adding tests for chempy.cpv

Author: ye11owSub

modules/chempy/cpv.py

@@ -23,41 +23,43 @@
 
 import math
 import random
-import copy
 
 RSMALL4 = 0.0001
 
 #------------------------------------------------------------------------------
-def get_null():
+def get_null() -> list[float]:
     return [0.0,0.0,0.0]
 
 #------------------------------------------------------------------------------
-def get_identity():
+def get_identity() -> list[list[float]]:
     return [[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0]]
 
 #------------------------------------------------------------------------------
-def distance_sq(v1, v2):
+def distance_sq(v1: list[float], v2: list[float]) -> float:
     d0 = v2[0] - v1[0]
     d1 = v2[1] - v1[1]
     d2 = v2[2] - v1[2]
     return (d0*d0) + (d1*d1) + (d2*d2)
 
 #------------------------------------------------------------------------------
-def distance(v1, v2):
+def distance(v1: list[float], v2: list[float]) -> float:
     d0 = v2[0] - v1[0]
     d1 = v2[1] - v1[1]
     d2 = v2[2] - v1[2]
     return math.sqrt((d0*d0) + (d1*d1) + (d2*d2))
 
 #------------------------------------------------------------------------------
-def length(v):
+def length(v: list[float]) -> float:
     return math.sqrt(v[0]*v[0] + v[1]*v[1] + v[2]*v[2])
 
 #------------------------------------------------------------------------------
-def random_displacement(v,radius):
-    r_vect = lambda r=random.random:[r()-0.5,r()-0.5,r()-0.5]
+def _random_vector() -> list[float]:
+    r = random.random
+    return [r()-0.5,r()-0.5,r()-0.5]
+
+def random_displacement(v: list[float], radius: float) -> list[float]:
     while 1:
-        vect = r_vect()
+        vect = _random_vector()
         v_len = length(vect)
         if (v_len<=0.5):
             break;
@@ -68,92 +70,85 @@ def random_displacement(v,radius):
         return v
 
 #------------------------------------------------------------------------------
-def random_sphere(v,radius):
-    r_vect = lambda r=random.random:[r()-0.5,r()-0.5,r()-0.5]
+def random_sphere(v: list[float], radius: float) -> list[float]:
     while 1:
-        vect = r_vect()
+        vect = _random_vector()
         v_len = length(vect)
         if (v_len<=0.5) and (v_len!=0.0):
             break;
     return add(v,scale([vect[0], vect[1], vect[2]],2*radius/v_len))
 
 #------------------------------------------------------------------------------
-def random_vector():
-    r_vect = lambda r=random.random:[r()-0.5,r()-0.5,r()-0.5]
+def random_vector() -> list[float]:
     while 1:
-        vect = r_vect()
+        vect = _random_vector()
         if length(vect)<=0.5:
             break;
     return scale([vect[0], vect[1], vect[2]],2.0)
 
 #------------------------------------------------------------------------------
-def add(v1,v2):
+def add(v1: list[float], v2: list[float]) -> list[float]:
     return [v1[0]+v2[0],v1[1]+v2[1],v1[2]+v2[2]]
 
 #------------------------------------------------------------------------------
-def average(v1,v2):
+def average(v1: list[float], v2: list[float]) -> list[float]:
     return [(v1[0]+v2[0])/2.0,(v1[1]+v2[1])/2.0,(v1[2]+v2[2])/2.0]
 
 #------------------------------------------------------------------------------
-def scale(v,factor):
+def scale(v: list[float], factor: float) -> list[float]:
     return [v[0]*factor,v[1]*factor,v[2]*factor]
 
 #------------------------------------------------------------------------------
-def negate(v):
+def negate(v: list[float]) -> list[float]:
     return [-v[0],-v[1],-v[2]]
 
 #------------------------------------------------------------------------------
-def sub(v1,v2):
+def reverse(v: list[float]) -> list[float]:
+    return [ -v[0], -v[1], -v[2] ]
+
+#------------------------------------------------------------------------------
+def sub(v1: list[float], v2: list[float]) -> list[float]:
     return [v1[0]-v2[0],v1[1]-v2[1],v1[2]-v2[2]]
 
 #------------------------------------------------------------------------------
-def dot_product(v1,v2):
+def dot_product(v1: list[float], v2: list[float]) -> float:
   return v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2]
 
 #------------------------------------------------------------------------------
-def cross_product(v1,v2):
+def cross_product(v1: list[float], v2: list[float]) -> list[float]:
   return [(v1[1]*v2[2]) - (v1[2]*v2[1]),
              (v1[2]*v2[0]) - (v1[0]*v2[2]),
              (v1[0]*v2[1]) - (v1[1]*v2[0])]
 
 #------------------------------------------------------------------------------
-def transform(m,v):
+def transform(m: list[list[float]], v: list[float]) -> list[float]:
     return [m[0][0]*v[0] + m[0][1]*v[1] + m[0][2]*v[2],
               m[1][0]*v[0] + m[1][1]*v[1] + m[1][2]*v[2],
               m[2][0]*v[0] + m[2][1]*v[1] + m[2][2]*v[2]]
 
