From 47b578f2b307f9cefaece81891a9a32662068838 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 12 Dec 2019 17:22:30 -0600
Subject: [PATCH] Set origin of arbd box using structure in mrdna script
---
bin/mrdna | 6 ++++--
mrdna/model/arbdmodel.py | 12 ++++++++++--
mrdna/segmentmodel.py | 1 +
3 files changed, 15 insertions(+), 4 deletions(-)
diff --git a/bin/mrdna b/bin/mrdna
index 4e603d7..f539741 100755
--- a/bin/mrdna
+++ b/bin/mrdna
@@ -9,6 +9,7 @@ import re
import pathlib
from mrdna import __version__ as __version__
from mrdna.simulate import multiresolution_simulation as simulate
+import numpy as np
"""Easy multiresolution simulations of DNA nanotechnology objects using ARBD"""
@@ -107,8 +108,9 @@ def main():
model = read_model( str(infile), debye_length=args.debye_length, temperature=args.temperature )
if args.dimensions is None:
- model.dimensions = [max(f,2500)
- for f in model.dimensions_from_structure( padding_factor=2.5 )]
+ dim = model.dimensions_from_structure( padding_factor=2.5 )
+ model.dimensions = dim
+ model.origin = model.get_center()-0.5*np.array(model.dimensions)
else:
model.dimensions = args.dimensions
diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py
index 197bddb..dd173d2 100644
--- a/mrdna/model/arbdmodel.py
+++ b/mrdna/model/arbdmodel.py
@@ -628,10 +628,11 @@ class PdbModel(Transformable, Parent):
class ArbdModel(PdbModel):
- def __init__(self, children, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6, cutoff=50, decompPeriod=10000, pairlistDistance=None, nonbondedResolution=0.1, remove_duplicate_bonded_terms=True, extra_bd_file_lines=""):
+ def __init__(self, children, dimensions=(1000,1000,1000), origin=None, temperature=291, timestep=50e-6, cutoff=50, decompPeriod=10000, pairlistDistance=None, nonbondedResolution=0.1, remove_duplicate_bonded_terms=True, extra_bd_file_lines=""):
PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms)
self.temperature = temperature
+ self.origin = origin
self.timestep = timestep
self.cutoff = cutoff
@@ -837,8 +838,15 @@ class ArbdModel(PdbModel):
params['outputPeriod'] = outputPeriod
for k,v in zip('XYZ', self.dimensions):
- params['origin'+k] = -v*0.5
params['dim'+k] = v
+
+ if self.origin is None:
+ for k,v in zip('XYZ', self.dimensions):
+ params['origin'+k] = -v*0.5
+ else:
+ for k,v in zip('XYZ', self.origin):
+ params['origin'+k] = v
+
params['pairlistDistance'] -= params['cutoff']
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 0273c5d..bebf3c7 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -1541,6 +1541,7 @@ class SegmentModel(ArbdModel):
def __init__(self, segments=[], local_twist=True, escapable_twist=True,
max_basepairs_per_bead=7,
max_nucleotides_per_bead=4,
+ origin = None,
dimensions=(5000,5000,5000), temperature=291,
timestep=50e-6, cutoff=50,
decompPeriod=10000, pairlistDistance=None,
--
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