Author: bugman
Date: Sun Mar 24 21:23:46 2013
New Revision: 19147
URL: http://svn.gna.org/viewcvs/relax?rev=19147&view=rev
Log:
More removals of the now dead parser argument for the structure.read_pdb user
function.
Modified:
trunk/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
trunk/test_suite/system_tests/bmrb.py
trunk/test_suite/system_tests/scripts/interatomic_tests.py
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
trunk/test_suite/system_tests/scripts/model_free/tylers_peptide.py
trunk/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
trunk/test_suite/system_tests/scripts/palmer_omp.py
Modified: trunk/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/n_state_model/conformation_analysis_rdc%2Bpcs.py?rev=19147&r1=19146&r2=19147&view=diff
==============================================================================
--- trunk/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
(original)
+++ trunk/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py Sun
Mar 24 21:23:46 2013
@@ -47,7 +47,7 @@
for file in files:
print(file)
if search('.pdb$', file):
- structure.read_pdb(file=file, parser='internal', set_model_num=num,
set_mol_name='conf')
+ structure.read_pdb(file=file, set_model_num=num, set_mol_name='conf')
num += 1
NUM_STR = num - 1
@@ -109,7 +109,7 @@
# Load all the tag structures.
NUM_TAG = 1000
for i in range(NUM_TAG):
- structure.read_pdb(file='LactoseMCMM4_'+`i+1`,
dir='../../../structures/tag_1000/080704_MCMM4_aligned-forEd1000',
parser='internal', set_model_num=i+1, set_mol_name='tag')
+ structure.read_pdb(file='LactoseMCMM4_'+`i+1`,
dir='../../../structures/tag_1000/080704_MCMM4_aligned-forEd1000',
set_model_num=i+1, set_mol_name='tag')
# Load the lanthanide atoms.
structure.load_spins(spin_id=':4@C1', ave_pos=False)
Modified: trunk/test_suite/system_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/bmrb.py?rev=19147&r1=19146&r2=19147&view=diff
==============================================================================
--- trunk/test_suite/system_tests/bmrb.py (original)
+++ trunk/test_suite/system_tests/bmrb.py Sun Mar 24 21:23:46 2013
@@ -240,7 +240,7 @@
# Load the PDB file.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
- self.interpreter.structure.read_pdb(file='1RTE_H_trunc.pdb',
dir=path, read_mol=None, set_mol_name=None, read_model=None,
set_model_num=None, parser='internal', alt_loc='A')
+ self.interpreter.structure.read_pdb(file='1RTE_H_trunc.pdb',
dir=path, read_mol=None, set_mol_name=None, read_model=None,
set_model_num=None, alt_loc='A')
# Set up the 15N and 1H spins.
self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True)
Modified: trunk/test_suite/system_tests/scripts/interatomic_tests.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/interatomic_tests.py?rev=19147&r1=19146&r2=19147&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/interatomic_tests.py (original)
+++ trunk/test_suite/system_tests/scripts/interatomic_tests.py Sun Mar 24
21:23:46 2013
@@ -16,7 +16,7 @@
# Load the structures.
NUM_STR = 4
for i in range(NUM_STR):
- self._execute_uf(uf_name='structure.read_pdb',
file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, parser='internal',
set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
+ self._execute_uf(uf_name='structure.read_pdb',
file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, set_model_num=i+1,
set_mol_name='lactose_MCMM4_S1')
# Load the sequence information.
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C*',
ave_pos=False)
Modified:
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py?rev=19147&r1=19146&r2=19147&view=diff
==============================================================================
---
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
(original)
+++
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
Sun Mar 24 21:23:46 2013
@@ -44,7 +44,7 @@
data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' +
sep + 'model_free' + sep + 'bug_20213_asn_sidechain' + sep
# Load PDB file
-structure.read_pdb(file='./1U06-H_trunc.pdb', dir=data_path, read_mol=1,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal',
alt_loc='A')
+structure.read_pdb(file='./1U06-H_trunc.pdb', dir=data_path, read_mol=1,
set_mol_name=None, read_model=None, set_model_num=None, alt_loc='A')
# Set up spins and isotopes
structure.load_spins(spin_id=':47@N*', ave_pos=True)
Modified: trunk/test_suite/system_tests/scripts/model_free/tylers_peptide.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/model_free/tylers_peptide.py?rev=19147&r1=19146&r2=19147&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/model_free/tylers_peptide.py
(original)
+++ trunk/test_suite/system_tests/scripts/model_free/tylers_peptide.py Sun
Mar 24 21:23:46 2013
@@ -17,7 +17,7 @@
spin.name(name='N')
model_free.remove_tm(spin_id=None)
sequence.display()
-structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=DATA_PATH+'structures', parser='internal')
+structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=DATA_PATH+'structures')
structure.get_pos("@N")
structure.get_pos("@H")
dipole_pair.unit_vectors()
Modified:
trunk/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py?rev=19147&r1=19146&r2=19147&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
(original)
+++ trunk/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
Sun Mar 24 21:23:46 2013
@@ -24,7 +24,7 @@
# Load the structures.
NUM_STR = 4
for i in range(NUM_STR):
- self._execute_uf(uf_name='structure.read_pdb',
file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, parser='internal',
set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
+ self._execute_uf(uf_name='structure.read_pdb',
file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, set_model_num=i+1,
set_mol_name='lactose_MCMM4_S1')
# Set up the 13C and 1H spins information.
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C*',
ave_pos=False)
@@ -76,7 +76,7 @@
# Load all the tag structures.
NUM_TAG = 10
for i in range(NUM_TAG):
- self._execute_uf(uf_name='structure.read_pdb',
file='tag_MCMM4_'+repr(i+1), dir=str_path, parser='internal',
set_model_num=i+1, set_mol_name='tag')
+ self._execute_uf(uf_name='structure.read_pdb',
file='tag_MCMM4_'+repr(i+1), dir=str_path, set_model_num=i+1,
set_mol_name='tag')
# Load the lanthanide atoms.
self._execute_uf(uf_name='structure.load_spins', spin_id='@C1',
ave_pos=False)
Modified: trunk/test_suite/system_tests/scripts/palmer_omp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/palmer_omp.py?rev=19147&r1=19146&r2=19147&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/palmer_omp.py (original)
+++ trunk/test_suite/system_tests/scripts/palmer_omp.py Sun Mar 24 21:23:46
2013
@@ -33,7 +33,7 @@
sequence.copy('data')
# Read a PDB file.
- structure.read_pdb(file='1F35_N_H_trunc.pdb',
dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures', parser='internal')
+ structure.read_pdb(file='1F35_N_H_trunc.pdb',
dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures')
# Select only 3 spins (residues 9, 10, and 11).
deselect.all()
r19147 - in /trunk: sample_scripts/n_state_model/ test_suite/system_tests/ test_suite/system_tests/scripts/ test_suite/syste...