From a82c07bc000b9affec65b19435ba3a63c9d66ed2 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Sat, 22 Sep 2018 13:22:40 -0500
Subject: [PATCH] Reinstated fixed atoms for atomic simulations
---
mrdna/model/arbdmodel.py | 18 +++++++++++-------
mrdna/readers/segmentmodel_from_lists.py | 12 ------------
mrdna/readers/segmentmodel_from_pdb.py | 2 ++
mrdna/segmentmodel.py | 2 +-
4 files changed, 14 insertions(+), 20 deletions(-)
diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py
index 17afaf7..cb85a16 100644
--- a/mrdna/model/arbdmodel.py
+++ b/mrdna/model/arbdmodel.py
@@ -481,7 +481,7 @@ class PdbModel(Transformable, Parent):
def _updateParticleOrder(self):
pass
- def writePdb(self, filename):
+ def writePdb(self, filename, beta_from_fixed=False):
if self.cacheInvalid:
self._updateParticleOrder()
with open(filename,'w') as fh:
@@ -501,6 +501,9 @@ class PdbModel(Transformable, Parent):
idx = "{:>6d}".format(idx)
data['idx'] = idx
+ if beta_from_fixed:
+ data['beta'] = 1 if 'fixed' in p.__dict__ else 0
+
pos = p.collapsedPosition()
dig = [max(int(np.log10(np.abs(x)+1e-6)//1),0)+1 for x in pos]
for d in dig: assert( d <= 7 )
@@ -1105,12 +1108,12 @@ cellBasisVector3 0 0 {cellZ}
if {{$nLast == 0}} {{
temperature 300
- # fixedAtoms on
- # fixedAtomsForces on
- # fixedAtomsFile $prefix.pdb
- # fixedAtomsCol B
- # minimize 2400
- # fixedAtoms off
+ fixedAtoms on
+ fixedAtomsForces on
+ fixedAtomsFile $prefix.fixed.pdb
+ fixedAtomsCol B
+ minimize 2400
+ fixedAtoms off
minimize 2400
}} else {{
bincoordinates {output_directory}/$prefix-$nLast.restart.coor
@@ -1127,6 +1130,7 @@ run {num_steps:d}
if output_directory == '': output_directory='.'
self.writePdb( output_name + ".pdb" )
+ self.writePdb( output_name + ".fixed.pdb", beta_from_fixed=True )
self.writePsf( output_name + ".psf" )
self.write_namd_configuration( output_name, output_directory = output_directory )
os.sync()
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index a83645b..8d53e24 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -70,18 +70,6 @@ def basepairs_and_stacks_to_helixmap(basepairs,stacks_above):
return helixmap, helixrank, is_fwd
-def SegmentModelFromPdb(*args,**kwargs):
- u = mda.Universe(*args,**kwargs)
- for a in u.select_atoms("resname DT* and name C7").atoms:
- a.name = "C5M"
-
- ## Find basepairs and base stacks
- centers,transforms = find_base_position_orientation(u)
- bps = find_basepairs(u, centers, transforms)
- stacks = find_stacks(u, centers, transforms)
-
- ## Build map from residue index to helix index
-
def set_splines(seg, coordinates, hid, hmap, hrank, fwd, orientation=None):
maxrank = np.max( hrank[hmap==hid] )
if maxrank == 0:
diff --git a/mrdna/readers/segmentmodel_from_pdb.py b/mrdna/readers/segmentmodel_from_pdb.py
index 3cbb683..e00e3d7 100644
--- a/mrdna/readers/segmentmodel_from_pdb.py
+++ b/mrdna/readers/segmentmodel_from_pdb.py
@@ -258,6 +258,8 @@ def SegmentModelFromPdb(*args,**kwargs):
bps = find_basepairs(u, centers, transforms)
stacks = find_stacks(u, centers, transforms)
+ pdb.set_trace()
+
## Find three-prime ends
three_prime = -np.ones(bps.shape, dtype=np.int)
for s in u.segments:
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index af50091..4dee89b 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -638,7 +638,6 @@ class Segment(ConnectableElement, Group):
if scale is not None and scale != 1:
for a in atoms:
a.position = scale*a.position
- a.fixed = 1
atoms.position = pos - atoms.atoms_by_name["C1'"].collapsedPosition()
else:
if scale is not None and scale != 1:
@@ -649,6 +648,7 @@ class Segment(ConnectableElement, Group):
for a in atoms:
if a.name[-1] in ("'","P","T"):
a.position = scale*(a.position-r0) + r0
+ else:
a.fixed = 1
atoms.position = pos
--
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