Author: bugman
Date: Wed Oct 7 14:29:55 2009
New Revision: 9627
URL: http://svn.gna.org/viewcvs/relax?rev=9627&view=rev
Log:
Wrote the relax_io.write_spin_data_file() function.
This writes spin specific data to a file (can be STDOUT). It will replace
the write_header()
and write_body() functions of generic_fns.sequence.
Modified:
1.3/generic_fns/rdc.py
1.3/relax_io.py
Modified: 1.3/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/rdc.py?rev=9627&r1=9626&r2=9627&view=diff
==============================================================================
--- 1.3/generic_fns/rdc.py (original)
+++ 1.3/generic_fns/rdc.py Wed Oct 7 14:29:55 2009
@@ -30,7 +30,7 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
from generic_fns import pipes
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSpinError,
RelaxRDCError
-from relax_io import read_spin_data_file
+from relax_io import read_spin_data_file, write_spin_data_file
def add_data_to_spin(spin=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, values=None, errors=None, sim=False):
@@ -422,7 +422,9 @@
#####################
# Loop over the RDC data.
- print(("\n%-50s %-15s %-15s" % ("spin_id", "value", "error")))
+ spin_ids = []
+ values = []
+ errors = []
for data in read_spin_data_file(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col, sep=sep,
spin_id=spin_id):
# Unpack.
if data_col and error_col:
@@ -461,8 +463,13 @@
# Append the error.
spin.rdc_err.append(error)
- # Print out.
- print(("%-50s %15s %15s" % (id, value, error)))
+ # Append the data for print out.
+ spin_ids.append(id)
+ values.append(value)
+ errors.append(error)
+
+ # Print out.
+ write_spin_data_file(spin_ids=spin_ids, data=values, data_name='RDCs',
error=errors, error_name='RDC_error')
# Global (non-spin specific) data.
Modified: 1.3/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_io.py?rev=9627&r1=9626&r2=9627&view=diff
==============================================================================
--- 1.3/relax_io.py (original)
+++ 1.3/relax_io.py Wed Oct 7 14:29:55 2009
@@ -473,8 +473,6 @@
molecule name, residue name and number, and/or spin name and number.
- @keyword id: The alignment tensor ID string.
- @type id: str
@keyword file: The name of the file to open.
@type file: str
@keyword dir: The directory containing the file (defaults to
the current directory
@@ -509,7 +507,8 @@
@type error_col: int or None
@keyword sep: The column separator which, if None, defaults to
whitespace.
@type sep: str or None
- @keyword spin_id: The spin ID string.
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all
+ spins.
@type spin_id: None or str
@return: A list of the spin specific data is yielded.
The format is a list
consisting of the spin ID string, the data value
(if data_col is give),
@@ -665,6 +664,249 @@
raise RelaxNoInPathError(binary)
+def write_spin_data_file(file=sys.stdout, dir=None, sep=None, spin_ids=None,
mol_names=None, res_nums=None, res_names=None, spin_nums=None,
spin_names=None, force=False, data=None, data_name=None, data_length=20,
data_format=None, error=None, error_name=None, error_length=20,
error_format=None):
+ """Generator function for reading the spin specific data from file.
+
+ Description
+ ===========
+
+ This function writes a columnar formatted file where each line
corresponds to a spin system.
+ Spin identification is either through a spin ID string or through
columns containing the
+ molecule name, residue name and number, and/or spin name and number.
+
+
+ @keyword file: The name of the file to write the data to (or
alternatively an already opened file object).
+ @type file: str or file object
+ @keyword dir: The directory to place the file into (defaults
to the current directory if None and the file argument is not a file object).
+ @type dir: str or None
+ @keyword sep: The column separator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ @keyword spin_ids: The list of spin ID strings.
+ @type spin_ids: None or list of str
+ @keyword mol_names: The list of molecule names.
+ @type mol_names: None or list of str
+ @keyword res_nums: The list of residue numbers.
+ @type res_nums: None or list of int
+ @keyword res_names: The list of residue names.
+ @type res_names: None or list of str
+ @keyword spin_nums: The list of spin numbers.
