Author: bugman
Date: Thu Feb 18 14:43:04 2010
New Revision: 10733
URL: http://svn.gna.org/viewcvs/relax?rev=10733&view=rev
Log:
The interpreter is now imported and set up. User function calls are now
passed through this class.
Modified:
1.3/auto_analyses/stereochem_analysis.py
Modified: 1.3/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/stereochem_analysis.py?rev=10733&r1=10732&r2=10733&view=diff
==============================================================================
--- 1.3/auto_analyses/stereochem_analysis.py (original)
+++ 1.3/auto_analyses/stereochem_analysis.py Thu Feb 18 14:43:04 2010
@@ -56,6 +56,7 @@
from generic_fns import pipes
from generic_fns.selection import spin_loop
from physical_constants import dipolar_constant, g1H, g13C
+from prompt.interpreter import Interpreter
from relax_io import mkdir_nofail
@@ -94,6 +95,11 @@
self.lower_lim_rdc=lower_lim_rdc
self.upper_lim_rdc=upper_lim_rdc
+ # Load the interpreter.
+ self.interpreter = Interpreter(show_script=False, quit=False,
raise_relax_error=True)
+ self.interpreter.populate_self()
+ self.interpreter.on(verbose=False)
+
# Create a directory for log files.
if self.log:
mkdir_nofail("logs")
@@ -406,24 +412,24 @@
out_sorted.write("%-20s%20s\n" % ("# Ensemble", "NOE_volation"))
# Create the data pipe.
- pipe.create("noe_viol_%s" % config, "N-state")
+ self.interpreter.pipe.create("noe_viol_%s" % config, "N-state")
# Read the first structure.
- structure.read_pdb("ensembles" + sep + config + "0.pdb",
set_mol_name=config, set_model_num=range(1, self.num_models+1),
parser="internal")
+ self.interpreter.structure.read_pdb("ensembles" + sep + config +
"0.pdb", set_mol_name=config, set_model_num=range(1, self.num_models+1),
parser="internal")
# Load all protons as the sequence.
- structure.load_spins("@H*", ave_pos=False)
+ self.interpreter.structure.load_spins("@H*", ave_pos=False)
# Create the pseudo-atoms.
for i in range(len(self.pseudo)):
- spin.create_pseudo(spin_name=self.pseudo[i][0],
members=self.pseudo[i][1], averaging="linear")
- sequence.display()
+
self.interpreter.spin.create_pseudo(spin_name=self.pseudo[i][0],
members=self.pseudo[i][1], averaging="linear")
+ self.interpreter.sequence.display()
# Read the NOE list.
- noe.read_restraints(file=self.noe_file)
+ self.interpreter.noe.read_restraints(file=self.noe_file)
# Set up the N-state model.
- n_state_model.select_model(model="fixed")
+ self.interpreter.n_state_model.select_model(model="fixed")
# Print out.
print("\n"*2 + "# Set up complete #" + "\n"*10)
@@ -437,16 +443,16 @@
sys.stderr.write(config + repr(ens) + "\n")
# Delete the old structures and rename the molecule.
- structure.delete()
+ self.interpreter.structure.delete()
# Read the ensemble.
- structure.read_pdb("ensembles" + sep + config + repr(ens) +
".pdb", set_mol_name=config, set_model_num=range(1, self.num_models+1),
parser="internal")
+ self.interpreter.structure.read_pdb("ensembles" + sep +
config + repr(ens) + ".pdb", set_mol_name=config, set_model_num=range(1,
self.num_models+1), parser="internal")
# Get the atomic positions.
- structure.get_pos(ave_pos=False)
+ self.interpreter.structure.get_pos(ave_pos=False)
# Calculate the average NOE potential.
- calc()
+ self.interpreter.calc()
# Sum the violations.
cdp.sum_viol = 0.0
@@ -459,7 +465,7 @@
out.write("%-20i%30.15f\n" % (ens, cdp.sum_viol))
# Save the state.
- results.write(file="%s_results_%s" % (config, ens), dir=dir,
force=True)
+ self.interpreter.results.write(file="%s_results_%s" %
(config, ens), dir=dir, force=True)
# Sort the NOE violations.
noe_viol.sort()
@@ -473,7 +479,7 @@
"""Perform the RDC part of the analysis."""
# Redirect STDOUT to a log file.
- if log:
+ if self.log:
sys.stdout = open("logs" + sep + "RDC_%s_analysis.log" %
self.rdc_name, 'w')
# The dipolar constant.
@@ -495,32 +501,32 @@
out_sorted.write("%-20s%20s\n" % ("# Ensemble",
"RDC_Q_factor(pales)"))
# Create the data pipe.
- pipe.create("rdc_analysis_%s" % config, "N-state")
+ self.interpreter.pipe.create("rdc_analysis_%s" % config,
"N-state")
# Read the first structure.
- structure.read_pdb("ensembles_superimposed" + sep + config +
"0.pdb", set_mol_name=config, set_model_num=range(1, self.num_models+1),
parser="internal")
+ self.interpreter.structure.read_pdb("ensembles_superimposed" +
sep + config + "0.pdb", set_mol_name=config, set_model_num=range(1,
self.num_models+1), parser="internal")
