Author: bugman
Date: Thu Feb 18 16:48:48 2010
New Revision: 10740
URL: http://svn.gna.org/viewcvs/relax?rev=10740&view=rev
Log:
The stereochem_analysis auto-analysis is now placing all generated files into
the desired results dir.
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=10740&r1=10739&r2=10740&view=diff
==============================================================================
--- 1.3/auto_analyses/stereochem_analysis.py (original)
+++ 1.3/auto_analyses/stereochem_analysis.py Thu Feb 18 16:48:48 2010
@@ -112,7 +112,7 @@
# Create a directory for log files.
if self.log:
- mkdir_nofail("logs")
+ mkdir_nofail(self.results_dir + sep + "logs")
def run(self):
@@ -184,8 +184,8 @@
print("Generating NOE violation Grace plots.")
# Open the output files.
- grace_curve = open("NOE_viol_curve.agr", 'w')
- grace_dist = open("NOE_viol_dist.agr", 'w')
+ grace_curve = open(self.results_dir+sep+"NOE_viol_curve.agr",
'w')
+ grace_dist = open(self.results_dir+sep+"NOE_viol_dist.agr", 'w')
# S-curve header.
colours = [4, 2] # Blue and red.
@@ -230,7 +230,7 @@
grace_dist.write("@target G0.S"+repr(i)+"\n@type xy\n")
# Open the results file and read the data.
- file = open("NOE_viol_" + self.configs[i] + "_sorted")
+ file = open(self.results_dir+sep+"NOE_viol_" +
self.configs[i] + "_sorted")
lines = file.readlines()
file.close()
@@ -266,8 +266,8 @@
print("Generating RDC Q-factor Grace plots.")
# Open the Grace output files.
- grace_curve = open("RDC_%s_curve.agr" % self.rdc_name, 'w')
- grace_dist = open("RDC_%s_dist.agr" % self.rdc_name, 'w')
+ grace_curve = open(self.results_dir+sep+"RDC_%s_curve.agr" %
self.rdc_name, 'w')
+ grace_dist = open(self.results_dir+sep+"RDC_%s_dist.agr" %
self.rdc_name, 'w')
# S-curve header.
colours = [4, 2] # Blue and red.
@@ -312,7 +312,7 @@
grace_dist.write("@target G0.S%s\n@type xy\n" % i)
# Open the results file and read the data.
- file = open("Q_factors_" + self.configs[i] + "_sorted")
+ file = open(self.results_dir+sep+"Q_factors_" +
self.configs[i] + "_sorted")
lines = file.readlines()
file.close()
@@ -349,7 +349,7 @@
print("Generating NOE-RDC correlation Grace plots.")
# Open the Grace output files.
- grace_file = open("correlation_plot.agr", 'w')
+ grace_file = open(self.results_dir+sep+"correlation_plot.agr",
'w')
# Grace header.
colours = [4, 2] # Blue and red.
@@ -377,12 +377,12 @@
grace_file.write("@target G0.S%s\n@type xy\n" % i)
# Open the NOE results file and read the data.
- file = open("NOE_viol_" + self.configs[i])
+ file = open(self.results_dir+sep+"NOE_viol_" +
self.configs[i])
noe_lines = file.readlines()
file.close()
# Open the RDC results file and read the data.
- file = open("Q_factors_" + self.configs[i])
+ file = open(self.results_dir+sep+"Q_factors_" +
self.configs[i])
rdc_lines = file.readlines()
file.close()
@@ -404,10 +404,10 @@
# Redirect STDOUT to a log file.
if self.log:
- sys.stdout = open("logs" + sep + "NOE_viol.log", 'w')
+ sys.stdout = open(self.results_dir+sep+"logs" + sep +
"NOE_viol.log", 'w')
# Create a directory for the save files.
- dir = "NOE_results"
+ dir = self.results_dir + sep + "NOE_results"
mkdir_nofail(dir=dir)
# Loop over the configurations.
@@ -416,8 +416,8 @@
print("\n"*10 + "# Set up for config " + config + " #" + "\n")
# Open the results file.
- out = open("NOE_viol_" + config, 'w')
- out_sorted = open("NOE_viol_" + config + "_sorted", 'w')
+ out = open(self.results_dir+sep+"NOE_viol_" + config, 'w')
+ out_sorted = open(self.results_dir+sep+"NOE_viol_" + config +
"_sorted", 'w')
out.write("%-20s%20s\n" % ("# Ensemble", "NOE_volation"))
out_sorted.write("%-20s%20s\n" % ("# Ensemble", "NOE_volation"))
@@ -425,7 +425,7 @@
self.interpreter.pipe.create("noe_viol_%s" % config, "N-state")
# Read the first structure.
- 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")
+ self.interpreter.structure.read_pdb("ensembles" + sep + config +
"0.pdb", dir=self.results_dir, set_mol_name=config, set_model_num=range(1,
self.num_models+1), parser="internal")
# Load all protons as the sequence.
self.interpreter.structure.load_spins("@H*", ave_pos=False)
@@ -456,7 +456,7 @@
self.interpreter.structure.delete()