+ @type spin_nums: None or list of int
+ @keyword spin_names: The list of spin names.
+ @type spin_names: None or list of str
+ @keyword force: A flag which if True will cause an existing file
to be overwritten.
+ @type force: bool
+ @keyword data: A list of the data to write out. The first
dimension corresponds to the spins. A second dimension can also be given if
multiple data sets across multiple columns are desired.
+ @type data: list or list of lists
+ @keyword data_name: A name corresponding to the data argument. If
the data argument is a list of lists, then this must also be a list with the
same length as the second dimension of the data arg.
+ @type data_name: str or list of str
+ @keyword data_length: The length of the data columns.
+ @type data_length: int
+ @keyword data_format: The optional python formatting string for the
data columns, e.g. "%-30s".
+ @type data_format: None or str
+ @keyword error: A list of the errors to write out. The first
dimension corresponds to the spins. A second dimension can also be given if
multiple data sets across multiple columns are desired. These will be
inter-dispersed between the data columns, if the data is given. If the data
arg is not None, then this must have the same dimensions as that object.
+ @type error: list or list of lists
+ @keyword error_name: A name corresponding to the error argument. If
the error argument is a list of lists, then this must also be a list with the
same length at the second dimension of the error arg.
+ @type error_name: str or list of str
+ @keyword error_length: The length of the error columns.
+ @type error_length: int
+ @keyword error_format: The optional python formatting string for the
error columns, e.g. "%-30s".
+ @type error_format: None or str
+ """
+
+ # Data argument tests.
+ if data:
+ # Data is a list of lists.
+ if isinstance(data[0], list):
+ # Data and data_name don't match.
+ if not isinstance(data_name, list):
+ raise RelaxError("The data_name arg '%s' must be a list as
the data argument is a list of lists." % data_name)
+
+ # Error doesn't match.
+ if error and (len(data) != len(error) or len(data[0]) !=
len(error[0])):
+ raise RelaxError("The data arg:\n%s\n\ndoes not have the
same dimensions as the error arg:\n%s." % (data, error))
+
+ # Data is a simple list.
+ else:
+ # Data and data_name don't match.
+ if not isinstance(data_name, str):
+ raise RelaxError("The data_name arg '%s' must be a string as
the data argument is a simple list." % data_name)
+
+ # Error doesn't match.
+ if error and len(data) != len(error):
+ raise RelaxError("The data arg:\n%s\n\ndoes not have the
same dimensions as the error arg:\n%s." % (data, error))
+
+ # Error argument tests.
+ if error:
+ # Error is a list of lists.
+ if isinstance(error[0], list):
+ # Error and error_name don't match.
+ if not isinstance(error_name, list):
+ raise RelaxError("The error_name arg '%s' must be a list as
the error argument is a list of lists." % error_name)
+
+ # Error is a simple list.
+ else:
+ # Error and error_name don't match.
+ if not isinstance(error_name, str):
+ raise RelaxError("The error_name arg '%s' must be a string
as the error argument is a simple list." % error_name)
+
+ # Number of spins check.
+ args = [spin_ids, mol_names, res_nums, res_names, spin_nums, spin_names]
+ arg_names = ['spin_ids', 'mol_names', 'res_nums', 'res_names',
'spin_nums', 'spin_names']
+ N = None
+ first_arg = None
+ first_arg_name = None
+ for i in range(len(args)):
+ if isinstance(args[i], list):
+ # First list match.
+ if N == None:
+ N = len(args[i])
+ first_arg = args[i]
+ first_arg_name = arg_names[i]
+
+ # Length check.
+ if len(args[i]) != N:
+ raise RelaxError("The %s and %s arguments do not have the
same number of spins ('%s' vs. '%s' respectively)." % (first_arg_name,
arg_names[i], len(first_arg), len(args[i])))
+
+ # Nothing?!?
+ if N == None:
+ raise RelaxError("No spin ID data is present.")
+
+ # Data and error length check.
