MultiOptPy 1.20.2__py3-none-any.whl

multioptpy/Utils/bond_connectivity.py

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+
+import numpy as np
+
+from multioptpy.Parameters.parameter import covalent_radii_lib, UnitValueLib
+from multioptpy.Utils.calc_tools import calc_bond_length_from_vec, calc_angle_from_vec, calc_dihedral_angle_from_vec
+
+class BondConnectivity:#Bohr
+    def __init__(self):
+        self.covalent_radii_lib_func = covalent_radii_lib#function
+        self.covalent_radii_threshold = 1.1
+        
+        return
+    
+    def distance_matrix(self, coord):#coord:natoms × 3, ndarray (Bohr unit)
+        natom = len(coord)
+        
+        distance_mat = np.zeros((natom, natom), dtype="float64")
+        tmp_mat = np.zeros((natom), dtype="float64")
+        for i in range(natom):
+            tmp_mat = coord - coord[i]
+            distance_mat[i] = np.linalg.norm(tmp_mat, axis=1)
+            distance_mat[i][i] = 0.0
+        return distance_mat
+    
+    def bondlength_matrix(self, element_list):
+        natom = len(element_list)
+        bond_length_mat = np.zeros((natom, natom), dtype="float64")
+        radii_list = np.array([self.covalent_radii_lib_func(elem) for elem in element_list], dtype="float64")
+        for i in range(natom):
+            bond_length_mat[i] = (radii_list + radii_list[i]) * self.covalent_radii_threshold
+            bond_length_mat[i][i] = -1.0
+        return bond_length_mat#Bohr
+
+    def bond_connect_matrix(self, element_list, coord):
+        
+        distance_mat = self.distance_matrix(coord)
+        bond_length_matrix = self.bondlength_matrix(element_list)
+        connectivity_mat = np.where(distance_mat <= bond_length_matrix, 1, 0)
+                  
+        return connectivity_mat
+
+
+    def bond_connect_table(self, connectivity_mat):
+        natom = len(connectivity_mat)
+
+        bond_table = []
+        for i in range(natom):
+            for j in range(natom):
+                if i > j:
+                    continue
+                if connectivity_mat[i, j] == 1:
+                    bond_table.append([i, j])
+                    
+        return bond_table
+    
+    def angle_connect_table(self, bond_connect_matrix):
+        angle_connect_table = []
+
+        for i in range(len(bond_connect_matrix)):
+            for j in range(len(bond_connect_matrix)):
+                if bond_connect_matrix[i][j] == 1:
+                    for n in range(j+1, len(bond_connect_matrix[i])):
+                        if bond_connect_matrix[i][n] == 1 and bond_connect_matrix[j][n] == 0:
+                            angle_connect_table.append([j, i, n])
+                        
+                
+        return angle_connect_table
+    
+    def dihedral_angle_connect_table(self, bond_connect_matrix):
+        dihedral_angle_connect_table = []
+        angle_connect_table = self.angle_connect_table(bond_connect_matrix)
+        for i in range(len(angle_connect_table)):
+            for j in range(i+1, len(angle_connect_table)):
+                if (angle_connect_table[i][1] == angle_connect_table[j][1] and angle_connect_table[i][2] == angle_connect_table[j][2]) or (angle_connect_table[i][1] == angle_connect_table[j][2] and angle_connect_table[i][2] == angle_connect_table[j][1]):
+                    
+                    candidate_dac_table = [angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2], angle_connect_table[j][0]]
+                    
+                    if bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[3]] == 1:# or bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[3]] == 1:
+                        dihedral_angle_connect_table.append(candidate_dac_table)
+                        continue
+                        
+                    candidate_dac_table = [angle_connect_table[j][0], angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2]]
+                    
+                    if bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[0]] == 1:# or bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[0]] == 1:
+                        dihedral_angle_connect_table.append(candidate_dac_table)   
+                        continue
+                        
+                
+                if (angle_connect_table[i][1] == angle_connect_table[j][1] and angle_connect_table[i][0] == angle_connect_table[j][0]) or (angle_connect_table[i][1] == angle_connect_table[j][0] and angle_connect_table[i][0] == angle_connect_table[j][1]):
