Author: bugman
Date: Thu Dec 11 11:15:46 2008
New Revision: 8190
URL: http://svn.gna.org/viewcvs/relax?rev=8190&view=rev
Log:
Merged revisions 8186-8189 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8186 | bugman | 2008-12-10 18:46:37 +0100 (Wed, 10 Dec 2008) | 3 lines
Added tests of structure.load_spins() to all the structure system tests.
........
r8187 | bugman | 2008-12-11 10:33:32 +0100 (Thu, 11 Dec 2008) | 10 lines
Partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).
The problem fixed here is that of the missing molecule container. This was
caused by the weirdness
of the Scientific python PDB reader splitting one modified lactose molecule
into 2 molecules. The
lactose part was unnamed, while the modifier was named after the residues
'UNK'. The
generic_fns.mol_res_spin.return_molecule() function was having problems
with this concept of the
first molecule unnamed and the second named. This is now fixed and the
unnamed molecule can be
retrieved.
........
r8188 | bugman | 2008-12-11 10:53:22 +0100 (Thu, 11 Dec 2008) | 8 lines
Another partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).
This problem was trigged by the internal reader (where the problem lies)
together with the
gromacs_phthalic_acid.pdb file. The issue was that the
__fill_object_from_pdb() was operating on
all structures currently loaded into relax. Hence with the 2 models of
this PDB file, the first
molecule had all the atoms of the first and second PDB models combined.
........
r8189 | bugman | 2008-12-11 11:14:00 +0100 (Thu, 11 Dec 2008) | 9 lines
Final fixes for bug #12735 (https://gna.org/bugs/index.php?12735).
The last problem was again triggered by the Scientific python PDB reader
weirdness. Residues ending
in '+' were being treated by the PDB reader as a different molecule. But
then the molecule names
LYS+, ARG+, etc. were causing problems as '+' was being treated as regular
expression when matching
molecule names. Therefore the '+' character has been stripped from all
molecule, residue, and atom
names.
........
Modified:
branches/ave_noe/ (props changed)
branches/ave_noe/generic_fns/mol_res_spin.py
branches/ave_noe/generic_fns/structure/internal.py
branches/ave_noe/generic_fns/structure/main.py
branches/ave_noe/test_suite/system_tests/structure.py
Propchange: branches/ave_noe/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Dec 11 11:15:46 2008
@@ -1,1 +1,1 @@
-/1.3:1-8184
+/1.3:1-8189
Modified: branches/ave_noe/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/mol_res_spin.py?rev=8190&r1=8189&r2=8190&view=diff
==============================================================================
--- branches/ave_noe/generic_fns/mol_res_spin.py (original)
+++ branches/ave_noe/generic_fns/mol_res_spin.py Thu Dec 11 11:15:46 2008
@@ -1601,6 +1601,10 @@
for mol in dp.mol:
# Skip the molecule if there is no match to the selection.
if mol not in select_obj:
+ continue
+
+ # Skip named molecules if the selection is None.
+ if selection == None and mol.name != None:
continue
# Store the molecule container.
Modified: branches/ave_noe/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/structure/internal.py?rev=8190&r1=8189&r2=8190&view=diff
==============================================================================
--- branches/ave_noe/generic_fns/structure/internal.py (original)
+++ branches/ave_noe/generic_fns/structure/internal.py Thu Dec 11 11:15:46
2008
@@ -904,6 +904,7 @@
print "Loading all structures from the PDB file."
# Loop over all models in the PDB file.
+ i = 0
for model_num, records in self.__parse_models(file_path):
# Only load the desired model.
if model != None and model != model_num:
@@ -917,7 +918,10 @@
self.add_struct(name=name, model=model_num, file=file,
path=path, str=Structure_container(), struct_index=struct_index)
# Fill the structural data object.
- self.__fill_object_from_pdb(records, struct_index=struct_index)
+ self.__fill_object_from_pdb(records, struct_index=i)
+
+ # Increment the structure index.
