Initial commit corrections

.gitignore

+FORTRAN_vscode/
+__pycache__/
+.venv/
+.vscode/

main.py

+import tooba_f as tbf
+
+P1=(0,1,0)
+P2=(1,1,0)
+print(tbf.angle_between3D(P1,P2))
+
+
+tbf.last_fr_export(trajfile='traj.trr')

tooba_f.py

+import numpy as np
+import scipy.optimize
+
+from mpl_toolkits.mplot3d import Axes3D
+import matplotlib.pyplot as plt
+
+def fitPlaneLTSQ(XYZ):
+    (rows, cols) = XYZ.shape
+    G = np.ones((rows, 3))
+    G[:, 0] = XYZ[:, 0]  #X
+    G[:, 1] = XYZ[:, 1]  #Y
+    Z = XYZ[:, 2]
+    (a, b, c),resid,rank,s = np.linalg.lstsq(G, Z, rcond=None)
+    normal = (a, b, -1)
+    nn = np.linalg.norm(normal)
+    normal = normal / nn
+    return (c, normal)
+
+def angle_between2D(p1, p2):
+    #arctan2 is anticlockwise
+    ang1 = np.arctan2(*p1[::-1])
+    ang2 = np.arctan2(*p2[::-1])
+    angle=np.rad2deg((ang1 - ang2) % (2 * np.pi)) #degree
+    if angle<180:
+        return angle
+    else:
+        return 360 - angle
+
+def angle_between3D(v1, v2):
+# v1 is your firsr vector
+# v2 is your second vector
+    angle = np.arccos(np.dot(v1, v2) / (np.linalg.norm(v1) * np.linalg.norm(v2))) #rad
+    angle=180*angle/np.pi #degrees
+    if angle<180:
+        return angle
+    else:
+        return 360 - angle
+
+def plot_surf(data, normal):
+    #Plot surface
+    fig = plt.figure()
+    ax = fig.gca(projection='3d')
+
+    # plot fitted plane
+    maxx = np.max(data[:,0])
+    maxy = np.max(data[:,1])
+    minx = np.min(data[:,0])
+    miny = np.min(data[:,1])
+
+    point = np.array([0.0, 0.0, c])
+    d = -point.dot(normal)
+
+    # plot original points
+    ax.scatter(data[:, 0], data[:, 1], data[:, 2])
+
+    # compute needed points for plane plotting
+    xx, yy = np.meshgrid([minx, maxx], [miny, maxy])
+    z = (-normal[0]*xx - normal[1]*yy - d)*1. / normal[2]
+
+    # plot plane
+    ax.plot_surface(xx, yy, z, alpha=0.2)
+
+    ax.set_xlabel('x')
+    ax.set_ylabel('y')
+    ax.set_zlabel('z')
+    plt.show()
+
+def count_frames(trajfile='traj.trr'):
+    from pytrr import (
+        read_trr_header,
+        read_trr_data,
+        skip_trr_data,
+        )
+
+    cnt_fr=0
+    with open(trajfile, 'rb') as inputfile:
+        for i in range(1000):
+            try: 
+                header = read_trr_header(inputfile)
+                #print('Step: {step}, time: {time}'.format(**header))
+                skip_trr_data(inputfile, header)
+                cnt_fr=cnt_fr+1
+            except EOFError:
+                pass
+    return cnt_fr
+
+def last_fr_export(trajfile='traj.trr'):
+    from pytrr import (
+        read_trr_header,
+        read_trr_data,
+        skip_trr_data,
+        )
+    cnt_fr=count_frames(trajfile)
+    with open(trajfile, 'rb') as inputfile:
+        for i in range(cnt_fr-1):
+            header = read_trr_header(inputfile)
+            #print('Step: {step}, time: {time}'.format(**header))
+            skip_trr_data(inputfile, header)
+        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])
+
+#Random data
+#data = np.random.randn(100, 3)/3
+#data[:, 2] /=10
+
+#Find surface of points-> for lipid plane
+#c, normal = fitPlaneLTSQ(data)
+#print('Normal of surface is: ',normal)
+
+#Angle between two lines-> for finding tilt
+#P1=(normal[0],normal[1], normal[2])
+#P2=(0,0,-0.99998042)
+
+#print('Line is: ',P2)
+#print('Angle between vectors is: ',angle_between3D(P1,P2))
+
+#Fit line to points->for lipid chain
+#from scipy import stats
+#slope, intercept, r_value, p_value, std_err = stats.linregress(data[:,0],data[:,1])
+#print('y=',slope,'x+',intercept)
+#print('r_value',r_value)
+
+#Angle between two lines-> for finding tilt
+#P1=(normal[0],normal[1])
+#P2=(1,1)
+
+#print('Line is: ',P2)
+#print('Angle between lines is: ',angle_between2D(P1,P2))
+
+#plot_surf(data=data, normal=normal)
+
+

toobba.code-workspace

+{
+	"folders": [
+		{
+			"path": "."
+		}
+	]
+}
\ No newline at end of file