+                    
+                    candidate_dac_table = [angle_connect_table[j][2], angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2]]
+                    if bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[0]] == 1:#bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[0]] == 1 or 
+                        dihedral_angle_connect_table.append(candidate_dac_table)            
+                        continue    
+                
+                    candidate_dac_table = [angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2], angle_connect_table[j][2]]
+                    
+                    if bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[3]] == 1:# or bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[3]] == 1:
+                        dihedral_angle_connect_table.append(candidate_dac_table)   
+                        continue
+                
+                if (angle_connect_table[i][1] == angle_connect_table[j][0] and angle_connect_table[i][2] == angle_connect_table[j][1]) or (angle_connect_table[i][1] == angle_connect_table[j][1] and angle_connect_table[i][2] == angle_connect_table[j][0]):
+                    
+                    candidate_dac_table = [angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2], angle_connect_table[j][2]]
+                    
+                    if bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[3]] == 1:# or bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[3]] == 1:
+                        dihedral_angle_connect_table.append(candidate_dac_table)   
+                        continue       
+                        
+                    candidate_dac_table = [angle_connect_table[j][2], angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2]]
+                    
+                    if bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[0]] == 1:#or bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[0]] == 1:
+                        dihedral_angle_connect_table.append(candidate_dac_table)     
+                        continue
+                
+                if (angle_connect_table[i][0] == angle_connect_table[j][1] and angle_connect_table[i][1] == angle_connect_table[j][2]) or (angle_connect_table[i][0] == angle_connect_table[j][2] and angle_connect_table[i][1] == angle_connect_table[j][1]):
+                  
+                    candidate_dac_table = [angle_connect_table[j][0], angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2]]
+                    if bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[0]] == 1:#or bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[0]] == 1:
+                        dihedral_angle_connect_table.append(candidate_dac_table)    
+                        continue
+                        
+                    candidate_dac_table = [angle_connect_table[i][0], angle_connect_table[i][1], angle_connect_table[i][2], angle_connect_table[j][0]]
+                    if bond_connect_matrix[candidate_dac_table[2]][candidate_dac_table[3]] == 1:# or bond_connect_matrix[candidate_dac_table[1]][candidate_dac_table[3]] == 1:
+                        dihedral_angle_connect_table.append(candidate_dac_table)              
+                        continue
+                
+        return dihedral_angle_connect_table
+    
+    def connectivity_table(self, coord, element_list):
+        b_C_mat = self.bond_connect_matrix(element_list, coord)
+        connectivity_table = [self.bond_connect_table(b_C_mat), self.angle_connect_table(b_C_mat), self.dihedral_angle_connect_table(b_C_mat)]
+        
+        return connectivity_table
+    
+
+def judge_shape_condition(geom_num_list, shape_condition_list):
+    finish_flag = None
+    if geom_num_list is None:
+        return False
+    elif len(shape_condition_list) % 3 != 0:
+        print("Error: shape_condition_list")
+        return True
+
+
+    for idx in range(int(len(shape_condition_list)/3)):
+        label = shape_condition_list[3*idx+2].split(",")
+        atom_num = len(label)
+        if atom_num == 2:
+            bond_length = float(shape_condition_list[3*idx])
+            condition = str(shape_condition_list[3*idx+1]) #gt or lt
+            print("bond condition: ", label, condition, bond_length)
+            vec_1 = geom_num_list[int(label[0])-1]
+            vec_2 = geom_num_list[int(label[1])-1]
+            current_bond_length = calc_bond_length_from_vec(vec_1, vec_2) * UnitValueLib().bohr2angstroms
