Commit f584d0d1 authored by cmaffeo2's avatar cmaffeo2
Browse files

Small updates to run script, flushing output of beadmodel

parent f864b0cf
......@@ -326,6 +326,7 @@ class beadModel():
for line in process.stdout:
# for line in iter(process.stdout.readline, b''):
sys.stdout.write(line)
sys.stdout.flush()
# sys.stdout.write(line.decode(sys.stdout.encoding))
# -------------------------- #
......
......@@ -395,7 +395,8 @@ class beadModelTwist():
for line in process.stdout:
# for line in iter(process.stdout.readline, b''):
sys.stdout.write(line)
# sys.stdout.write(line.decode(sys.stdout.encoding))
sys.stdout.flush()
# sys.stdout.write(line.decode(sys.stdout.encoding))
# -------------------------- #
# Methods for building model #
......
......@@ -168,7 +168,7 @@ def simulateDesign(inFile, outPrefix, numCoarsestSteps=5000000, gpu=0, shiftEule
# ------------------------------- #
stepId = [i for i in range(5)]
numSteps = [int(0.2*numCoarsestSteps), int(0.8*numCoarsestSteps)]
numSteps = [int(0.05*numCoarsestSteps), int(0.95*numCoarsestSteps)]
timestep = [200e-6, 200e-6]
lastModel = None
......@@ -192,13 +192,13 @@ def simulateDesign(inFile, outPrefix, numCoarsestSteps=5000000, gpu=0, shiftEule
if i == 1:
coords = readArbdCoords( "output/%s.0.restart" % lastOut )
else:
coords = readAvgArbdCoords("%s.psf" % out, "%s.ideal.pdb" % lastOut,
coords = readAvgArbdCoords("%s.psf" % lastOut, "%s.ideal.pdb" % lastOut,
"output/%s.0.dcd" % lastOut )
model.backmap( lastModel, coords,
dsDnaHelixNeighborDist=100, dsDnaAllNeighborDist=50,
ssDnaHelixNeighborDist=50)
if i > 0: model.simulate(out, **args)
model.simulate(out, **args)
lastModel = model
coords = readAvgArbdCoords(
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment