Author: bugman
Date: Tue Apr 8 14:39:03 2008
New Revision: 5430
URL: http://svn.gna.org/viewcvs/relax?rev=5430&view=rev
Log:
Merged generic_fns.sequence.load_PDB_sequence() into
generic_fns.structure.main.load_spins().
Modified:
1.3/generic_fns/sequence.py
1.3/generic_fns/structure/main.py
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=5430&r1=5429&r2=5430&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Tue Apr 8 14:39:03 2008
@@ -55,120 +55,6 @@
# Write the data.
write_body(file=sys.stdout, 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)
-
-
-def load_PDB_sequence(spin_id=None):
- """Function for loading the sequence out of a PDB file.
-
- @param spin_id: The molecule, residue, and spin identifier string.
- @type spin_id: str
- """
-
- # Print out.
- print "\nLoading the sequence from the PDB file.\n"
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Reassign the sequence of the first structure.
- if cdp.structure.structures[0].peptide_chains:
- chains = cdp.structure.structures[0].peptide_chains
- molecule = 'protein'
- elif cdp.structure.structures[0].nucleotide_chains:
- chains = cdp.structure.structures[0].nucleotide_chains
- molecule = 'nucleic acid'
- else:
- raise RelaxNoPdbChainError
-
- # Split up the selection string.
- mol_token, res_token, spin_token = tokenise(spin_id)
-
- # Parse the tokens.
- molecules = parse_token(mol_token)
- residues = parse_token(res_token)
- spins = parse_token(spin_token)
-
- # Init some indecies.
- mol_index = 0
- res_index = 0
- spin_index = 0
-
- # Loop over the molecules.
- for chain in chains:
- # The name of the molecule.
- if chain.chain_id:
- mol_name = chain.chain_id
- elif chain.segment_id:
- mol_name = chain.segment_id
- else:
- mol_name = None
-
- # Skip non-matching molecules.
- if mol_token and mol_name not in molecules:
- continue
-
- # Add the molecule if there is a molecule name (otherwise everything
goes into the default first MolecularContainer).
- if 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)
-
- # Loop over the residues.
- for res in chain.residues:
- # The residue name and number.
- if molecule == 'nucleic acid':
- res_name = res.name[-1]
- else:
- res_name = res.name
- res_num = res.number
-
- # Skip non-matching residues.
- if res_token and not (res_name in residues or res_num in
residues):
- continue
-
- # 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)
-
- # Loop over the spins.
- for atom in res.atom_list:
- # The spin name and number.
- spin_name = atom.name
- spin_num = atom.properties['serial_number']
-
- # Skip non-matching spins.
- if spin_token and not (spin_name in spins or spin_num in
spins):
- continue
-
- # Replace the first empty residue.
- if spin_index == 0 and
cdp.mol[mol_index].res[res_index].spin[0].name == None:
- cdp.mol[mol_index].res[res_index].spin[0].name =
spin_name
- cdp.mol[mol_index].res[res_index].spin[0].num = spin_num
-
- # Create a new residue.
- else:
- # Add the residue.
-
cdp.mol[mol_index].res[res_index].spin.add_item(spin_name=spin_name,
spin_num=spin_num)
-
- # Increment the residue index.
- spin_index = spin_index + 1
-
- # Increment the residue index.
- res_index = res_index + 1
-
- # Increment the molecule index.
- mol_index = mol_index + 1
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):
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=5430&r1=5429&r2=5430&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Tue Apr 8 14:39:03 2008
@@ -39,16 +39,119 @@
def load_spins(spin_id=None):
"""Load the spins from the structural object into the relax data store.
- @keyword spin_id: The spin identification string.
- @type spin_id: str
+ @keyword spin_id: The molecule, residue, and spin identifier string.
+ @type spin_id: str
"""
# Test if the current data pipe exists.
if not relax_data_store.current_pipe:
raise RelaxNoPipeError
+ # Print out.
+ print "Generating the spins from the loaded structure.\n"
+
# Alias the current data pipe.
cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Reassign the sequence of the first structure.
+ if cdp.structure.structures[0].peptide_chains:
+ chains = cdp.structure.structures[0].peptide_chains
+ molecule = 'protein'
+ elif cdp.structure.structures[0].nucleotide_chains:
+ chains = cdp.structure.structures[0].nucleotide_chains
+ molecule = 'nucleic acid'
+ else:
+ raise RelaxNoPdbChainError
+
+ # Split up the selection string.
+ mol_token, res_token, spin_token = tokenise(spin_id)
+
+ # Parse the tokens.
+ molecules = parse_token(mol_token)
+ residues = parse_token(res_token)
+ spins = parse_token(spin_token)
+
+ # Init some indecies.
+ mol_index = 0
+ res_index = 0
+ spin_index = 0
+
+ # Loop over the molecules.
+ for chain in chains:
+ # The name of the molecule.
+ if chain.chain_id:
+ mol_name = chain.chain_id
+ elif chain.segment_id:
+ mol_name = chain.segment_id
+ else:
+ mol_name = None
+
+ # Skip non-matching molecules.
+ if mol_token and mol_name not in molecules:
+ continue
+
+ # Add the molecule if there is a molecule name (otherwise everything
goes into the default first MolecularContainer).
+ if 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)
+
+ # Loop over the residues.
+ for res in chain.residues:
+ # The residue name and number.
+ if molecule == 'nucleic acid':
+ res_name = res.name[-1]
+ else:
+ res_name = res.name
+ res_num = res.number
+
+ # Skip non-matching residues.
+ if res_token and not (res_name in residues or res_num in
residues):
+ continue
+
+ # 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)
+
+ # Loop over the spins.
+ for atom in res.atom_list:
+ # The spin name and number.
+ spin_name = atom.name
+ spin_num = atom.properties['serial_number']
+
+ # Skip non-matching spins.
+ if spin_token and not (spin_name in spins or spin_num in
spins):
+ continue
+
+ # Replace the first empty residue.
+ if spin_index == 0 and
cdp.mol[mol_index].res[res_index].spin[0].name == None:
+ cdp.mol[mol_index].res[res_index].spin[0].name =
spin_name
+ cdp.mol[mol_index].res[res_index].spin[0].num = spin_num
+
+ # Create a new residue.
+ else:
+ # Add the residue.
+
cdp.mol[mol_index].res[res_index].spin.add_item(spin_name=spin_name,
spin_num=spin_num)
+
+ # Increment the residue index.
+ spin_index = spin_index + 1
+
+ # Increment the residue index.
+ res_index = res_index + 1
+
+ # Increment the molecule index.
+ mol_index = mol_index + 1
def read_pdb(file=None, dir=None, model=None, parser='scientific',
fail=True, verbosity=1):
r5430 - in /1.3/generic_fns: sequence.py structure/main.py