bmatrix

In this module the elements of the Wilson B-Matrix are calculated

bmatrix.B_Matrix_Entry_Angle_AtomA(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-Matrix entries for the in-plane angle bending coordinate (ABC) for Atom A

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_Angle_AtomB(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-Matrix entries for the in-plane angle bending coordinate (ABC) for Atom B

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_Angle_AtomC(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-Matrix entries for the in-plane angle bending coordinate (ABC) for Atom C

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_BondLength(Coordinates_AtomA, Coordinates_AtomB) → float

Calculates the B-Matrix entries for the bond stretching coordinate

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B

bmatrix.B_Matrix_Entry_LinearAngleFirstPlane_AtomA(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-matrix entries for the linear angle bending coordinate for atom A

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_LinearAngleFirstPlane_AtomB(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-matrix entries for the linear angle bending coordinate for atom B

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_LinearAngleFirstPlane_AtomC(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-matrix entries for the linear angle bending coordinate for atom C

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_LinearAngleSecondPlane_AtomA(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-matrix entries for the perpendicular plane in the linear case (atom C)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_LinearAngleSecondPlane_AtomB(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-matrix entries for the perpendicular plane in the linear case (atom B)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_LinearAngleSecondPlane_AtomC(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculates the B-matrix entries for the perpendicular plane in the linear case (atom C)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coordinates of atom A
Coordinates_AtomB:: a tuple of the x,y,z coordinates of atom B
Coordinates_AtomC:: a tuple of the x,y,z coordinates of atom C

bmatrix.B_Matrix_Entry_OutOfPlane_AtomA(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the out-of-plane coordinate (atom A)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.B_Matrix_Entry_OutOfPlane_AtomB(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the out-of-plane coordinate (atom B)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.B_Matrix_Entry_OutOfPlane_AtomC(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the out-of-plane coordinate (atom C)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.B_Matrix_Entry_OutOfPlane_AtomD(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the out-of-plane coordinate (atom D)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.B_Matrix_Entry_Torsion_AtomA(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the torsion coordinate (AtomA)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.B_Matrix_Entry_Torsion_AtomB(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the torsion coordinate (AtomB)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.B_Matrix_Entry_Torsion_AtomC(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the torsion coordinate (AtomB)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.B_Matrix_Entry_Torsion_AtomD(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculates the B-matrix elements for the torsion coordinate (AtomD)

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the x,y,z coords of atom C
Coordinates_AtomC:: a tuple of the x,y,z coords of atom D

bmatrix.b_matrix(atoms, bonds, angles, linear_angles, out_of_plane, dihedrals, idof) → array

Generates the Wilson B matrix and evaluates the elements using the functions defined in the script

Attributes:

atoms:: a object of the molecule class
bonds:: a list of tuples where each tuple is a bond (A,B)
angles:: a list of tuples where each tuple is a angle (A,B,C)
linear_angles:: a list of tuples where each tuple is a linear angle (A,B,C)
out_of_plane:: a list of tuples where each tuples is a out-of-plane angle (A,B,C,D)
dihedrals:: a list of tuples where each tuple is a dihedral angle (A,B,C,D)
idof:: the vibrational degrees of freedom of the molecule (int)

bmatrix.bond_angle(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC) → float

Calculate the bond angle between atom A, B and C using their coordinates

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomC:: a tuple of the coordinates of atom C

bmatrix.bond_length(Coordinates_AtomA, Coordinates_AtomB) → float

Calculates the bond_length using the euclidean norm between two coordinates

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom a
Coordinates_AtomB:: a tuple of the x,y,z coords of atom b

bmatrix.torsion_angle(Coordinates_AtomA, Coordinates_AtomB, Coordinates_AtomC, Coordinates_AtomD) → float

Calculate the torsion angle between atoms A,B,C and D. The dihedral angle is the angle between the two intersecting planes where a set of three atoms define a half-plane

Attributes:

Coordinates_AtomA:: a tuple of the x,y,z coords of atom A
Coordinates_AtomB:: a tuple of the x,y,z coords of atom B
Coordinates_AtomD:: a tuple of the x,y,z coords of atom C
Coordinates_AtomD:: a tuple of the x,y,z coords of atom D