Commit d9626894 authored by cmaffeo2's avatar cmaffeo2
Browse files

Updated simulate.py to fix ENM name, copy force field

parent b7c3f69d
......@@ -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
......
......@@ -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
......
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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