Author: bugman
Date: Thu Nov 30 11:13:59 2006
New Revision: 2899
URL: http://svn.gna.org/viewcvs/relax?rev=2899&view=rev
Log:
Ported r2893 to r2897 from the 1.3 line.
The command used was:
svn merge -r2892:2897 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
This includes a number of bug fixes:
Bug #7755 (https://gna.org/bugs/?7755).
Bug #7890 (https://gna.org/bugs/?7890).
Bug #7891 (https://gna.org/bugs/?7891).
The revisions also include a print out when spin systems are eliminated
through the 'eliminate()'
user function.
Modified:
1.2/generic_fns/monte_carlo.py
1.2/specific_fns/model_free.py
Modified: 1.2/generic_fns/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/monte_carlo.py?rev=2899&r1=2898&r2=2899&view=diff
==============================================================================
--- 1.2/generic_fns/monte_carlo.py (original)
+++ 1.2/generic_fns/monte_carlo.py Thu Nov 30 11:13:59 2006
@@ -22,6 +22,7 @@
from copy import deepcopy
from math import sqrt
+from Numeric import ones
from random import gauss
@@ -306,7 +307,7 @@
self.relax.data.sim_state[self.run] = 1
- def select_all_sims(self, number=None, select_sim=None):
+ def select_all_sims(self, number=None, all_select_sim=None):
"""Function for setting the select flag of all simulations of all
instances to one."""
# Function type.
@@ -320,19 +321,31 @@
num_instances = count_num_instances(self.run)
# Create the selected simulation array with all simulations selected.
- if select_sim == None:
- select_sim = []
- for i in xrange(number):
- select_sim.append(1)
+ if all_select_sim == None:
+ select_sim = ones(number)
# Loop over the instances.
for instance in xrange(num_instances):
+ # Set up the selected simulation array.
+ if all_select_sim != None:
+ select_sim = all_select_sim[instance].tolist()
+
# Set the selected simulation array.
set_selected_sim(self.run, instance, select_sim)
- def setup(self, run=None, number=None, select_sim=None):
- """Function for setting up Monte Carlo simulations."""
+ def setup(self, run=None, number=None, all_select_sim=None):
+ """Function for setting up Monte Carlo simulations.
+
+ @param run: The name of the run.
+ @type run: str
+ @param number: The number of Monte Carlo simulations to set
up.
+ @type number: int
+ @params all_select_sim: The selection status of the Monte Carlo
simulations. The first
+ dimension of this matrix corresponds to the simulation and the
second corresponds to the
+ instance.
+ @type all_select_sim: Numeric matrix (int)
+ """
# Arguments.
self.run = run
@@ -350,10 +363,7 @@
self.relax.data.sim_number = {}
# Add the simulation number.
- if select_sim:
- self.relax.data.sim_number[self.run] = len(select_sim)
- else:
- self.relax.data.sim_number[self.run] = number
+ self.relax.data.sim_number[self.run] = number
# Create the data structure 'sim_state'.
if not hasattr(self.relax.data, 'sim_state'):
@@ -363,4 +373,4 @@
self.relax.data.sim_state[self.run] = 1
# Select all simulations.
- self.select_all_sims(number=number, select_sim=select_sim)
+ self.select_all_sims(number=number, all_select_sim=all_select_sim)
Modified: 1.2/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2899&r1=2898&r2=2899&view=diff
==============================================================================
--- 1.2/specific_fns/model_free.py (original)
+++ 1.2/specific_fns/model_free.py Thu Nov 30 11:13:59 2006
@@ -1420,10 +1420,12 @@
# Local tm.
if name == 'local_tm' and value >= c1:
+ print "The local tm parameter of " + `value` + " is greater than
" + `c1` + ", eliminating spin system " + `self.relax.data.res[run][i].num` +
" " + self.relax.data.res[run][i].name + " of the run " + `run`
return 1
# Internal correlation times.
if match('t[efs]', name) and value >= c2 * tm:
+ print "The " + name + " value of " + `value` + " is greater than
" + `c2 * tm` + ", eliminating spin system " +
`self.relax.data.res[run][i].num` + " " + self.relax.data.res[run][i].name +
" of the run " + `run`
return 1
# Accept model.
@@ -3343,7 +3345,7 @@
nucleus_set = 0
sim_num = None
sims = []
- select_sim = []
+ all_select_sim = []
diff_data_set = 0
diff_error_set = 0
diff_sim_set = None
@@ -3397,11 +3399,14 @@
except:
raise RelaxError, "The simulation number '%s' is
invalid." % sim_num
- # Update the sims array.
