Author: bugman
Date: Wed Oct 28 18:59:00 2009
New Revision: 9837
URL: http://svn.gna.org/viewcvs/relax?rev=9837&view=rev
Log:
The polymer type and one letter code sequence are being placed into the BMRB
file.
The new molecule.type() user function has been created for this.
Modified:
branches/bmrb/generic_fns/mol_res_spin.py
branches/bmrb/prompt/molecule.py
Modified: branches/bmrb/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/mol_res_spin.py?rev=9837&r1=9836&r2=9837&view=diff
==============================================================================
--- branches/bmrb/generic_fns/mol_res_spin.py (original)
+++ branches/bmrb/generic_fns/mol_res_spin.py Wed Oct 28 18:59:00 2009
@@ -38,7 +38,7 @@
# Python module imports.
from numpy import array
from re import split
-from string import count, strip
+from string import count, strip, upper
from textwrap import fill
from warnings import warn
@@ -514,28 +514,31 @@
@type version: str
"""
- # Get the molecule names.
- mol_names = get_molecule_names()
-
- # Loop over the names.
- for i in range(len(mol_names)):
+ # Loop over the molecules.
+ for mol in molecule_loop():
# Test that the molecule has a name!
- if not mol_names[i]:
+ if not mol.name:
raise RelaxError("All molecules must be named.")
+ # Test that the molecule has a type!
+ if not hasattr(mol, 'type') or not mol.type:
+ raise RelaxError("The molecule type for the '%s' molecule must
be specified, please use the appropriate molecule user function to set this."
% mol.name)
+
# Get the residue names and numbers.
- res_names = get_residue_names("#" + mol_names[i])
- res_nums = get_residue_nums("#" + mol_names[i])
+ res_names = get_residue_names("#" + mol.name)
+ res_nums = get_residue_nums("#" + mol.name)
+
+ # Get the one letter codes.
+ polymer_seq_code = one_letter_code(res_names)
# Find the molecule type.
- if len(res_nums) < 4:
+ if mol.type in ['organic molecule', 'other']:
mol_type = 'non-polymer'
- warn(RelaxWarning("The molecule '%s' is assumed to be a
non-polymer, i.e. an organic molecule, ligand, metal ion, etc. It should not
be a solvent molecule!"))
else:
mol_type = 'polymer'
# Add the entity.
- star.entity.add(mol_name=mol_names[i], mol_type=mol_type,
res_nums=res_nums, res_names=res_names)
+ star.entity.add(mol_name=mol.name, mol_type=mol_type,
polymer_type=mol.type, polymer_seq_code=polymer_seq_code, res_nums=res_nums,
res_names=res_names)
def copy_molecule(pipe_from=None, mol_from=None, pipe_to=None, mol_to=None):
@@ -1693,6 +1696,61 @@
warn(RelaxWarning("The spin '%s' is already numbered. Set the
force flag to renumber." % id))
else:
spin.num = number
+
+
+def one_letter_code(res_names):
+ """Convert the list of residue names into a string of one letter residue
codes.
+
+ Standard amino acids are converted to the one letter code. Unknown
residues are labelled as 'X'.
+
+
+ @param res_names: A list of residue names.
+ @type res_names: list or str
+ @return: The one letter codes for the residues.
+ @rtype: str
+ """
+
+ # The amino acid translation table.
+ aa_table = [
+ ['Alanine', 'ALA', 'A'],
+ ['Arginine', 'ARG', 'R'],
+ ['Asparagine', 'ASN', 'N'],
+ ['Aspartic acid', 'ASP', 'D'],
+ ['Cysteine', 'CYS', 'C'],
+ ['Glutamic acid', 'GLU', 'E'],
+ ['Glutamine', 'GLN', 'Q'],
+ ['Glycine', 'GLY', 'G'],
+ ['Histidine', 'HIS', 'H'],
+ ['Isoleucine', 'ILE', 'I'],
+ ['Leucine', 'LEU', 'L'],
+ ['Lysine', 'LYS', 'K'],
+ ['Methionine', 'MET', 'M'],
+ ['Phenylalanine', 'PHE', 'F'],
+ ['Proline', 'PRO', 'P'],
+ ['Serine', 'SER', 'S'],
+ ['Threonine', 'THR', 'T'],
+ ['Tryptophan', 'TRP', 'W'],
+ ['Tyrosine', 'TYR', 'Y'],
+ ['Valine', 'VAL', 'V']
+ ]
+
+ # Translate.
