Author: bugman
Date: Mon Feb 4 18:06:15 2008
New Revision: 4910
URL: http://svn.gna.org/viewcvs/relax?rev=4910&view=rev
Log:
Huge redesign of the load_PDB_sequence() function (and converted it to the
new relax design).
This new function should give much more flexibility and abstraction in the
mapping from the
molecular structure to the relax mol-res-spin data structure.
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=4910&r1=4909&r2=4910&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Mon Feb 4 18:06:15 2008
@@ -22,9 +22,9 @@
# relax module imports.
from data import Data as relax_data_store
+from generic_fns.selection import count_spins, parse_token, spin_loop,
tokenise
from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxSequenceError
from relax_io import extract_data, open_write_file, strip
-from generic_fns.selection import count_spins, spin_loop
import sys
@@ -57,44 +57,118 @@
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():
+def load_PDB_sequence(spin_id=None):
"""Function for loading the sequence out of a PDB file.
- This needs to be modified to handle multiple peptide chains.
+ @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 relax_data_store.pdb[run].structures[0].peptide_chains:
- res =
relax_data_store.pdb[run].structures[0].peptide_chains[0].residues
+ if cdp.structure.structures[0].peptide_chains:
+ chains = cdp.structure.structures[0].peptide_chains
molecule = 'protein'
- elif relax_data_store.pdb[run].structures[0].nucleotide_chains:
- res =
relax_data_store.pdb[run].structures[0].nucleotide_chains[0].residues
+ elif cdp.structure.structures[0].nucleotide_chains:
+ chains = cdp.structure.structures[0].nucleotide_chains
molecule = 'nucleic acid'
else:
raise RelaxNoPdbChainError
- # Add the run to 'relax_data_store.res'.
- relax_data_store.res.add_list(run)
-
- # Loop over the sequence.
- for i in xrange(len(res)):
- # Append a data container.
- relax_data_store.res[run].add_item()
-
- # Residue number.
- relax_data_store.res[run][i].num = res[i].number
-
- # Residue name.
- if molecule == 'nucleic acid':
- relax_data_store.res[run][i].name = res[i].name[-1]
+ # 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:
- relax_data_store.res[run][i].name = res[i].name
-
- # Select the residue.
- relax_data_store.res[run][i].select = 1
+ 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 = chain.name
+
+ # Create a new molecule.
+ else:
+ # Add the molecule.
+ cdp.mol.add_item(mol_name=chain.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):
r4910 - /1.3/generic_fns/sequence.py