 #------------------------------------------------------------------------------
-def inverse_transform(m,v):
+def inverse_transform(m: list[list[float]], v: list[float]) -> list[float]:
     return [m[0][0]*v[0] + m[1][0]*v[1] + m[2][0]*v[2],
             m[0][1]*v[0] + m[1][1]*v[1] + m[2][1]*v[2],
             m[0][2]*v[0] + m[1][2]*v[1] + m[2][2]*v[2]]
 
 #------------------------------------------------------------------------------
-def multiply(m1,m2): # HAVEN'T YET VERIFIED THAT THIS CONFORMS TO STANDARD DEFT
-    return [[m1[0][0]*m2[0][0] + m1[0][1]*m2[1][0] + m1[0][2]*m2[2][0],
-                m1[1][0]*m2[0][0] + m1[1][1]*m2[1][0] + m1[1][2]*m2[2][0],
-                m1[2][0]*m2[0][0] + m1[2][1]*m2[1][0] + m1[2][2]*m2[2][0]],
-              [m1[0][0]*m2[0][1] + m1[0][1]*m2[1][1] + m1[0][2]*m2[2][1],
-                m1[1][0]*m2[0][1] + m1[1][1]*m2[1][1] + m1[1][2]*m2[2][1],
-                m1[2][0]*m2[0][1] + m1[2][1]*m2[1][1] + m1[2][2]*m2[2][1]],
-              [m1[0][0]*m2[0][2] + m1[0][1]*m2[1][2] + m1[0][2]*m2[2][2],
-                m1[1][0]*m2[0][2] + m1[1][1]*m2[1][2] + m1[1][2]*m2[2][2],
-                m1[2][0]*m2[0][2] + m1[2][1]*m2[1][2] + m1[2][2]*m2[2][2]]]
+def multiply(m1: list[list[float]], m2: list[list[float]]) -> list[list[float]]:
+   # HAVEN'T YET VERIFIED THAT THIS CONFORMS TO STANDARD DEFT
+   # upd: no, it's not(fixed)
 
-#------------------------------------------------------------------------------
-def transpose(m1):
-    return [[m1[0][0],
-             m1[1][0],
-             m1[2][0]],
-            [m1[0][1],
-             m1[1][1],
-             m1[2][1]],
-            [m1[0][2],
-             m1[1][2],
-             m1[2][2]]]
+   return [[m1[0][0]*m2[0][0] + m1[0][1]*m2[1][0] + m1[0][2]*m2[2][0],
+               m1[0][0]*m2[0][1] + m1[0][1]*m2[1][1] + m1[0][2]*m2[2][1],
+               m1[0][0]*m2[0][2] + m1[0][1]*m2[1][2] + m1[0][2]*m2[2][2]],
+             [m1[1][0]*m2[0][0] + m1[1][1]*m2[1][0] + m1[1][2]*m2[2][0],
+               m1[1][0]*m2[0][1] + m1[1][1]*m2[1][1] + m1[1][2]*m2[2][1],
+               m1[1][0]*m2[0][2] + m1[1][1]*m2[1][2] + m1[1][2]*m2[2][2]],
+             [m1[2][0]*m2[0][0] + m1[2][1]*m2[1][0] + m1[2][2]*m2[2][0],
+               m1[2][0]*m2[0][1] + m1[2][1]*m2[1][1] + m1[2][2]*m2[2][1],
+               m1[2][0]*m2[0][2] + m1[2][1]*m2[1][2] + m1[2][2]*m2[2][2]]]
 
 #------------------------------------------------------------------------------
-def get_system2(x,y):
+def get_system2(x: list[float],y: list[float]) -> list[list[float]]:
     z = cross_product(x,y)
     z = normalize(z)
     y = cross_product(z,x);
@@ -162,24 +157,24 @@ def get_system2(x,y):
     return [x,y,z]
 
 #------------------------------------------------------------------------------
-def scale_system(s,factor):
+def scale_system(s: list[list[float]], factor: float) -> list[list[float]]:
     r = []
     for a in s:
         r.append([a[0]*factor,a[1]*factor,a[2]*factor])
     return r
 
 #------------------------------------------------------------------------------
-def transpose(m):
+def transpose(m: list[list[float]]) -> list[list[float]]:
     return [[m[0][0], m[1][0], m[2][0]],
               [m[0][1], m[1][1], m[2][1]],
               [m[0][2], m[1][2], m[2][2]]]
 
 #------------------------------------------------------------------------------
-def transform_about_point(m,v,p):
+def transform_about_point(m: list[list[float]], v: list[float], p: list[float]) -> list[float]:
     return add(transform(m,sub(v,p)),p)
 
 #------------------------------------------------------------------------------
-def get_angle(v1,v2): # v1,v2 must be unit vectors
+def get_angle(v1: list[float], v2: list[float]) -> float: # v1,v2 must be unit vectors
     denom = (math.sqrt(((v1[0]*v1[0]) + (v1[1]*v1[1]) + (v1[2]*v1[2]))) *
                 math.sqrt(((v2[0]*v2[0]) + (v2[1]*v2[1]) + (v2[2]*v2[2]))))
     if denom>1e-10:
@@ -190,7 +185,7 @@ def get_angle(v1,v2): # v1,v2 must be unit vectors
     return result
 
 #------------------------------------------------------------------------------
-def get_angle_formed_by(p1,p2,p3): # angle formed by three positions in space
+def get_angle_formed_by(p1: list[float], p2: list[float], p3: list[float]) -> float: # angle formed by three positions in space
 
     # based on code submitted by Paul Sherwood
     r1 = distance(p1,p2)
@@ -207,37 +202,33 @@ def get_angle_formed_by(p1,p2,p3): # angle formed by three positions in space
     return theta;
 
 #------------------------------------------------------------------------------
-def project(v,n):
+def project(v: list[float], n: list[float]) -> list[float]:
     dot = v[0]*n[0] + v[1]*n[1] + v[2]*n[2]
     return [ dot * n[0], dot * n[1], dot * n[2] ]
 
 #------------------------------------------------------------------------------
-def remove_component(v, n):
+def remove_component(v: list[float], n: list[float]) -> list[float]:
     dot = v[0]*n[0] + v[1]*n[1] + v[2]*n[2]
     return [v[0] - dot * n[0], v[1] - dot * n[1], v[2] - dot * n[2]]
 
 #------------------------------------------------------------------------------
-def normalize(v):
+def normalize(v: list[float]) -> list[float]:
     vlen = math.sqrt((v[0]*v[0]) + (v[1]*v[1]) + (v[2]*v[2]))
     if vlen>RSMALL4:
         return [v[0]/vlen,v[1]/vlen,v[2]/vlen]
     else:
         return get_null()
 
 #------------------------------------------------------------------------------
-def reverse(v):
-    return [ -v[0], -v[1], -v[2] ]
-
-#------------------------------------------------------------------------------
-def normalize_failsafe(v):
+def normalize_failsafe(v: list[float]) -> list[float]:
     vlen = math.sqrt((v[0]*v[0]) + (v[1]*v[1]) + (v[2]*v[2]))
     if vlen>RSMALL4:
         return [v[0]/vlen,v[1]/vlen,v[2]/vlen]
     else:
         return [1.0,0.0,0.0]
 
 #------------------------------------------------------------------------------
-def rotation_matrix(angle,axis):
+def rotation_matrix(angle: float, axis: list[float]) -> list[list[float]]:
 
     x=axis[0]
     y=axis[1]
@@ -271,7 +262,7 @@ def rotation_matrix(angle,axis):
               [ (one_c * zx) - ys, (one_c * yz) + xs, (one_c * zz) + c ]]
 
 #------------------------------------------------------------------------------
-def transform_array(rot_mtx,vec_array):
+def transform_array(rot_mtx: list[list[float]], vec_array: list[list[float]]) -> list[list[float]]:
 
     '''transform_array( matrix, vector_array ) -> vector_array
 
@@ -280,7 +271,7 @@ def transform_array(rot_mtx,vec_array):
     return [transform(rot_mtx, x) for x in vec_array]
 
 #------------------------------------------------------------------------------
-def translate_array(trans_vec,vec_array):
+def translate_array(trans_vec: list[float], vec_array: list[list[float]]):
 
     '''translate_array(trans_vec,vec_array) -> vec_array
 
@@ -291,17 +282,17 @@ def translate_array(trans_vec,vec_array):
     return [add(trans_vec, x) for x in vec_array]
 
 #------------------------------------------------------------------------------
-def fit_apply(fit_result,vec_array):
+def fit_apply(fit_result: tuple[list[float], list[float], list[list[float]], float], vec_array: list[list[float]]) -> list[list[float]]:
     '''fit_apply(fir_result,vec_array) -> vec_array
-    
+
     Applies a fit result to an array of vectors
     '''
 
     t1, mt2, m = fit_result[:3]
     return [add(t1, transform(m, add(mt2, x))) for x in vec_array]
 
 #------------------------------------------------------------------------------
-def fit(target_array, source_array):
+def fit(target_array: list[list[float]], source_array: list[list[float]]) -> tuple[list[float], list[float], list[list[float]], float] | None:
 
     '''fit(target_array, source_array) -> (t1, t2, rot_mtx, rmsd) [fit_result]
 
@@ -370,7 +361,6 @@ def fit(target_array, source_array):
     iters = 0
     while (iters < maxiter):
         iters = iters + 1
-        ix = (iters-1)%ndim
         iy = iters%ndim
         iz = (iters+1)%ndim
         sig = corr_mtx[iz][iy] - corr_mtx[iy][iz]