diff --git a/bin/enrgmd b/bin/enrgmd
index 84d64893178a7b8921d64664fc53fae52796c47a..aa90fcf7459a37db0fc79f86d448aedc9dc165cd 100755
--- a/bin/enrgmd
+++ b/bin/enrgmd
@@ -42,13 +42,19 @@ if __name__ == '__main__':
from mrdna.readers import read_atomic_pdb as read_model
else:
raise Exception("Unrecognized input file '{}'".format(infile))
-
- model = read_model( str(infile) )
if args.output_prefix is not None:
prefix = args.output_prefix
directory = args.directory
+ if prefix == infile.stem and extension == ".pdb":
+ print("Are you sure you want to overwrite '{}'? (you may provide '-o' option) [y/N]".format(infile))
+ if input() not in ("y","Y","yes","Y","Yes","YES"):
+ import sys
+ sys.exit(1)
+
+ model = read_model( str(infile) )
+
d_orig = os.getcwd()
try:
if directory is None:
diff --git a/bin/mrdna b/bin/mrdna
index 4364474450fe9488b9f9f623f42d558e216d2b45..41f47a92b464f2e112900296d5abc87e4f1d4744 100755
--- a/bin/mrdna
+++ b/bin/mrdna
@@ -24,8 +24,10 @@ parser.add_argument('--fine-steps', type=float, default=1e7,
parser.add_argument('--backbone-scale', type=float, default=1.0,
help='Factor to scale DNA backbone in atomic model; try 0.25 to avoid clashes for atomistic simulations')
-parser.add_argument('--draw-cylinders', type=bool, default=False,
- help='whether or not to draw the cylinders')
+parser.add_argument('--draw-cylinders', nargs='?', const=True, type=bool, default=False,
+ help='Whether or not to draw the cylinders')
+parser.add_argument('--draw-tubes', nargs='?', const=True, type=bool, default=False,
+ help='Whether or not to draw the tubes')
parser.add_argument('input_file', type=str,
help="""Any of the following:
@@ -58,15 +60,30 @@ if __name__ == '__main__':
if args.output_prefix is not None:
prefix = args.output_prefix
- if args.draw_cylinders is not False:
- model = model
- model.vmd_cylinder_tcl()
- output_name = prefix+ ".cylinders.tcl"
+ if args.draw_cylinders is True:
+ output_name = prefix + ".cylinders.tcl"
+ model.vmd_cylinder_tcl( output_name )
+ if prefix == infile.stem and extension == ".pdb":
+ print("Are you sure you want to overwrite '{}'? (you may provide '-o' option) [y/N]".format(infile))
+ if input() not in ("y","Y","yes","Y","Yes","YES"):
+ import sys
+ sys.exit(1)
model._clear_beads()
- model._generate_atomic_model(scale=args.backbone_scale)
+ model._generate_atomic_model(scale=args.backbone_scale)
+ model.write_atomic_ENM( prefix )
+ model.atomic_simulate( output_name = prefix )
+ elif args.draw_tubes is True:
+ output_name = prefix + ".tubes.tcl"
+ model.vmd_tube_tcl( output_name )
+ if prefix == infile.stem and extension == ".pdb":
+ print("Are you sure you want to overwrite '{}'? (you may provide '-o' option) [y/N]".format(infile))
+ if input() not in ("y","Y","yes","Y","Yes","YES"):
+ import sys
+ sys.exit(1)
+ model._clear_beads()
+ model._generate_atomic_model(scale=args.backbone_scale)
model.write_atomic_ENM( prefix )
model.atomic_simulate( output_name = prefix )
-
else:
run_args = dict(
model = model,
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index e3d400988f368d455d7c9131cb3c62d8af3b7af7..fa10c4d1840768371f9e6db03431d3f29d29e228 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -2874,27 +2874,44 @@ proc calcforces {} {
print(angles[np.argmin(score)])
print(score)
- def vmd_cylinder_tcl(self, file_handle):
- raise NotImplementedError
-
- def draw_cylinder(segment):
- r0 = segment.start_position
- r1 = segment.end_position
-
- file_handle.write("")
- file_handle.write("")
+ def vmd_tube_tcl(self, file_name="drawTubes.tcl"):
+ with open(file_name, 'w') as tclFile:
+ tclFile.write("## beginning TCL script \n")
- ## material
- for s in self.segments:
- if isinstance(s,DoubleStrandedSegment):
- ...
- radius = 5
- elif isinstance(s,SingleStrandedSegment):
- ...
- else:
- raise(Exception)
+ def draw_tube(segment,radius_value=10, color="cyan", resolution=5):
+ tclFile.write("## Tube being drawn... \n")
+
+ contours = np.linspace(0,1, max(2,1+segment.num_nt//resolution) )
+ rs = [segment.contour_to_position(c) for c in contours]
+
+ radius_value = str(radius_value)
+ tclFile.write("graphics top color {} \n".format(str(color)))
+ for i in range(len(rs)-2):
+ r0 = rs[i]
+ r1 = rs[i+1]
+ filled = "yes" if i in (0,len(rs)-2) else "no"
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled {} \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value), filled))
+ tclFile.write("graphics top sphere {{ {} {} {} }} radius {} resolution 30\n".format(r1[0], r1[1], r1[2], str(radius_value)))
+ r0 = rs[-2]
+ r0 = rs[-1]
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value)))
- file_handle.write("")
+ ## material
+ tclFile.write("graphics top materials on \n")
+ tclFile.write("graphics top material AOEdgy \n")
+
+ ## iterate through the model segments
+ for s in self.segments:
+ if isinstance(s,DoubleStrandedSegment):
+ tclFile.write("## dsDNA! \n")
+ draw_tube(s,10,"cyan")
+ elif isinstance(s,SingleStrandedSegment):
+ tclFile.write("## ssDNA! \n")
+ draw_tube(s,3,"orange",resolution=1.5)
+ else:
+ raise Exception ("your model includes beads that are neither ssDNA nor dsDNA")
+ ## tclFile complete
+ tclFile.close()
def vmd_cylinder_tcl(self, file_name="drawCylinders.tcl"):
#raise NotImplementedError
@@ -2905,9 +2922,6 @@ proc calcforces {} {
r0 = segment.contour_to_position(0)
r1 = segment.contour_to_position(1)
- x0,y0,z0 = r0
- x1,y1,z1 = r1
-
radius_value = str(radius_value)
color = str(color)