- sims.append(sim_num)
+ # A new simulation number.
+ if sim_num not in sims:
+ # Update the sims array and append an empty array to the
selected sims array.
+ sims.append(sim_num)
+ all_select_sim.append([])
# Selected simulations.
- select_sim.append(self.file_line[self.col['select']])
+
all_select_sim[-1].append(int(self.file_line[self.col['select']]))
# Diffusion tensor data.
if self.data_set == 'value' and not diff_data_set:
@@ -3427,7 +3432,7 @@
if self.read_columnar_pdb(print_flag):
pdb = 1
- # XH vector.
+ # XH vector, heteronucleus, and proton.
if self.data_set == 'value':
self.read_columnar_xh_vect()
@@ -3439,7 +3444,14 @@
# Set up the simulations.
if len(sims):
- self.relax.generic.monte_carlo.setup(self.run,
select_sim=select_sim)
+ # Convert the selected simulation array of arrays into a Numeric
matrix and transpose it.
+ all_select_sim = transpose(array(all_select_sim))
+
+ # Set up the Monte Carlo simulations.
+ self.relax.generic.monte_carlo.setup(self.run, number=len(sims),
all_select_sim=all_select_sim)
+
+ # Turn the simulation state to off!
+ self.relax.data.sim_state[self.run] = 0
def read_columnar_sequence(self):
@@ -3470,6 +3482,10 @@
# Set the vector.
self.relax.generic.pdb.set_vector(run=self.run,
res=self.res_index, xh_vect=xh_vect)
+
+ # The heteronucleus and proton names.
+ self.relax.data.res[self.run][self.res_index].heteronuc =
self.file_line[self.col['pdb_heteronuc']]
+ self.relax.data.res[self.run][self.res_index].proton =
self.file_line[self.col['pdb_proton']]
def remove_tm(self, run, res_num):
@@ -4980,7 +4996,7 @@
xh_vect = replace(`data.xh_vect.tolist()`, ' ', '')
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='error', nucleus=nucleus,
model=model, equation=equation, params=params, param_set=self.param_set,
s2=s2, s2f=s2f, s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex,
r=r, csa=csa, diff_type=diff_type, diff_params=diff_params, pdb=pdb,
pdb_model=pdb_model, pdb_heteronuc=pdb_heteronuc, pdb_proton=pdb_proton,
xh_vect=xh_vect, ri_labels=ri_labels, remap_table=remap_table,
frq_labels=frq_labels, frq=frq, ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='error', nucleus=nucleus,
model=model, equation=equation, params=params, param_set=self.param_set,
s2=s2, s2f=s2f, s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex,
r=r, csa=csa, diff_type=diff_type, diff_params=diff_params, pdb=pdb,
pdb_model=pdb_model, pdb_heteronuc=data.heteronuc, pdb_proton=data.proton,
xh_vect=xh_vect, ri_labels=ri_labels, remap_table=remap_table,
frq_labels=frq_labels, frq=frq, ri=ri, ri_error=ri_error)
# Simulation values.
@@ -5169,7 +5185,7 @@
xh_vect = replace(`data.xh_vect.tolist()`, ' ', '')
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, select_sim=select_sim,
data_set='sim_'+`i`, nucleus=nucleus, model=model, equation=equation,
params=params, param_set=self.param_set, s2=s2, s2f=s2f, s2s=s2s,
local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa, chi2=chi2,
i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=pdb_heteronuc, pdb_proton=pdb_proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, select_sim=select_sim,
data_set='sim_'+`i`, nucleus=nucleus, model=model, equation=equation,
params=params, param_set=self.param_set, s2=s2, s2f=s2f, s2s=s2s,
local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa, chi2=chi2,
i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=data.heteronuc, pdb_proton=data.proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
r2899 - in /1.2: generic_fns/monte_carlo.py specific_fns/model_free.py