Author: bugman
Date: Thu Jun 13 10:22:24 2013
New Revision: 20081
URL: http://svn.gna.org/viewcvs/relax?rev=20081&view=rev
Log:
Removed the pipe_control.dipole_pair module as its contents is now in
pipe_control.interatomic.
Removed:
trunk/pipe_control/dipole_pair.py
Removed: trunk/pipe_control/dipole_pair.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/dipole_pair.py?rev=20080&view=auto
==============================================================================
--- trunk/pipe_control/dipole_pair.py (original)
+++ trunk/pipe_control/dipole_pair.py (removed)
@@ -1,401 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module for the manipulation of relaxation data."""
-
-# Python module imports.
-from numpy import float64, zeros
-from numpy.linalg import norm
-import sys
-from warnings import warn
-
-# relax module imports.
-from lib.arg_check import is_float
-from pipe_control.interatomic import create_interatom, exists_data,
interatomic_loop, return_interatom
-from pipe_control.mol_res_spin import Selection, exists_mol_res_spin_data,
return_spin, spin_loop
-from pipe_control import pipes
-from lib.errors import RelaxError, RelaxNoInteratomError
-from lib.io import extract_data, write_data
-from lib.warnings import RelaxWarning, RelaxZeroVectorWarning
-
-
-def define(spin_id1=None, spin_id2=None, pipe=None, direct_bond=False,
verbose=True):
- """Set up the magnetic dipole-dipole interaction.
-
- @keyword spin_id1: The spin identifier string of the first spin of
the pair.
- @type spin_id1: str
- @keyword spin_id2: The spin identifier string of the second spin of
the pair.
- @type spin_id2: str
- @param pipe: The data pipe to operate on. Defaults to the
current data pipe.
- @type pipe: str
- @keyword direct_bond: A flag specifying if the two spins are directly
bonded.
- @type direct_bond: bool
- @keyword verbose: A flag which if True will result in printouts of
the created interatomoic data containers.
- @type verbose: bool
- """
-
- # The data pipe.
- if pipe == None:
- pipe = pipes.cdp_name()
-
- # Get the data pipe.
- dp = pipes.get_pipe(pipe)
-
- # Loop over both spin selections.
- ids = []
- for spin1, mol_name1, res_num1, res_name1, id1 in spin_loop(spin_id1,
pipe=pipe, full_info=True, return_id=True):
- for spin2, mol_name2, res_num2, res_name2, id2 in
spin_loop(spin_id2, pipe=pipe, full_info=True, return_id=True):
- # Directly bonded atoms.
- if direct_bond:
- # Different molecules.
- if mol_name1 != mol_name2:
- continue
-
- # From structural info.
- if hasattr(dp, 'structure') and
dp.structure.get_molecule(mol_name1, model=1):
- if not dp.structure.are_bonded(atom_id1=id1,
atom_id2=id2):
- continue
-
- # From the residue info.
- else:
- # No element info.
- if not hasattr(spin1, 'element'):
- raise RelaxError("The spin '%s' does not have the
element type set." % id1)
- if not hasattr(spin2, 'element'):
- raise RelaxError("The spin '%s' does not have the
element type set." % id2)
-
- # Backbone NH and CH pairs.
- pair = False
- if (spin1.element == 'N' and spin2.element == 'H') or
(spin2.element == 'N' and spin1.element == 'H'):
- pair = True
- elif (spin1.element == 'C' and spin2.element == 'H') or
(spin2.element == 'C' and spin1.element == 'H'):
- pair = True
-
- # Same residue, so skip.
- if pair and res_num1 != None and res_num1 != res_num2:
- continue
- elif pair and res_num1 == None and res_name1 !=
res_name2:
- continue
-
- # Get the interatomic data object, if it exists.
- interatom = return_interatom(id1, id2, pipe=pipe)
-
- # Create the container if needed.
- if interatom == None:
- interatom = create_interatom(spin_id1=id1, spin_id2=id2,
pipe=pipe)
-
- # Check that this has not already been set up.
- if interatom.dipole_pair:
- raise RelaxError("The magnetic dipole-dipole interaction
already exists between the spins '%s' and '%s'." % (id1, id2))
-
- # Set a flag indicating that a dipole-dipole interaction is
present.
- interatom.dipole_pair = True
-
- # Store the IDs for the printout.
- ids.append([repr(id1), repr(id2)])
-
- # No matches, so fail!
- if not len(ids):
- # Find the problem.
- count1 = 0
- count2 = 0
- for spin in spin_loop(spin_id1):
- count1 += 1
- for spin in spin_loop(spin_id2):
- count2 += 1
-
- # Report the problem.
- if count1 == 0 and count2 == 0:
- raise RelaxError("Neither spin IDs '%s' and '%s' match any
spins." % (spin_id1, spin_id2))
- elif count1 == 0:
- raise RelaxError("The spin ID '%s' matches no spins." % spin_id1)
- elif count2 == 0:
- raise RelaxError("The spin ID '%s' matches no spins." % spin_id2)
- else:
- raise RelaxError("Unknown error.")
