From d96268941dbe7d7ca9dea5300ac29572976775e8 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 17 Sep 2018 11:15:58 -0500
Subject: [PATCH] Updated simulate.py to fix ENM name, copy force field
---
bin/enrgmd | 2 +-
mrdna/readers/cadnano_segments.py | 1 +
mrdna/simulate.py | 8 +++++++-
3 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/bin/enrgmd b/bin/enrgmd
index 6360704..84d6489 100755
--- a/bin/enrgmd
+++ b/bin/enrgmd
@@ -64,7 +64,6 @@ http://dx.doi.org/10.1093/nar/gkw155
model._clear_beads()
model._generate_atomic_model(scale=args.backbone_scale)
model.write_atomic_ENM( prefix )
- model.atomic_simulate( output_name = prefix )
try:
shutil.copytree( get_resource_path("charmm36.nbfix"), "charmm36.nbfix" )
except FileExistsError:
@@ -73,6 +72,7 @@ http://dx.doi.org/10.1093/nar/gkw155
os.makedirs('output')
except FileExistsError:
...
+ model.atomic_simulate( output_name = prefix )
except:
raise
diff --git a/mrdna/readers/cadnano_segments.py b/mrdna/readers/cadnano_segments.py
index 708c4cb..849de60 100644
--- a/mrdna/readers/cadnano_segments.py
+++ b/mrdna/readers/cadnano_segments.py
@@ -9,6 +9,7 @@ from ..coords import readArbdCoords, readAvgArbdCoords
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
from ..model.dna_sequence import m13 as m13seq
+
## TODO: separate SegmentModel from ArbdModel so multiple parts can be combined
## TODO: catch circular strands in "get_5prime" cadnano calls
## TODO: handle special motifs
diff --git a/mrdna/simulate.py b/mrdna/simulate.py
index c648fb1..df93fc4 100644
--- a/mrdna/simulate.py
+++ b/mrdna/simulate.py
@@ -1,6 +1,8 @@
import os
import tempfile
from .coords import readArbdCoords, readAvgArbdCoords
+import shutil
+from . import get_resource_path
arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd
namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2"
@@ -97,7 +99,11 @@ def multiresolution_simulation( model, output_name,
model.update_splines(coordinates)
model._clear_beads()
model._generate_atomic_model(scale=backbone_scale)
- model.write_atomic_ENM( output_name )
+ try:
+ shutil.copytree( get_resource_path("charmm36.nbfix"), "charmm36.nbfix" )
+ except FileExistsError:
+ ...
+ model.write_atomic_ENM( output_prefix )
model.atomic_simulate( output_name = output_prefix )
ret = directory
--
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