Final small fixes before v1.10 release

src/target.py

@@ -843,7 +843,7 @@ def is_within_directory(directory, target):
                 prefix = os.path.commonprefix([abs_directory, abs_target])
                 return prefix == abs_directory
 
-            def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
+            def safe_extract(tar, path=".", members=None, numeric_owner=False):
                 for member in tar.getmembers():
                     member_path = os.path.join(path, member.name)
                     if not is_within_directory(path, member_path):

src/tinkerio.py

@@ -643,7 +643,7 @@ def evaluate_(self, xyzin, force=False, dipole=False):
         Result = OrderedDict()
         # If we want the dipoles (or just energies), analyze is the way to go.
         if dipole or (not force):
-            oanl = self.calltinker("analyze %s -k %s" % (xyzin, self.name), stdin="G,E,M", print_to_screen=False)
+            oanl = self.calltinker("analyze %s -k %s" % (xyzin, self.name), stdin="G E M", print_to_screen=False)
             # Read potential energy and dipole from file.
             eanl = []
             dip = []
@@ -986,7 +986,7 @@ def molecular_dynamics(self, nsteps, timestep, temperature=None, pressure=None,
         temps = np.array(temps)
 
         if verbose: logger.info("Post-processing to get the dipole moments\n")
-        oanl = self.calltinker("analyze %s-md.arc" % self.name, stdin="G,E,M", print_to_screen=False)
+        oanl = self.calltinker("analyze %s-md.arc" % self.name, stdin="G E M", print_to_screen=False)
 
         # Read potential energy and dipole from file.
         eanl = []
@@ -1006,7 +1006,7 @@ def molecular_dynamics(self, nsteps, timestep, temperature=None, pressure=None,
                 dip.append([float(s[i]) for i in range(-3,0)])
             if first_shot:
                 for key in eckeys:
-                    if strip.startswith(key):
+                    if strip.startswith(key) and isfloat(s[-2]):
                         if key in ecomp:
                             ecomp[key].append(float(s[-2])*4.184)
                         else:
@@ -1016,7 +1016,7 @@ def molecular_dynamics(self, nsteps, timestep, temperature=None, pressure=None,
                         havekeys.add(key)
             else:
                 for key in havekeys:
-                    if strip.startswith(key):
+                    if strip.startswith(key) and isfloat(s[-2]):
                         if key in ecomp:
                             ecomp[key].append(float(s[-2])*4.184)
                         else:

tools/drawforces/drawforces.vmd

@@ -60,7 +60,7 @@ proc min {x y} {expr {$x<$y? $x: $y}}
 # lot of vectors easily.
 # field has to be a list of pairs of xyz triples (center and vector).
 # the function returns a list of the graphics ids for easy deletion.
-proc vmd_draw_vector {mol cnt vec {scale 1.0} {res 35} {radius 0.05}} {
+proc vmd_draw_vector {mol cnt vec {scale 1.0} {res 35} {radius 0.1}} {
     global cid
 
     set camz [lindex [lindex [molinfo 0 get view_matrix] 0] 2]
@@ -81,7 +81,7 @@ proc vmd_draw_vector {mol cnt vec {scale 1.0} {res 35} {radius 0.05}} {
     # Choose a direction that is normal to the present vector.
     set offset [ vecscale $x3 [expr [expr $cid - 0.5] * 0.05] ]
     set cnt [ vecadd $cnt $offset ]
-    set radius [min [expr 0.1 * [veclength $vec]] $radius]
+    set radius [min [expr 0.3 * [veclength $vec]] $radius]
     return [list \
       [graphics $mol cylinder [vecsub $cnt $veczero] \
         [vecadd $cnt [vecscale 0.8 $vecfull]] \
@@ -91,7 +91,7 @@ proc vmd_draw_vector {mol cnt vec {scale 1.0} {res 35} {radius 0.05}} {
 	resolution $res]]
 }
 
-proc vmd_draw_vecfield {mol field {scale 1.0} {res 35} {radius 0.05}} {
+proc vmd_draw_vecfield {mol field {scale 1.0} {res 35} {radius 0.1}} {
     set gids ""
     foreach i $field {
         lassign $i cnt vec
@@ -121,7 +121,7 @@ proc do_frcdraw {args} {
         set cid 0
         foreach frcdata $frcdatas($frame) {
             graphics $molid color [ lindex $colors $cid ]
-            lappend frcgraphs [vmd_draw_vecfield $molid $frcdata 3.0 35 1.2]
+            lappend frcgraphs [vmd_draw_vecfield $molid $frcdata 3.0 35 0.1]
             incr cid
         }
     }