From f506105a42e71ad9d44350180969eb36ab2bf818 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 13 Aug 2019 15:12:41 -0500
Subject: [PATCH] Added ability to add custom extra lines to BD file using
extra_bd_file_lines attribute in arbdmodel
---
mrdna/model/arbdmodel.py | 6 +++++-
mrdna/segmentmodel.py | 11 +++++++----
2 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py
index 88d22b5..b374901 100644
--- a/mrdna/model/arbdmodel.py
+++ b/mrdna/model/arbdmodel.py
@@ -628,7 +628,7 @@ 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):
+ 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=""):
PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms)
self.temperature = temperature
@@ -641,6 +641,8 @@ class ArbdModel(PdbModel):
self.decompPeriod = decompPeriod
self.pairlistDistance = pairlistDistance
+ self.extra_bd_file_lines = extra_bd_file_lines
+
self.numParticles = 0
self.particles = []
self.type_counts = None
@@ -857,6 +859,8 @@ pairlistDistance {pairlistDistance}
origin {originX} {originY} {originZ}
systemSize {dimX} {dimY} {dimZ}
+
+{extra_bd_file_lines}
\n""".format(**params))
## Write entries for each type of particle
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 9adcc29..86550d1 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -436,7 +436,7 @@ class Segment(ConnectableElement, Group):
self.sequence = None
def __repr__(self):
- return "<{} {}[{:d}]>".format( type(self), self.name, self.num_nt )
+ return "<{} {}[{:d}]>".format( str(type(self)).split('.')[-1], self.name, self.num_nt )
def set_splines(self, contours, coords):
tck, u = interpolate.splprep( coords.T, u=contours, s=0, k=1)
@@ -1540,15 +1540,18 @@ class SegmentModel(ArbdModel):
dimensions=(5000,5000,5000), temperature=291,
timestep=50e-6, cutoff=50,
decompPeriod=10000, pairlistDistance=None,
- nonbondedResolution=0,DEBUG=0,
- debye_length = None
+ nonbondedResolution=0, DEBUG=0,
+ debye_length = None,
+ extra_bd_file_lines = "",
):
self.DEBUG = DEBUG
if DEBUG > 0: print("Building ARBD Model")
ArbdModel.__init__(self,segments,
dimensions, temperature, timestep, cutoff,
decompPeriod, pairlistDistance=None,
- nonbondedResolution=0)
+ nonbondedResolution = 0,
+ extra_bd_file_lines = extra_bd_file_lines
+ )
# self.max_basepairs_per_bead = max_basepairs_per_bead # dsDNA
--
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