# Read the ensemble.
- 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")
+ self.interpreter.structure.read_pdb("ensembles" + sep +
config + repr(ens) + ".pdb", dir=self.results_dir, set_mol_name=config,
set_model_num=range(1, self.num_models+1), parser="internal")
# Get the atomic positions.
self.interpreter.structure.get_pos(ave_pos=False)
@@ -490,13 +490,13 @@
# Redirect STDOUT to a log file.
if self.log:
- sys.stdout = open("logs" + sep + "RDC_%s_analysis.log" %
self.rdc_name, 'w')
+ sys.stdout = open(self.results_dir+sep+"logs" + sep +
"RDC_%s_analysis.log" % self.rdc_name, 'w')
# The dipolar constant.
d = 3.0 / (2.0*pi) * dipolar_constant(g13C, g1H, self.bond_length)
# Create a directory for the save files.
- dir = "RDC_%s_results" % self.rdc_name
+ dir = self.results_dir + sep + "RDC_%s_results" % self.rdc_name
mkdir_nofail(dir=dir)
# Loop over the configurations.
@@ -505,8 +505,8 @@
print("\n"*10 + "# Set up for config " + config + " #" + "\n")
# Open the results files.
- out = open("Q_factors_" + config, 'w')
- out_sorted = open("Q_factors_" + config + "_sorted", 'w')
+ out = open(self.results_dir+sep+"Q_factors_" + config, 'w')
+ out_sorted = open(self.results_dir+sep+"Q_factors_" + config +
"_sorted", 'w')
out.write("%-20s%20s%20s\n" % ("# Ensemble",
"RDC_Q_factor(pales)", "RDC_Q_factor(standard)"))
out_sorted.write("%-20s%20s\n" % ("# Ensemble",
"RDC_Q_factor(pales)"))
@@ -514,7 +514,7 @@
self.interpreter.pipe.create("rdc_analysis_%s" % config,
"N-state")
# Read the first structure.
- 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")
+ self.interpreter.structure.read_pdb("ensembles_superimposed" +
sep + config + "0.pdb", dir=self.results_dir, set_mol_name=config,
set_model_num=range(1, self.num_models+1), parser="internal")
# Load all protons as the sequence.
self.interpreter.structure.load_spins("@H*", ave_pos=False)
@@ -553,7 +553,7 @@
self.interpreter.structure.delete()
# Read the ensemble.
- 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")
+ self.interpreter.structure.read_pdb("ensembles_superimposed"
+ sep + config + repr(ens) + ".pdb", dir=self.results_dir,
set_mol_name=config, set_model_num=range(1, self.num_models+1),
parser="internal")
# Load the CH vectors for the H atoms.
self.interpreter.structure.vectors(spin_id="@H*",
attached="*C*", ave=False)
@@ -585,7 +585,7 @@
"""Generate the ensembles by random sampling of the snapshots."""
# Create the directory for the ensembles, if needed.
- mkdir_nofail(dir="ensembles")
+ mkdir_nofail(dir=self.results_dir + sep + "ensembles")
# Loop over the configurations.
for conf_index in range(len(self.configs)):
@@ -603,7 +603,7 @@
file_name = "ensembles" + sep + self.configs[conf_index] +
repr(ens) + ".pdb"
# Open the output file.
- out = open(file_name, 'w')
+ out = open(self.results_dir+sep+file_name, 'w')
# Header.
out.write("REM Structures: " + repr(rand) + "\n")
@@ -628,8 +628,8 @@
# Logging turned on.
if self.log:
- log = open("logs" + sep + "superimpose_molmol.stderr", 'w')
- sys.stdout = open("logs" + sep + "superimpose.log", 'w')
+ log = open(self.results_dir+sep+"logs" + sep +
"superimpose_molmol.stderr", 'w')
+ sys.stdout = open(self.results_dir+sep+"logs" + sep +
"superimpose.log", 'w')
# Loop over S and R.
for config in ["R", "S"]:
@@ -645,7 +645,7 @@
log.write("\n\n\nSuperimposing %s with Molmol, output to
%s.\n" % (file_in, file_out))
# Failure handling (if a failure occurred and this is rerun,
skip all existing files).
- if access(file_out, F_OK):
+ if access(self.results_dir+sep+file_out, F_OK):
continue
# Open the Molmol pipe.
@@ -655,14 +655,14 @@
stdin.write("InitAll yes\n")
# Read the PDB.
- stdin.write("ReadPdb " + file_in + "\n")
+ stdin.write("ReadPdb " + self.results_dir+sep+file_in + "\n")
# Fitting to mean.
stdin.write("Fit to_first 'selected'\n")
stdin.write("Fit to_mean 'selected'\n")
# Write the result.
- stdin.write("WritePdb " + file_out + "\n")
+ stdin.write("WritePdb " + self.results_dir+sep+file_out +
"\n")
# End Molmol.
stdin.close()
@@ -693,4 +693,4 @@
mol.atom_name[i] = mol.atom_name[i][1:] +
mol.atom_name[i][0]
# Replace the superimposed file.
- self.interpreter.structure.write_pdb(config + repr(ens) +
".pdb", dir="ensembles_superimposed", force=True)
+ self.interpreter.structure.write_pdb(config + repr(ens) +
".pdb", dir=self.results_dir+sep+"ensembles_superimposed", force=True)
r10740 - /1.3/auto_analyses/stereochem_analysis.py