# Load all protons as the sequence.
- structure.load_spins("@H*", ave_pos=False)
+ self.interpreter.structure.load_spins("@H*", ave_pos=False)
# Create the pseudo-atoms.
for i in range(len(self.pseudo)):
- spin.create_pseudo(spin_name=self.pseudo[i][0],
members=self.pseudo[i][1], averaging="linear")
- sequence.display()
+
self.interpreter.spin.create_pseudo(spin_name=self.pseudo[i][0],
members=self.pseudo[i][1], averaging="linear")
+ self.interpreter.sequence.display()
# Read the RDC data.
- rdc.read(align_id=self.rdc_file, file=self.rdc_file,
spin_id_col=self.rdc_spin_id_col, mol_name_col=self.rdc_mol_name_col,
res_num_col=self.rdc_res_num_col, res_name_col=self.rdc_res_name_col,
spin_num_col=self.rdc_spin_num_col, spin_name_col=self.rdc_spin_name_col,
data_col=self.rdc_data_col, error_col=self.rdc_error_col)
+ self.interpreter.rdc.read(align_id=self.rdc_file,
file=self.rdc_file, spin_id_col=self.rdc_spin_id_col,
mol_name_col=self.rdc_mol_name_col, res_num_col=self.rdc_res_num_col,
res_name_col=self.rdc_res_name_col, spin_num_col=self.rdc_spin_num_col,
spin_name_col=self.rdc_spin_name_col, data_col=self.rdc_data_col,
error_col=self.rdc_error_col)
# Set the values needed to calculate the dipolar constant.
- value.set(self.bond_length, "bond_length", spin_id="@H*")
- value.set(self.bond_length, "bond_length", spin_id="@Q*")
- value.set("13C", "heteronucleus", spin_id="@H*")
- value.set("13C", "heteronucleus", spin_id="@Q*")
- value.set("1H", "proton", spin_id="@H*")
- value.set("1H", "proton", spin_id="@Q*")
+ self.interpreter.value.set(self.bond_length, "bond_length",
spin_id="@H*")
+ self.interpreter.value.set(self.bond_length, "bond_length",
spin_id="@Q*")
+ self.interpreter.value.set("13C", "heteronucleus", spin_id="@H*")
+ self.interpreter.value.set("13C", "heteronucleus", spin_id="@Q*")
+ self.interpreter.value.set("1H", "proton", spin_id="@H*")
+ self.interpreter.value.set("1H", "proton", spin_id="@Q*")
# Set up the model.
- n_state_model.select_model(model="fixed")
+ self.interpreter.n_state_model.select_model(model="fixed")
# Print out.
print("\n"*2 + "# Set up complete #" + "\n"*10)
@@ -534,17 +540,17 @@
sys.stderr.write(config + repr(ens) + "\n")
# Delete the old structures.
- structure.delete()
+ self.interpreter.structure.delete()
# Read the ensemble.
- structure.read_pdb("ensembles_superimposed" + sep + config +
repr(ens) + ".pdb", set_mol_name=config, set_model_num=range(1,
self.num_models+1), parser="internal")
+ self.interpreter.structure.read_pdb("ensembles_superimposed"
+ sep + config + repr(ens) + ".pdb", set_mol_name=config,
set_model_num=range(1, self.num_models+1), parser="internal")
# Load the CH vectors for the H atoms.
- structure.vectors(spin_id="@H*", attached="*C*", ave=False)
+ self.interpreter.structure.vectors(spin_id="@H*",
attached="*C*", ave=False)
# Minimisation.
#grid_search(inc=4)
- minimise("simplex", constraints=False)
+ self.interpreter.minimise("simplex", constraints=False)
# Store and write out the Q-factors.
q_factors.append([cdp.q_rdc, ens])
@@ -555,7 +561,7 @@
cdp.align_tensor_Hz_5D = d * cdp.align_tensors[0].A_5D
# Save the state.
- results.write(file="%s_results_%s" % (config, ens), dir=dir,
force=True)
+ self.interpreter.results.write(file="%s_results_%s" %
(config, ens), dir=dir, force=True)
# Sort the NOE violations.
q_factors.sort()
@@ -661,9 +667,9 @@
stderr.close()
# Open the superimposed file in relax.
- reset()
- pipe.create('out', 'N-state')
- structure.read_pdb(file_out, parser="internal")
+ self.interpreter.reset()
+ self.interpreter.pipe.create('out', 'N-state')
+ self.interpreter.structure.read_pdb(file_out,
parser="internal")
# Fix the retarded MOLMOL proton naming.
for model in cdp.structure.structural_data:
@@ -677,4 +683,4 @@
mol.atom_name[i] = mol.atom_name[i][1:] +
mol.atom_name[i][0]
# Replace the superimposed file.
- structure.write_pdb(config + repr(ens) + ".pdb",
dir="ensembles_superimposed", force=True)
+ self.interpreter.structure.write_pdb(config + repr(ens) +
".pdb", dir="ensembles_superimposed", force=True)
r10733 - /1.3/auto_analyses/stereochem_analysis.py