Author: bugman
Date: Wed Oct 7 14:59:07 2009
New Revision: 9631
URL: http://svn.gna.org/viewcvs/relax?rev=9631&view=rev
Log:
Removed all dependence on write_body() and write_header() from the sequence
module.
Modified:
1.3/generic_fns/sequence.py
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=9631&r1=9630&r2=9631&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Wed Oct 7 14:59:07 2009
@@ -134,9 +134,9 @@
def display(sep=None, mol_name_flag=False, res_num_flag=False,
res_name_flag=False, spin_num_flag=False, spin_name_flag=False):
- """Function for displaying the molecule, residue, and/or spin sequence
data.
-
- This calls the write_body() function to do most of the work.
+ """Display the molecule, residue, and/or spin sequence data.
+
+ This calls the write() function to do most of the work.
@keyword sep: The column seperator which, if None,
defaults to whitespace.
@@ -163,7 +163,7 @@
raise RelaxNoSequenceError
# Write the data.
- write_body(file=sys.stdout, sep=sep, mol_name_flag=mol_name_flag,
res_num_flag=res_num_flag, res_name_flag=res_name_flag,
spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
+ write(file=sys.stdout, sep=sep, mol_name_flag=mol_name_flag,
res_num_flag=res_num_flag, res_name_flag=res_name_flag,
spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
def generate(mol_name=None, res_num=None, res_name=None, spin_num=None,
spin_name=None, pipe=None, select=True, verbose=True):
@@ -218,6 +218,7 @@
curr_spin = return_spin(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name),
pipe=pipe)
# A new spin.
+ new_data = False
if not curr_spin:
# Add the spin.
curr_res.spin.add_item(spin_name=spin_name, spin_num=spin_num)
@@ -225,12 +226,15 @@
# Get the spin.
curr_spin = return_spin(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name),
pipe=pipe)
+ # New data.
+ new_data = True
+
# Set the selection flag.
curr_spin.select = select
# Print out of all the spins.
- if verbose:
- write_line(sys.stdout, mol_name, res_num, res_name, spin_num,
spin_name, mol_name_flag=True, res_num_flag=True, res_name_flag=True,
spin_num_flag=True, spin_name_flag=True)
+ if new_data:
+ return mol_name, res_num, res_name, spin_num, spin_name
def read(file=None, dir=None, file_data=None, spin_id_col=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, sep=None, spin_id=None):
@@ -278,13 +282,28 @@
if exists_mol_res_spin_data():
raise RelaxSequenceError
- # Header print out.
- write_header(sys.stdout, mol_name_flag=True, res_num_flag=True,
res_name_flag=True, spin_num_flag=True, spin_name_flag=True)
+ # Init the data.
+ mol_names = []
+ res_nums = []
+ res_names = []
+ spin_nums = []
+ spin_names = []
# Generate the sequence.
for id in read_spin_data(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, sep=sep, spin_id=spin_id):
# Add the spin.
- generate(*spin_id_to_data_list(id))
+ new_spin = generate(*spin_id_to_data_list(id))
+
+ # Append the new spin.
+ if new_spin:
+ mol_names.append(new_spin[0])
+ res_nums.append(new_spin[1])
+ res_names.append(new_spin[2])
+ spin_nums.append(new_spin[3])
+ spin_names.append(new_spin[4])
+
+ # Write the data.
+ write_spin_data(mol_names=mol_names, res_nums=res_nums,
res_names=res_names, spin_nums=spin_nums, spin_names=spin_names)
def validate_sequence(data, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None):
@@ -358,9 +377,9 @@
def write(file, dir=None, sep=None, mol_name_flag=False, res_num_flag=False,
res_name_flag=False, spin_num_flag=False, spin_name_flag=False, force=False):
- """Function for writing molecule, residue, and/or sequence data.
-
- This calls the write_body() function to do most of the work.
+ """Write the molecule, residue, and/or sequence data.
+
+ This calls the relax_io.write_spin_data() function to do most of the
work.
@param file: The name of the file to write the data to.
@@ -391,11 +410,32 @@
if not count_spins():
raise RelaxNoSequenceError
- # Open the file for writing.
- seq_file = open_write_file(file, dir, force)
+ # Init the data.
+ mol_names = []
+ res_nums = []
+ res_names = []
+ spin_nums = []
+ spin_names = []
+
+ # Spin loop.
+ for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
+ mol_names.append(mol_name)
+ res_nums.append(res_num)
+ res_names.append(res_name)
+ spin_nums.append(spin.num)
+ spin_names.append(spin.name)
+
+ # Remove unwanted data.
+ if not mol_name_flag:
+ mol_names = None
+ if not res_num_flag:
+ res_nums = None
+ if not res_name_flag:
+ res_names = None
+ if not spin_num_flag:
+ spin_nums = None
+ if not spin_name_flag:
+ spin_names = None
# Write the data.
- write_body(file=seq_file, sep=sep, mol_name_flag=mol_name_flag,
res_num_flag=res_num_flag, res_name_flag=res_name_flag,
spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
-
- # Close the results file.
- seq_file.close()
+ write_spin_data(file=file, dir=dir, sep=sep, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names)
r9631 - /1.3/generic_fns/sequence.py