Begin domain decomposition function

CHANGELOG

@@ -6,6 +6,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.0.2] - 2020-05-04
+### Added
+- debug trr frames export
+- initial code fro domain decomposition function
+
+### Changed
+- None
+
+### Removed
+- None
+
 ## [0.0.1] - 2020-04-27
 ### Added
 - add gitignore

main.py

@@ -5,5 +5,6 @@ import tooba_f as tbf
 #print(tbf.angle_between3D(P1,P2))
 
 
-#tbf.last_fr_export(trajfile='traj.trr')
-tbf.read_gro('initial.gro')
\ No newline at end of file
+data_all=tbf.fr_export(trajfile='traj.trr',num_frames=10)
+#system,data_num,box_size,res_num,res_type,atom_type,atom_num,rest_dt = tbf.read_gro('initial.gro')
+tbf.domain_decomposition(data=data_all,dx=-1,dy=-1,dz=-1)
\ No newline at end of file

tooba_f.py

@@ -72,6 +72,11 @@ def plot_surf(data, normal, c):
     plt.show()
 
 def count_frames(trajfile='traj.trr'):
+    """
+    Count total frames of .trr file
+
+    parameters:     trajfile = [.trr]
+    """
     cnt_fr=0
     with open(trajfile, 'rb') as inputfile:
         for i in range(1000):
@@ -85,20 +90,45 @@ def count_frames(trajfile='traj.trr'):
     return cnt_fr
 
 def fr_export(trajfile='traj.trr', num_frames=1):
+    """
+    Export frames from gromacs .trr file. 
+
+    parameters:     trajfile = [.trr]
+                    num_frames = [number of frames to keep
+                                  counting from the end of file]
+    """
     cnt_fr=count_frames(trajfile)
+    data_all={}
     with open(trajfile, 'rb') as inputfile:
         for i in range(cnt_fr-num_frames):
             header = read_trr_header(inputfile)
             #print('Step: {step}, time: {time}'.format(**header))
             skip_trr_data(inputfile, header)
+        for i in range(cnt_fr-num_frames,cnt_fr):
             header = read_trr_header(inputfile)
             print('Step: {step}, time: {time}'.format(**header))
             data = read_trr_data(inputfile, header)
-        print(data.keys())
-        print(data['box'])
-        print(data['x'][0])
+            #print(data.keys())
+            #print(data['box'])
+            #print(data['x'][0])
+            step='{step}'.format(**header)
+            data_all[step]=data
+        return data_all
 
 def read_gro(gro):
+    """
+    Read .gro file and exports 
+    1. system name
+    2. data number
+    3. box size
+    4. residue number
+    5. residue type
+    6. atom type
+    7. atom number
+    8. free format data (x,y,z,v,u,w)
+
+    parameters:     gro = [.gro]
+    """
     cnt=0
     data_num=0
     res_num = [] 
@@ -124,3 +154,24 @@ def read_gro(gro):
                 box_size=line[:50]
         #print(system,data_num,box_size)
         return system,data_num,box_size,res_num,res_type,atom_type,atom_num,rest_dt
+
+def domain_decomposition(data,dx,dy,dz):
+    """
+    Identify residues that rely inside a subdomain 
+    of a rectangular box
+
+    """
+    print('xs ys zs x y z')
+    for step in data.keys():
+        #print(data[step]['box'])
+        #data[step]['box'][row][element]
+        xs=data[step]['box'][0][0]
+        ys=data[step]['box'][1][1]
+        zs=data[step]['box'][2][2]
+        #data[step]['x'][atom_num][x(0),y(1),z(3)]
+        x=data[step]['x'][0][0]
+        y=data[step]['x'][0][1]
+        z=data[step]['x'][0][2]
+        print(xs,ys,zs, x, y, z)
+    #Todo: identify points inside box that belong to same residue
+    #return
\ No newline at end of file