+            if condition == "gt":
+                if current_bond_length > bond_length:
+                    finish_flag = False
+                else:
+                    finish_flag = True
+                    break
+            elif condition == "lt":
+                if current_bond_length < bond_length:
+                    finish_flag = False
+                else:
+                    finish_flag = True
+                    break
+            else:
+                print("Error: shape_condition_list")
+                return True
+        
+        elif atom_num == 3:
+            angle = float(shape_condition_list[3*idx])
+            condition = str(shape_condition_list[3*idx+1]) #gt or lt
+            print("angle condition: ", label, condition, angle)
+            vec_1 = geom_num_list[int(label[0])-1] - geom_num_list[int(label[1])-1]
+            vec_2 = geom_num_list[int(label[2])-1] - geom_num_list[int(label[1])-1]
+            current_angle = np.rad2deg(calc_angle_from_vec(vec_1, vec_2))
+
+            if condition == "gt":
+                if current_angle > angle:
+                    finish_flag = False
+                else:
+                    finish_flag = True
+                    break
+            elif condition == "lt":
+                if current_angle < angle:
+                    finish_flag = False
+                else:
+                    finish_flag = True
+                    break
+            else:
+                print("Error: shape_condition_list")
+                return True
+        
+        elif atom_num == 4:
+            dihedral_angle = float(shape_condition_list[3*idx])
+            condition = str(shape_condition_list[3*idx+1])
+            print("dihedral angle condition: ", label, condition, dihedral_angle)
+            vec_1 = geom_num_list[int(label[0])-1] - geom_num_list[int(label[1])-1]
+            vec_2 = geom_num_list[int(label[1])-1] - geom_num_list[int(label[2])-1]
+            vec_3 = geom_num_list[int(label[2])-1] - geom_num_list[int(label[3])-1]
+
+            current_dihedral_angle = np.rad2deg(calc_dihedral_angle_from_vec(vec_1, vec_2, vec_3))
+
+            if condition == "gt":
+                if current_dihedral_angle > dihedral_angle:
+                    finish_flag = False
+                else:
+                    finish_flag = True
+                    break
+            elif condition == "lt":
+                if current_dihedral_angle < dihedral_angle:
+                    finish_flag = False
+                else:
+                    finish_flag = True
+                    break
+            else:
+                print("Error: shape_condition_list")
+                return True
+
+        else:
+            print("Error: shape_condition_list")
+            return True
+
+    return finish_flag
+
+
+
+
+
+if __name__ == "__main__":#test
+    BC = BondConnectivity()
+    words = ["C     0.184130020000      1.253523500000      0.322496160000"
+            ,"H     0.649324370000      0.314864420000      0.540242210000"
+            ,"H     0.649339210000      1.534270620000      1.244266980000"
+            ,"H     0.540802860000      1.757921690000     -0.551155350000"
+            ,"H   -10.075869980000      1.253539030000      0.322496160000"
+            ,"H   -10.475869980000      1.253539030000      0.322496160000"
+            ,"C    -1.355869979883      1.253542481111      0.322496160000"
+            ,"F    -1.850403239571      2.449475576521     -0.063047840000"
+            ,"F    -1.850429465316      0.321694576682     -0.520435840000"
+            ,"F    -1.850421234650      0.989475576632      1.550971160000"]
+    elements = []
+    coord = []
+    for word in words:
+        splited_word = word.split()
+       
+        elements.append(splited_word[0])
+        coord.append(list(map(float, splited_word[1:4])))
+    
+    coord = np.array(coord)/0.52917721067 #Bohr
+    print(BC.distance_matrix(coord))
+    print(BC.bondlength_matrix(elements))
+    
+    b_c_mat = BC.bond_connect_matrix(elements, coord)
+    print(b_c_mat)
+    #print(BC.bond_connect_table(b_c_mat))
+    print(np.array(BC.bond_connect_table(b_c_mat), dtype=np.int32)+1)
+    #print(BC.angle_connect_table(b_c_mat))
+    print(np.array(BC.angle_connect_table(b_c_mat), dtype=np.int32)+1)
+    #print(BC.dihedral_angle_connect_table(b_c_mat))
+    print(np.array(BC.dihedral_angle_connect_table(b_c_mat), dtype=np.int32)+1)
+