Author: bugman
Date: Thu Apr 24 00:12:24 2008
New Revision: 5964
URL: http://svn.gna.org/viewcvs/relax?rev=5964&view=rev
Log:
Spun off half of the read() function into the new generate() function.
The new function will be very useful for other parts of relax.
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=5964&r1=5963&r2=5964&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Thu Apr 24 00:12:24 2008
@@ -22,7 +22,7 @@
# relax module imports.
from data import Data as relax_data_store
-from generic_fns.selection import count_spins, exists_mol_res_spin_data,
spin_loop
+from generic_fns.selection import count_spins, exists_mol_res_spin_data,
generate_spin_id, return_molecule, return_residue, return_spin, spin_loop
from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxSequenceError
from relax_io import extract_data, open_write_file, strip
import sys
@@ -60,6 +60,54 @@
# 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)
+
+
+def generate(mol_name=None, res_num=None, res_name=None, spin_num=None,
spin_name=None):
+ """Generate the sequence item-by-item by adding a single
molecule/residue/spin container as necessary.
+
+ @keyword mol_name: The molecule name.
+ @type mol_name: bool
+ @keyword res_num: The residue number.
+ @type res_num: bool
+ @keyword res_name: The residue name.
+ @type res_name: bool
+ @keyword spin_num: The spin number.
+ @type spin_num: bool
+ @keyword spin_name: The spin name.
+ @type spin_name: bool
+ """
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Get the molecule.
+ curr_mol = return_molecule(generate_spin_id(mol_name=mol_name))
+
+ # A new molecule.
+ if not curr_mol:
+ # Add the molecule (and store it in the 'curr_mol' object).
+ cdp.mol.add_item(mol_name=mol_name)
+ curr_mol = cdp.mol[-1]
+
+ # Get the residue.
+ curr_res = return_residue(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name))
+
+ # A new residue.
+ if not curr_res:
+ # Add the residue (and store it in the 'curr_res' object).
+ curr_mol.res.add_item(res_name=res_name, res_num=res_num)
+ curr_res = curr_mol.res[-1]
+
+ # 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))
+
+ # A new spin.
+ if not curr_spin:
+ # Add the spin.
+ curr_res.spin.add_item(spin_name=spin_name, spin_num=spin_num)
+
+ # Print out of all the spins.
+ 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)
def read(file=None, dir=None, mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None):
@@ -122,15 +170,8 @@
if not file_data:
raise RelaxFileEmptyError
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
# Test if the sequence data is valid.
validate_sequence(file_data, 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)
-
- # Init some indecies.
- mol_index = 0
- res_index = 0
# 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)
@@ -154,41 +195,8 @@
if spin_name_col != None:
spin_name = file_data[i][spin_name_col]
- # A new molecule.
- if mol_name_col != None and cdp.mol[mol_index].name != mol_name:
- # Replace the first empty molecule.
- if mol_index == 0 and cdp.mol[0].name == None:
- cdp.mol[0].name = mol_name
-
- # Create a new molecule.
- else:
- # Add the molecule.
- cdp.mol.add_item(mol_name=mol_name)
-
- # Increment the molecule index.
- mol_index = mol_index + 1
-
- # A new residue.
- if res_name_col != None and cdp.mol[mol_index].res[res_index].num !=
res_num:
- # Replace the first empty residue.
- if res_index == 0 and cdp.mol[mol_index].res[0].name == None:
- cdp.mol[mol_index].res[0].name = res_name
- cdp.mol[mol_index].res[0].num = res_num
-
- # Create a new residue.
- else:
- # Add the residue.
- cdp.mol[mol_index].res.add_item(res_name=res_name,
res_num=res_num)
-
- # Increment the residue index.
- res_index = res_index + 1
-
- # A new spin.
- if spin_num_col != None:
-
cdp.mol[mol_index].res[res_index].spin.add_item(spin_name=spin_name,
spin_num=spin_num)
-
- # Print out of all the spins.
- 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)
+ # Generate the sequence.
+ generate(mol_name, res_num, res_name, spin_num, spin_name)
def validate_sequence(data, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None):
r5964 - /1.3/generic_fns/sequence.py