+ if data and len(data) != N:
+ raise RelaxError("The %s and data arguments do not have the same
number of spins ('%s' vs. '%s' respectively)." % (first_arg_name,
len(first_arg), len(data)))
+ if error and len(error) != N:
+ raise RelaxError("The %s and error arguments do not have the same
number of spins ('%s' vs. '%s' respectively)." % (first_arg_name,
len(first_arg), len(error)))
+
+ # No special separator character.
+ if sep == None:
+ sep = ''
+
+ # Open the file.
+ file = open_write_file(file_name=file, dir=dir)
+
+ # The column lengths.
+ len_spin_id = 10
+ len_mol_name = 10
+ len_res_num = 10
+ len_res_name = 10
+ len_spin_num = 10
+ len_spin_name = 10
+ len_args = [len_spin_id, len_mol_name, len_res_num, len_res_name,
len_spin_num, len_spin_name]
+
+ # Data and error formatting strings.
+ data_head_format = "%%-%ss" % data_length
+ if not data_format:
+ data_format = "%%%ss" % data_length
+ error_head_format = "%%-%ss" % error_length
+ if not error_format:
+ error_format = "%%%ss" % error_length
+
+ # The spin arguments.
+ args = [spin_ids, mol_names, res_nums, res_names, spin_nums, spin_names]
+ arg_names = ['spin_id', 'mol_name', 'res_num', 'res_name', 'spin_num',
'spin_name']
+
+
+ # Header.
+ #########
+
+ # Init.
+ file.write("\n")
+ prefix = '# '
+
+ # The spin ID info.
+ for i in range(len(args)):
+ if args[i]:
+ file.write(("%s%%-%ss%s" % (prefix, len_args[i], sep)) %
arg_names[i])
+ prefix = ' '
+
+ # The data.
+ if data:
+ # List of lists.
+ if isinstance(data[0], list):
+ # Loop over the list.
+ for i in range(len(data[0])):
+ # The data.
+ file.write((prefix+data_head_format+sep) % data_name[i])
+
+ # The error.
+ if error:
+ file.write((prefix+error_head_format+sep) %
error_name[i])
+
+ # Simple list.
+ else:
+ # The data.
+ file.write((prefix+data_head_format+sep) % data_name)
+
+ # The error.
+ if error:
+ file.write((prefix+error_head_format+sep) % error_name)
+
+ # Only errors.
+ elif error:
+ # List of lists.
+ if isinstance(error[0], list):
+ for i in range(len(error[0])):
+ file.write((prefix+error_head_format+sep) % error_name[i])
+
+ # Simple list.
+ else:
+ file.write((prefix+error_head_format+sep) % error_name)
+
+ # Terminate the line.
+ file.write("\n")
+
+
+ # Spin specific data.
+ #####################
+
+ # Loop over the spins.
+ for spin_index in range(N):
+ # The prefix.
+ prefix = ''
+
+ # The spin ID info.
+ for i in range(len(args)):
+ if args[i]:
+ file.write(("%s%%-%ss%s" % (prefix, len_args[i], sep)) %
args[i][spin_index])
+ prefix = ' '
+
+ # The data.
+ if data:
+ # List of lists.
+ if isinstance(data[0], list):
+ # Loop over the list.
+ for i in range(len(data[0])):
+ # The data.
+ file.write((prefix+data_format+sep) %
data[spin_index][i])
+
+ # The error.
+ if error:
+ file.write((prefix+error_format+sep) %
error[spin_index][i])
+
+ # Simple list.
+ else:
+ # The data.
+ file.write((prefix+data_format+sep) % data[spin_index])
+
+ # The error.
+ if error:
+ file.write((prefix+error_format+sep) % error[spin_index])
+
+ # Only errors.
+ elif error:
+ # List of lists.
+ if isinstance(error[0], list):
+ for i in range(len(error[0])):
+ file.write((prefix+error_format+sep) %
error[spin_index][i])
+
+ # Simple list.
+ else:
+ file.write((prefix+error_format+sep) % error[spin_index])
+
+ # End of the line.
+ file.write("\n")
+
+
class DummyFileObject:
def __init__(self):
r9627 - in /1.3: generic_fns/rdc.py relax_io.py