-
- # Print out.
- if verbose:
- print("Magnetic dipole-dipole interactions are now defined for the
following spins:\n")
- write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2"],
data=ids)
-
-
-def read_dist(file=None, dir=None, unit='meter', spin_id1_col=None,
spin_id2_col=None, data_col=None, sep=None):
- """Set up the magnetic dipole-dipole interaction.
-
- @keyword file: The name of the file to open.
- @type file: str
- @keyword dir: The directory containing the file (defaults to
the current directory if None).
- @type dir: str or None
- @keyword unit: The measurement unit. This can be either
'meter' or 'Angstrom'.
- @type unit: str
- @keyword spin_id1_col: The column containing the spin ID strings of the
first spin.
- @type spin_id1_col: int
- @keyword spin_id2_col: The column containing the spin ID strings of the
second spin.
- @type spin_id2_col: int
- @keyword data_col: The column containing the averaged distances in
meters.
- @type data_col: int or None
- @keyword sep: The column separator which, if None, defaults to
whitespace.
- @type sep: str or None
- """
-
- # Check the units.
- if unit not in ['meter', 'Angstrom']:
- raise RelaxError("The measurement unit of '%s' must be one of
'meter' or 'Angstrom'." % unit)
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Extract the data from the file.
- file_data = extract_data(file, dir, sep=sep)
-
- # Loop over the RDC data.
- data = []
- for line in file_data:
- # Invalid columns.
- if spin_id1_col > len(line):
- warn(RelaxWarning("The data %s is invalid, no first spin ID
column can be found." % line))
- continue
- if spin_id2_col > len(line):
- warn(RelaxWarning("The data %s is invalid, no second spin ID
column can be found." % line))
- continue
- if data_col and data_col > len(line):
- warn(RelaxWarning("The data %s is invalid, no data column can be
found." % line))
- continue
-
- # Unpack.
- spin_id1 = line[spin_id1_col-1]
- spin_id2 = line[spin_id2_col-1]
- ave_dist = None
- if data_col:
- ave_dist = line[data_col-1]
-
- # Convert and check the value.
- if ave_dist != None:
- try:
- ave_dist = float(ave_dist)
- except ValueError:
- warn(RelaxWarning("The averaged distance of '%s' from the
line %s is invalid." % (ave_dist, line)))
- continue
-
- # Unit conversion.
- if unit == 'Angstrom':
- ave_dist = ave_dist * 1e-10
-
- # Get the interatomic data container.
- interatom = return_interatom(spin_id1, spin_id2)
-
- # No container found.
- if interatom == None:
- raise RelaxNoInteratomError(spin_id1=spin_id1, spin_id2=spin_id2)
-
- # Store the averaged distance.
- interatom.r = ave_dist
-
- # Store the data for the printout.
- data.append([repr(interatom.spin_id1), repr(interatom.spin_id2),
repr(ave_dist)])
-
- # No data, so fail!
- if not len(data):
- raise RelaxError("No data could be extracted from the file.")
-
- # Print out.
- print("The following averaged distances have been read:\n")
- write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2",
"Ave_distance(meters)"], data=data)
-
-
-def set_dist(spin_id1=None, spin_id2=None, ave_dist=None, unit='meter'):
- """Set up the magnetic dipole-dipole interaction.
-
- @keyword spin_id1: The spin identifier string of the first spin of
the pair.
- @type spin_id1: str
- @keyword spin_id2: The spin identifier string of the second spin of
the pair.
- @type spin_id2: str
- @keyword ave_dist: The r^-3 averaged interatomic distance.
- @type ave_dist: float
- @keyword unit: The measurement unit. This can be either
'meter' or 'Angstrom'.
- @type unit: str
- """
-
- # Check the units.
- if unit not in ['meter', 'Angstrom']:
- raise RelaxError("The measurement unit of '%s' must be one of
'meter' or 'Angstrom'." % unit)
-
- # Unit conversion.
- if unit == 'Angstrom':
- ave_dist = ave_dist * 1e-10
-
- # Generate the selection objects.
- sel_obj1 = Selection(spin_id1)
- sel_obj2 = Selection(spin_id2)
-
- # Loop over the interatomic containers.
- data = []
- for interatom in interatomic_loop():
- # Get the spin info.
- mol_name1, res_num1, res_name1, spin1 =
return_spin(interatom.spin_id1, full_info=True)
- mol_name2, res_num2, res_name2, spin2 =
return_spin(interatom.spin_id2, full_info=True)
-
- # No match, either way.
