic_data data structure is a dictionary of arrays. The keys
correspond to the
@@ -62,6 +63,8 @@
This function will create the key-value pair for the given atom.
+ @param atomic_data: The dictionary to place the atomic data into.
+ @type atomic_data: dict
@param atom_id: The atom identifier. This is used as the key within
the dictionary.
@type atom_id: str
@param record_name: The record name, e.g. 'ATOM', 'HETATM', or 'TER'.
@@ -100,7 +103,7 @@
atomic_data[atom_id].append(element)
-def atom_connect(atom_id=None, bonded_id=None):
+def atom_connect(atomic_data=None, atom_id=None, bonded_id=None):
"""Function for connecting two atoms within the atomic_data data
structure.
The atomic_data data structure is a dictionary of arrays. The keys
correspond to the
@@ -123,6 +126,14 @@
The bonded_id atom number will then be appended to the atom_id array.
Because the
connections work both ways in the PDB file, the atom_id atom number will
be appended to the
bonded_id atom array as well.
+
+
+ @param atomic_data: The dictionary to place the atomic data into.
+ @type atomic_data: dict
+ @param atom_id: The atom identifier. This is used as the key within
the dictionary.
+ @type atom_id: str
+ @param bonded_id: The second atom identifier. This is used as the key
within the dictionary.
+ @type bonded_id: str
"""
# Find the atom number corresponding to atom_id.
@@ -145,42 +156,55 @@
def atomic_mass(element=None):
- """Return the atomic mass of the given element."""
+ """Return the atomic mass of the given element.
+
+ @param element: The name of the element to return the atomic mass of.
+ @type element: str
+ @return: The relative atomic mass.
+ @rtype: float
+ """
# Proton.
if element == 'H' or element == 'Q':
- return 1.00794
+ return ArH
# Carbon.
elif element == 'C':
- return 12.0107
+ return ArC
# Nitrogen.
elif element == 'N':
- return 14.0067
+ return ArN
# Oxygen.
elif element == 'O':
- return 15.9994
+ return ArO
# Sulphur.
elif element == 'S':
- return 32.065
+ return ArS
# Unknown.
else:
raise RelaxError, "The mass of the element " + `element` + " has not
yet been programmed into relax."
-def autoscale_tensor(method=None):
- """Automatically determine an appropriate scaling factor for display
- of the diffusion tensor"""
-
+def autoscale_tensor(method='mass'):
+ """Automatically determine an appropriate scaling factor for display of
the diffusion tensor.
+
+ @param method: The method used to determine the scaling of the
diffusion tensor object.
+ @type method: str
+ @return: The scaling factor.
+ @rtype: float
+ """
+
+ # Centre of mass method.
if method == 'mass':
com, mass = centre_of_mass(return_mass=True)
scale = mass * 6.8e-11
return scale
+ # Autoscaling method.
warn(RelaxWarning("Autoscale method %s not implimented. Reverting to
scale=1.8e-6 A.s" % method))
return 1.8e-6
Modified: branches/N_state_model/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/physical_constants.py?rev=5039&r1=5038&r2=5039&view=diff
==============================================================================
--- branches/N_state_model/physical_constants.py (original)
+++ branches/N_state_model/physical_constants.py Wed Feb 20 09:55:12 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007 Edward d'Auvergne
#
+# Copyright (C) 2007-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -24,6 +24,9 @@
from math import pi
+# Misc. constants.
+##################
+
# Planck's constant.
h = 6.62606876 * 1e-34
@@ -33,12 +36,19 @@
# The magnetic constant or the permeability of vacuum.
mu0 = 4.0 * pi * 1e-7
+
+# CSA and bond lengths.
+#######################
+
# The 15N CSA in the NH bond (default value).
N15_CSA = -172 * 1e-6
# The length of the NH bond (default value).
NH_BOND_LENGTH = 1.02 * 1e-10
+
+# Gyromagnetic ratios.
+######################
# The 13C gyromagnetic ratio.
g13C = 6.728 * 1e7
@@ -54,3 +64,22 @@
# The 31P gyromagnetic ratio.
g31P = 10.841 * 1e7
+
+
+# Relative atomic masses.
+#########################
+
+# Proton.
+ArH = 1.00794
+
+# Carbon.
+ArC = 12.0107
+
+# Nitrogen.
+ArN = 14.0067
+
+# Oxygen.
+ArO = 15.9994
+
+# Sulphur.
+ArS = 32.065
r5039 - in /branches/N_state_model: ./ generic_fns/structure.py physical_constants.py