Corrections

CHANGELOG

@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - code for assign coordinates to subdomain
 - code for creating vectors for each tail of lipid in subdomain
 - code for creating surface for heads of lipids in subdomain
+- code for calculating the angle between surface and vectors for every step, sudomain and resid
+- clean main.py
 
 ### Changed
 - change output in def atomid_data() to include resid

main.py

 import tooba_f as tbf
-
-#P1=(0,1,0)
-#P2=(1,1,0)
-#print(tbf.angle_between3D(P1,P2))
-
+###################################################
+#NOTICE:    resids of head in each subdomain may differ in tail case
+#           keep all atoms of group in the first occurent subdomain
+#           in case of tail is the one closest to the head, hence
+#           the code is a good approximation 
+###################################################
+TRAJ='traj.trr'
+NUM_FR=1
+GRO='initial.gro'
+HEAD=True
+HD_GROUP={'MMA':['C1', 'C2']}
+TAIL=True
+TL_GROUP={'MMA':['C3', 'C4', 'C5']}
+###################################################
 #Read .trr file
-data_all=tbf.fr_export(trajfile='traj.trr',num_frames=1)
+data_all=tbf.fr_export(trajfile=TRAJ,num_frames=NUM_FR)
 #Read .gro file
-_,data_num,_,res_num,res_type,atom_type,atom_num,_ = tbf.read_gro('initial.gro')
+_,data_num,_,res_num,res_type,atom_type,atom_num,_ = tbf.read_gro(GRO)
 #Create subdomains coordinates
 box_p=tbf.domain_decomposition(data=data_all,dx=2,dy=2,dz=2)
 
 ###################################################
-HEAD=False
 if HEAD==True:
     #Find atom type index in lists created above
-    group_ndx=tbf.atomid_data(res_num, atom_type, atom_num, group={'MMA':['C1', 'C2']})
+    group_ndx=tbf.atomid_data(res_num, atom_type, atom_num, group=HD_GROUP)
     #Assign desired atoms (from above function) to subdomains
     ##result1: {step:{res:{atom_type:{atom_num:(subX,subYsubZ)}}}}
     ##result2: {step:{res:{atom_type:{(subX,subYsubZ):[atom_num]}}}}
@@ -24,16 +32,16 @@ if HEAD==True:
     coord_norm,_=tbf.sub_coord(box=box_res, data=data_all, res_num=res_num)
     #Creates dictionary with c, normal per subdomain for each frame
     surf=tbf.coord2norm(coord_norm,img=True)
-
 ###################################################
-TAIL=True
 if TAIL==True:
     #Find atom type index in lists created above
-    group_ndx=tbf.atomid_data(res_num, atom_type, atom_num, group={'MMA':['C3', 'C4', 'C5']})
+    group_ndx=tbf.atomid_data(res_num, atom_type, atom_num, group=TL_GROUP)
     #Assign desired atoms (from above function) to subdomains
     ##result1: {step:{res:{atom_type:{atom_num:(subX,subYsubZ)}}}}
     ##result2: {step:{res:{atom_type:{(subX,subYsubZ):[atom_num]}}}}
     _,box_res=tbf.atom2grid(data_all,box_p, group_ndx)
     #Creates dictionary with coordinates per subdomain for each frame
     _,coord_vector=tbf.sub_coord(box=box_res, data=data_all, res_num=res_num)
-    vector=tbf.coord2vector(coord_vector)
\ No newline at end of file
+    vector=tbf.coord2vector(coord_vector)
+###################################################
+tbf.SurfVector_angle(surf,vector)
\ No newline at end of file

tooba_f.py

@@ -404,10 +404,9 @@ def coord2vector(coord_vector):
     Use the coord_vector from 'def sub_coord' and replaces XYZ coordinates
     with vector of best fit line
 
-    parameters:         coord = {step:{subdomain:array[[X1,Y1,Z1] ... [Xn,Yn,Zn]]}}
-                        img = True or False
-    
-    output:             dictionary = {step:{subdomain:[x, y, z]}
+    parameters:         coord = {step:{subdomain:{resid:[[X1,Y1,Z1] ... [Xn,Yn,Zn]]}}
+        
+    output:             dictionary = {step:{subdomain:{resid:[x, y, z]}}
     """
     vector={}
     for step in coord_vector.keys():
@@ -417,4 +416,26 @@ def coord2vector(coord_vector):
             for resid in coord_vector[step][subdomain].keys():
                 vv = points2vector(np.array(coord_vector[step][subdomain][resid]))
                 vector[step][subdomain][resid]=vv
-    return vector
\ No newline at end of file
+    return vector
+
+def SurfVector_angle(surf,vector):
+    """
+    Use the surf and vector from 'def coord2norm' and 'def coord2vector'
+    and calculate the angle between them for every step, sudomain and resid
+
+    parameters:         surf = {step:{subdomain:{c:int, normal:array[]}}}
+                        vector = {step:{subdomain:{resid:[x, y, z]}}
+    
+    output:             angle = {step:{subdomain:{resid:angle}}
+    """
+    angle={}
+    for step in surf.keys():
+        angle[step]={}
+        for sudomain in surf[step].keys():
+            angle[step][sudomain]={}
+            for resid in vector[step][sudomain].keys():
+                P1=tuple(surf[step][sudomain]['normal'])
+                P2=tuple(vector[step][sudomain][resid])
+                #print(tbf.angle_between3D(P1,P2))
+                angle[step][sudomain][resid]=angle_between3D(P1,P2)
+    return angle
\ No newline at end of file