- if not (sel_obj1.contains_spin(spin_num=spin1.num,
spin_name=spin1.name, res_num=res_num1, res_name=res_name1, mol=mol_name1)
and sel_obj2.contains_spin(spin_num=spin2.num, spin_name=spin2.name,
res_num=res_num2, res_name=res_name2, mol=mol_name2)) and not
(sel_obj2.contains_spin(spin_num=spin1.num, spin_name=spin1.name,
res_num=res_num1, res_name=res_name1, mol=mol_name1) and
sel_obj1.contains_spin(spin_num=spin2.num, spin_name=spin2.name,
res_num=res_num2, res_name=res_name2, mol=mol_name2)):
- continue
-
- # Store the averaged distance.
- interatom.r = ave_dist
-
- # Store the data for the printout.
- data.append([repr(interatom.spin_id1), repr(interatom.spin_id2),
repr(ave_dist)])
-
- # No data, so fail!
- if not len(data):
- raise RelaxError("No data could be set.")
-
- # Print out.
- print("The following averaged distances have been set:\n")
- write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2",
"Ave_distance(meters)"], data=data)
-
-
-def unit_vectors(ave=True):
- """Extract the bond vectors from the loaded structures and store them in
the spin container.
-
- @keyword ave: A flag which if True will cause the average of
all vectors to be calculated.
- @type ave: bool
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if interatomic data exists.
- if not exists_data():
- raise RelaxNoInteratomError
-
- # Print out.
- if ave:
- print("Averaging all vectors.")
- else:
- print("No averaging of the vectors.")
-
- # Loop over the interatomic data containers.
- no_vectors = True
- pos_info = False
- for interatom in interatomic_loop():
- # Get the spin info.
- spin1 = return_spin(interatom.spin_id1)
- spin2 = return_spin(interatom.spin_id2)
-
- # No positional information.
- if not hasattr(spin1, 'pos'):
- continue
- if not hasattr(spin2, 'pos'):
- continue
-
- # Positional information flag.
- pos_info = True
-
- # Both single positions.
- if is_float(spin1.pos[0], raise_error=False) and
is_float(spin2.pos[0], raise_error=False):
- # The vector.
- vector_list = [spin2.pos - spin1.pos]
-
- # A single and multiple position pair.
- elif is_float(spin1.pos[0], raise_error=False) or
is_float(spin2.pos[0], raise_error=False):
- # The first spin has multiple positions.
- if is_float(spin2.pos[0], raise_error=False):
- vector_list = []
- for i in range(len(spin1.pos)):
- vector_list.append(spin2.pos - spin1.pos[i])
-
- # The second spin has multiple positions.
- else:
- vector_list = []
- for i in range(len(spin2.pos)):
- vector_list.append(spin2.pos[i] - spin1.pos)
-
- # Both spins have multiple positions.
- else:
- # Non-matching number of positions.
- if len(spin1.pos) != len(spin2.pos):
- raise RelaxError("The spin '%s' consists of %s positions
whereas the spin '%s' consists of %s - these numbers must match." %
(interatom.spin_id1, len(spin1.pos), interatom.spin_id1, len(spin1.pos)))
-
- # Calculate all vectors.
- vector_list = []
- for i in range(len(spin1.pos)):
- vector_list.append(spin2.pos[i] - spin1.pos[i])
-
- # Unit vectors.
- for i in range(len(vector_list)):
- # Normalisation factor.
- norm_factor = norm(vector_list[i])
-
- # Test for zero length.
- if norm_factor == 0.0:
- warn(RelaxZeroVectorWarning(id))
-
- # Calculate the normalised vector.
- else:
- vector_list[i] = vector_list[i] / norm_factor
-
- # Average.
- if ave:
- ave_vector = zeros(3, float64)
- for i in range(len(vector_list)):
- ave_vector = ave_vector + vector_list[i]
- vector_list = [ave_vector / len(vector_list)]
-
- # Convert to a single vector if needed.
- if len(vector_list) == 1:
- vector_list = vector_list[0]
-
- # Store the unit vector(s).
- setattr(interatom, 'vector', vector_list)
-
- # We have a vector!
- no_vectors = False
-
- # Print out.
- num = 1
- if not is_float(vector_list[0], raise_error=False):
- num = len(vector_list)
- plural = 's'
- if num == 1:
- plural = ''
- if spin1.name:
- spin1_str = spin1.name
- else:
- spin1_str = spin1.num
- if spin2.name:
- spin2_str = spin2.name
- else:
- spin2_str = spin2.num
- print("Calculated %s %s-%s unit vector%s between the spins '%s' and
'%s'." % (num, spin1_str, spin2_str, plural, interatom.spin_id1,
interatom.spin_id2))
-
- # Catch the problem of no positional information being present.
- if not pos_info:
- raise RelaxError("Positional information could not be found for any
spins.")
-
- # Right, catch the problem of missing vectors to prevent massive user
confusion!
- if no_vectors:
- raise RelaxError("No vectors could be extracted.")
r20081 - /trunk/pipe_control/dipole_pair.py