From bad59dec75b9fc8fbb2f4135dd6b1ac14ed1216b Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 6 Sep 2018 18:26:00 -0500
Subject: [PATCH] Modified simulation protocol to try loading files without
'.0' suffix
---
mrdna/simulate.py | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/mrdna/simulate.py b/mrdna/simulate.py
index 8d9cc11..fef95d0 100644
--- a/mrdna/simulate.py
+++ b/mrdna/simulate.py
@@ -46,7 +46,10 @@ def multiresolution_simulation( model, output_name,
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
## TODO Remove long bonds
model.simulate( outputPrefix = output_prefix, numSteps=0.05*coarse_steps, **simargs )
- coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
+ try:
+ coordinates = readArbdCoords('%s.restart' % full_output_prefix)
+ except:
+ coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
output_prefix = "%s-1" % output_name
model._update_segment_positions(coordinates)
model.simulate( outputPrefix = output_prefix, numSteps=0.95*coarse_steps, **simargs )
@@ -54,7 +57,10 @@ def multiresolution_simulation( model, output_name,
output_prefix = "%s-1" % output_name
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
model.simulate( outputPrefix = output_prefix, numSteps=coarse_steps, **simargs )
- coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
+ try:
+ coordinates = readArbdCoords('%s.restart' % full_output_prefix)
+ except:
+ coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
""" Fine simulation """
@@ -66,7 +72,10 @@ def multiresolution_simulation( model, output_name,
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
- coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
+ try:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix, rmsdThreshold=1)
+ except:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
""" Freeze twist """
@@ -76,7 +85,10 @@ def multiresolution_simulation( model, output_name,
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=False )
model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
- coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix )
+ try:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix )
+ except:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix )
""" Atomic simulation """
--
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