+ seq = ''
+ for res in res_names:
+ # Aa match.
+ match = False
+ for i in range(len(aa_table)):
+ if upper(res) == aa_table[i][1]:
+ seq = seq + aa_table[i][2]
+ match = True
+ break
+
+ # No match.
+ if not match:
+ seq = seq + 'X'
+
+ # Return the sequence.
+ return seq
def parse_token(token, verbosity=False):
@@ -2622,3 +2680,46 @@
# Return the three tokens.
return mol_token, res_token, spin_token
+
+
+def type_molecule(mol_id, type=None, force=False):
+ """Set the molecule type.
+
+ @param mol_id: The molecule identification string.
+ @type mol_id: str
+ @param type: The molecule type.
+ @type type: str
+ @keyword force: A flag which if True will cause the molecule type to
be overwritten.
+ @type force: bool
+ """
+
+ # Check.
+ allowed = ['organic molecule',
+ 'DNA/RNA hybrid',
+ 'polydeoxyribonucleotide',
+ 'polypeptide(D)',
+ 'polypeptide(L)',
+ 'polyribonucleotide',
+ 'polysaccharide(D)',
+ 'polysaccharide(L)'
+ 'other'
+ ]
+ if type not in allowed:
+ raise RelaxError("The molecule type '%s' must be one of %s." %
(type, allowed))
+
+ # Disallow residue and spin selections.
+ select_obj = Selection(mol_id)
+ if select_obj.has_residues():
+ raise RelaxResSelectDisallowError
+ if select_obj.has_spins():
+ raise RelaxSpinSelectDisallowError
+
+ # Change the molecule types.
+ for mol in molecule_loop(mol_id):
+ if hasattr(mol, 'type') and not force:
+ warn(RelaxWarning("The molecule '%s' already has its type set.
Set the force flag to change." % mol_id))
+ else:
+ mol.type = type
+
+
+
Modified: branches/bmrb/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/molecule.py?rev=9837&r1=9836&r2=9837&view=diff
==============================================================================
--- branches/bmrb/prompt/molecule.py (original)
+++ branches/bmrb/prompt/molecule.py Wed Oct 28 18:59:00 2009
@@ -30,7 +30,7 @@
# relax module imports.
from base_class import User_fn_class
import check
-from generic_fns.mol_res_spin import copy_molecule, create_molecule,
delete_molecule, display_molecule, id_string_doc, name_molecule
+from generic_fns.mol_res_spin import copy_molecule, create_molecule,
delete_molecule, display_molecule, id_string_doc, name_molecule, type_molecule
class Molecule(User_fn_class):
@@ -230,6 +230,62 @@
name_molecule(mol_id=mol_id, name=name, force=force)
+ def type(self, mol_id=None, type=None, force=False):
+ """Set the molecule type (mainly used for BMRB submission).
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ mol_id: The molecule identification string corresponding to one or
more molecules.
+
+ type: The molecule type.
+
+ force: A flag which if True will cause the molecule to type to be
overwritten.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This function allows the type of the molecule to be specified. It
can be one of:
+
+ 'organic molecule',
+ 'DNA/RNA hybrid',
+ 'polydeoxyribonucleotide',
+ 'polypeptide(D)',
+ 'polypeptide(L)',
+ 'polyribonucleotide',
+ 'polysaccharide(D)',
+ 'polysaccharide(L)',
+ 'other'.
+
+
+
+ Examples
+ ~~~~~~~~
+
+ To set the molecule 'Ap4Aase' to the 'polypeptide(L)' type, type one
of:
+
+ relax> molecule.type('#Ap4Aase', 'polypeptide(L)', True)
+ relax> molecule.type(mol_id='#Ap4Aase', type='polypeptide(L)',
force=True)
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "molecule.type("
+ text = text + "mol_id=" + repr(mol_id)
+ text = text + ", type=" + repr(type)
+ text = text + ", force=" + repr(force) + ")"
+ print(text)
+
+ # The argument checks.
+ check.is_str(mol_id, 'molecule identification string',
can_be_none=True)
+ check.is_str(type, 'molecule type')
+ check.is_bool(force, 'force flag')
+
+ # Execute the functional code.
+ type_molecule(mol_id=mol_id, type=type, force=force)
+
+
# Docstring modification.
#########################
r9837 - in /branches/bmrb: generic_fns/mol_res_spin.py prompt/molecule.py