Author: bugman
Date: Tue Apr 8 15:10:12 2008
New Revision: 5431
URL: http://svn.gna.org/viewcvs/relax?rev=5431&view=rev
Log:
Completion of generic_fns.structure.main.load_spins() and allowed atom
selections in atom_loop().
The generic_fns.structure.main.load_spins() function now uses the structural
data object API method
atom_loop() to generate the molecule, residue, and spin sequence in the relax
data store. The
sequence generation code is mainly from the old load_PDB_sequence() function.
The Scientific Python data object atom_loop() generator method has been
updated to allow for only
selected atoms to be yielded.
Modified:
1.3/generic_fns/sequence.py
1.3/generic_fns/structure/main.py
1.3/generic_fns/structure/scientific.py
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=5431&r1=5430&r2=5431&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Tue Apr 8 15:10:12 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,
parse_token, spin_loop, tokenise
+from generic_fns.selection import count_spins, exists_mol_res_spin_data,
spin_loop
from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxSequenceError
from relax_io import extract_data, open_write_file, strip
import sys
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=5431&r1=5430&r2=5431&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Tue Apr 8 15:10:12 2008
@@ -53,105 +53,40 @@
# 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
+ # Loop over all atoms of the spin_id selection.
+ for mol_name, res_num, res_name, atom_num, atom_name, pos in
cdp.structure.atom_loop(spin_id=spin_id, pos=True):
+ # Get the corresponding molecule container.
+ mol_cont = return_molecule('#' + mol_name)
+
+ # Add the molecule if it doesn't exist.
+ if mol_name and mol_cont == None:
+ # Add the molecule.
+ cdp.mol.add_item(mol_name=mol_name)
+
+ # Get the container.
+ mol_cont = cdp.mol[-1]
+
+ # Get the corresponding residue container (residue name is ignored
because only the number is unique).
+ res_cont = return_residue(':' + `res_num`)
+
+ # Add the residue if it doesn't exist.
+ if res_num and res_name and res_cont == None:
+ # Add the residue.
+ mol_cont.res.add_item(res_name=res_name, res_num=res_num)
+
+ # Get the container.
+ res_cont = mol_cont.res[-1]
+
+ # Get the corresponding spin container (spin name is ignored because
only the number is unique).
+ spin_cont = return_spin(':' + `spin_num`)
+
+ # Add the spin if it doesn't exist.
+ if spin_name and spin_cont == None:
+ # Add the spin.
+ res_cont.spin.add_item(spin_name=spin_name, spin_num=spin_num)
+
+ # Get the container.
+ spin_cont = res_cont.spin[-1]
def read_pdb(file=None, dir=None, model=None, parser='scientific',
fail=True, verbosity=1):
Modified: 1.3/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=5431&r1=5430&r2=5431&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Tue Apr 8 15:10:12 2008
@@ -39,6 +39,7 @@
# relax module imports.
from api_base import Str_object
from data import Data as relax_data_store
+from generic_fns.selection import parse_token, tokenise
from relax_errors import RelaxNoPdbChainError, RelaxNoResError,
RelaxPdbLoadError
from relax_warnings import RelaxNoAtomWarning, RelaxZeroVectorWarning
@@ -63,15 +64,29 @@
array of len 3)
"""
+ # Split up the selection string.
+ mol_token, res_token, atom_token = tokenise(atom_id)
+
+ # Parse the tokens.
+ molecules = parse_token(mol_token)
+ residues = parse_token(res_token)
+ atoms = parse_token(atom_token)
+
# Loop over the loaded structures.
for struct in self.structural_data:
# Protein.
if struct.peptide_chains:
chains = struct.peptide_chains
+ molecule = 'protein'
# RNA/DNA.
elif struct.nucleotide_chains:
chains = struct.nucleotide_chains
+ molecule = 'nucleic acid'
+
+ # We have a problem!
+ else:
+ raise RelaxNoPdbChainError
# Loop over the chains (each of which will be treated as a new
molecule).
for chain in chains:
@@ -83,11 +98,22 @@
else:
mol_name = None
+ # Skip non-matching molecules.
+ if mol_token and mol_name not in molecules:
+ continue
+
# Loop over the residues of the protein in the PDB file.
for res in chain.residues:
# Residue number and name.
+ if molecule == 'nucleic acid':
+ res_name = res.name[-1]
+ else:
+ res_name = res.name
res_num = res.number
- res_name = res.name
+
+ # Skip non-matching residues.
+ if res_token and not (res_name in residues or res_num in
residues):
+ continue
# Loop over the atoms of the residue.
for atom in res:
@@ -95,6 +121,10 @@
atom_num = atom.properties['serial_number']
atom_name = atom.properties['element']
pos = atom.position.array
+
+ # Skip non-matching atoms.
+ if atom_token and not (atom_name in atoms or
atom_num in atoms):
+ continue
# Yield the information.
if pos:
r5431 - in /1.3/generic_fns: sequence.py structure/main.py structure/scientific.py