Updates

PCA/PCAmovies.py

@@ -251,7 +251,7 @@ def setup_swp(self,zrange=None,nframes:int=300,framerate:int=15):
 
     #     return self.data.R@wt0
 
-
+    #%% xtc writers
     def xtc_from_weight(self,wt,rho_index:int,filename:str='temp.xtc',
                         nframes:int=150,framerate:int=15,scaling:float=1):
         """
@@ -304,8 +304,8 @@ def xtc_from_PCamp(self,PCamp,rho_index:int,filename:str='temp.xtc',nframes:int=
                        framerate:int=15,scaling:float=1):
 
         timescale=self.PCARef.sens.info['z0'][rho_index]
-        step=np.round(10**timescale*1e12/self.PCARef.source.select.traj.dt/framerate).astype(int)
-        step=1
+        step=np.round(10**timescale*1e12/self.PCARef.source.select.traj.dt/framerate/3).astype(int)
+        # step=1
         if step==0:step=1
         if step*nframes>PCamp.shape[1]:
             step=np.round(PCamp.shape[1]/nframes).astype(int)
@@ -321,15 +321,15 @@ def xtc_from_PCamp(self,PCamp,rho_index:int,filename:str='temp.xtc',nframes:int=
 
         self._xtc=filename
 
-        self.options.TimescaleIndicator(tau=np.ones(nframes)*step*self.pca.select.traj.dt)
+        self.options.TimescaleIndicator(tau=np.ones(nframes)*step*self.pca.select.traj.dt/1e3)
 
         return self
 
 
 
 
 
-
+    #%% Display modes
     def xtc_rho(self,rho_index:int,frac:float=0.75,filename:str='temp.xtc',
                       nframes:int=150,framerate:int=15,scaling:float=1):
         """
@@ -399,12 +399,14 @@ def xtc_bond(self,index:int,rho_index:int,frac:float=0.75,filename:str='temp.xtc
 
     def xtc_impulse(self,index:int,rho_index:int,frac:float=0.75,filename:str='temp.xtc',
                  nframes:int=150,framerate:int=15,scaling:float=1):
-        PCamp=self.pca.Impulse.PCamp_bond(index)
+        PCamp=self.pca.Impulse.PCamp_bond(index)[:,1:]
         wt=self.pca.Weighting.bond(index=index,rho_index=rho_index)
 
         self.xtc_from_PCamp(PCamp=(PCamp.T*wt).T, rho_index=rho_index,filename=filename,
                             nframes=nframes,framerate=framerate,scaling=scaling)
 
+        self.options.commands=['~ribbon #{0}','show #{0}']
+
         return self
 
     def xtc_noweight(self,rho_index:int=None,mode_index:int=None,filename:str='temp.xtc',
@@ -685,9 +687,21 @@ class Options():
     def __init__(self,pca_movie):
         self.dict={}
         self.pca_movie=pca_movie
-
+        self._commands=[]
+
+    @property
+    def commands(self):
+        return self._commands
+    @commands.setter
+    def commands(self,value):
+        if isinstance(value,str):
+            value=[value]
+        assert isinstance(value,list),'Commands must be a list'
+        self._commands=value
+
     def __call__(self):
         for f in self.dict.values():f()
+        self.run_commands()
 
     def clear(self):
         for k in self.dict:
@@ -708,6 +722,10 @@ def add_event(self,name,*args):
 
     def remove_event(self,name):
         self.CMX.remove_event(self.CMXid,name)
+
+    def run_commands(self):
+        for cmd in self.commands:
+            self.CMX.command_line(self.CMXid,cmd.format(self.pca_movie.molsys.movie.mdlnums[0]))
 
     def TimescaleIndicator(self,tau=None,remove:bool=False):
         """
@@ -725,12 +743,15 @@ def TimescaleIndicator(self,tau=None,remove:bool=False):
         None.
 
         """
-        if tau is None:tau=10**self.pca_movie.setup['tscale_swp']*1e9
+
         if remove:
             if __name__ in self.dict:self.dict.pop(__name__)
             return
+        if tau is None:tau=10**self.pca_movie.setup['tscale_swp']*1e9
         if tau is not None:
-            self.dict['TimescaleIndicator']=lambda tau=tau:self.add_event('TimescaleIndicator', tau)
+            self.dict['TimescaleIndicator']=\
+                lambda tau=tau:self.add_event('TimescaleIndicator', tau,
+                                              self.pca_movie.molsys.movie.mdlnums[1])
         return self
 
     def Detectors(self,index=None,rho_index=None,remove:bool=False):

PCA/testPCA.py

@@ -15,7 +15,7 @@
 
 pca=PCA(select)
 pca.select_bond('15N',resids=np.concatenate([np.arange(225,248),np.arange(261,281)]))
-pca.select_bond('15N')
+# pca.select_bond('15N')
 pca.select_atoms('all')
 
 

chimeraX/CMXEvents.py

@@ -46,21 +46,21 @@ def cleanup(self):
 
 
 class TimescaleIndicator():
-    def __init__(self, cmx, tau):
+    def __init__(self, cmx, tau, mn:int=-1):
         self.cmx = cmx
         self.session = cmx.session
-        self.model = self.session.models[-1]
+        self.model = self.session.models[mn]
         self.tau = tau
         self.i = -1
         self.label = label_create(self.session, 'timescale',  # Create a 2d label
-                                  text='1 s: {:.0f} ps'.format(self.tau[1] * 1e3),
+                                  text='1 s: {:.0f} ps'.format(self.tau[0] * 1e3),
                                   xpos=0.02, ypos=.05, size=50)
 
     def __call__(self):
         i = self.model.active_coordset_id - 1
         if i != self.i:
             tau = self.tau[i] * 1e3
-            if i == 0 and False:
+            if i == 0:
                 text = '1 s: {:.0f} ps'.format(self.tau[1] * 1e3)
             elif tau < 1e3:
                 text = '1 s: {:.0f} ps'.format(tau)