+ i = i + 1
# Loading worked.
return True
Modified: branches/ave_noe/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/structure/main.py?rev=8190&r1=8189&r2=8190&view=diff
==============================================================================
--- branches/ave_noe/generic_fns/structure/main.py (original)
+++ branches/ave_noe/generic_fns/structure/main.py Thu Dec 11 11:15:46 2008
@@ -25,6 +25,7 @@
from numpy import dot, float64, ndarray, zeros
from os import F_OK, access
from re import search
+from string import replace
import sys
from warnings import warn
@@ -70,6 +71,15 @@
# Loop over all atoms of the spin_id selection.
for mol_name, res_num, res_name, atom_num, atom_name, element, pos in
cdp.structure.atom_loop(atom_id=spin_id, str_id=str_id, mol_name_flag=True,
res_num_flag=True, res_name_flag=True, atom_num_flag=True,
atom_name_flag=True, element_flag=True, pos_flag=True, ave=ave_pos):
+
+ # Remove the '+' regular expression character from the mol, res, and
spin names!
+ if mol_name and search('\+', mol_name):
+ mol_name = replace(mol_name, '+', '')
+ if res_name and search('\+', res_name):
+ res_name = replace(res_name, '+', '')
+ if atom_name and search('\+', atom_name):
+ atom_name = replace(atom_name, '+', '')
+
# Initialise the identification string.
id = ''
@@ -81,9 +91,9 @@
# The container.
mol_cont = return_molecule(id)
- # The is only one molecule and it is unnamed.
- elif cdp.mol[0].name == None and len(cdp.mol) == 1:
- mol_cont = cdp.mol[0]
+ # Get the unnamed molecule, assuming there is only one.
+ else:
+ mol_cont = return_molecule()
# Add the molecule if it doesn't exist.
if mol_cont == None:
Modified: branches/ave_noe/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/test_suite/system_tests/structure.py?rev=8190&r1=8189&r2=8190&view=diff
==============================================================================
--- branches/ave_noe/test_suite/system_tests/structure.py (original)
+++ branches/ave_noe/test_suite/system_tests/structure.py Thu Dec 11 11:15:46
2008
@@ -139,6 +139,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='1F35_N_H_molmol.pdb',
dir=path, parser='internal')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_internal2(self):
"""Load the 'Ap4Aase_res1-12.pdb' PDB file (using the internal
structural object PDB reader)."""
@@ -149,6 +155,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=path, parser='internal')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_internal3(self):
"""Load the 'gromacs_phthalic_acid.pdb' PDB file (using the internal
structural object PDB reader)."""
@@ -159,6 +171,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='internal')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_internal4(self):
"""Load the 'tylers_peptide_trunc.pdb' PDB file (using the internal
structural object PDB reader)."""
@@ -169,6 +187,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=path, parser='internal')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_internal5(self):
"""Load the 'lactose_MCMM4_S1_1.pdb' PDB file (using the internal
structural object PDB reader)."""
@@ -179,6 +203,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, parser='internal')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_scientific1(self):
"""Load the '1F35_N_H_molmol.pdb' PDB file (using the Scientific
python structural object PDB reader)."""
@@ -189,6 +219,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='1F35_N_H_molmol.pdb',
dir=path, parser='scientific')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_scientific2(self):
"""Load the 'Ap4Aase_res1-12.pdb' PDB file (using the Scientific
python structural object PDB reader)."""
@@ -199,6 +235,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=path, parser='scientific')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_scientific3(self):
"""Load the 'gromacs_phthalic_acid.pdb' PDB file (using the
Scientific python structural object PDB reader)."""
@@ -209,6 +251,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='scientific')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_scientific4(self):
"""Load the 'tylers_peptide_trunc.pdb' PDB file (using the
Scientific python structural object PDB reader)."""
@@ -219,6 +267,12 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=path, parser='scientific')
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
def test_read_pdb_scientific5(self):
"""Load the 'lactose_MCMM4_S1_1.pdb' PDB file (using the Scientific
python structural object PDB reader)."""
@@ -229,5 +283,8 @@
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, parser='scientific')
-
-
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
r8190 - in /branches/ave_noe: ./ generic_fns/ generic_fns/structure/ test_suite/system_tests/