Currently, the AtomVect module defines ten functions. Two functions are documented on other pages. The AtomVector() function is used to create a new Atom Vector (AV). This is documented on the [New] page. The MapAndVector() function is used to create a new Atom Map and Atom Vector from an Atom Vector file (AVF). This is documented on the [Files] page. This page documents these eight functions: Angle Distance DotPerAtom DotProduct Extract Torsion Reduction TransMatrix DotProduct The DotProduct() function takes two AV arguments, and forms the scalar product of the two vectors and returns the scalar value. Function Name Number of Arguments Return Type Return Value DotProduct 2 Python float the scalar product Keyword Argument Value Preset Value - required the first AV - - required the second AV - The AVs must be conformal, but may otherwise be of any variant. Example: >>> from Yup.Taro.AtomVect import * >>> A = AtomVector( numatom=2, sample='UNIFORM' ) >>> B = AtomVector( numatom=2, sample='GAUSSIAN' ) >>> A AtomVector[2:3] { -0.0277413 0.648549 0.382733 -0.0690634 -0.89526 0.656545 } >>> B AtomVector[2:3] { -0.402081 1.03964 1.3343 1.02185 -0.919675 -0.921506 } >>> DotProduct( A, B ) 1.3438602284342707 >>> Page Index DotPerAtom The DotPerAtom() function takes two AV arguments, and forms the scalar product for each atom, across the dimension axis. The result is an AV with one dimension and the same number of atoms as the AVs in the argument list. The vector equivalent is the vector product operator. Function Name Number of Arguments Return Type Return Value DotPerAtom 2 AtomVector the scalar product for each atom Keyword Argument Value Preset Value - required the first AV - - required the second AV - The AVs must be conformal. The dimension axis may be of any length. This is quite different from the Vector product operator where the number of dimensions must be exactly three. This example is a follow-on to the previous one: >>> DotPerAtom( A, B ) AtomVector[2:1] { 1.19609 0.147766 } >>> Note that the result is an AV which is printed since it is not assigned to a variable. Page Index Reduction The Reduction() function takes the AV specified in the first argument and returns a new AV which is the reduction of the first AV in the dimension specified in the second argument. Function Name Number of Arguments Return Type Return Value Reduction 2 AtomVector the reduced AV Keyword Argument Value Preset Value - required the AV to be reduced - - required the dimension to be reduced - The dimension to be reduced must be 0 (the atoms axis) or 1 (the dimension axis) only. No other value is acceptable. The reduction is the sum of the items of the axis that is to be reduced. Continuing with the example: >>> Reduction( A, 0 ) AtomVector[1:3] { -0.0968047 -0.246712 1.03928 } >>> Reduction( B, 1 ) AtomVector[2:1] { 1.97186 -0.81933 } >>> Reduction( DotPerAtom( A, B ), 0 ) AtomVector[1:1] { 1.34386 } >>> Note the last example, and compare with the last result in the first example. Page Index Extract The Extract() function takes the AV specified in the first argument and returns an extract (slice) of it. The source AV must be Entire but can be Anonymous. The extract is from the atom number specified in the second argument to the atom number one less than the number specified in the optional last argument. If the last argument is not provided, a one-atom extract will be returned. The normal way of obtaining an extract AV is by subscripting with an atom map as key. This function provides for the cases when subscripting is not possible or convenient. Function Name Number of Arguments Return Type Return Value Extract 3 AtomVector the extract AV Keyword Argument Value Preset Value - required the source AV - - required first atom number of the extract - - optional one more than the last atom number of the extract - If the last argument is not specified, it is assumed to be one more than the number specified in the second argument. In other words, Extract( A, i ) is a one-atom slice of Atom Vector A at atom-i; this is equivalent to Extract( A, i, i + 1 ). Whether the source AV is mapped or anonymous, the resulting extract is always anonymous. Page Index TransMatrix The TransMatrix() function returns a tuple containing the first 12 elements of the transformation matrix that correspond to the three rotation angles and three displacements that are supplied. This function uses the same subroutine as the transform() method. Function Name Number of Arguments Return Type Return Value TransMatrix 2 tuple of doubles the transformation matrix Keyword Argument Value Preset Value - required tuple of three floating point values (radians) - - optional tuple of three floating point values (Angstroms) ( 0.0, 0.0, 0.0 ) The values of the first argument are checked. The values must be between minus and plus PI. This function does not yield the last row of the transformation matrix which is always [0 0 0 1]. At this time, the rotation is carried out in a left handed coordinate frame. First, a rotation about the Z-axis by the angle specified in the first argument. Then about the new Y-axis by the angle supplied in the second argument. The final rotation is about the twice rotated Z-axis by the angle supplied in the third argument. The translations are to be carried last, by the amounts supplied in the last three arguments. The specifics of the rotation are not important. If these operations are changed in the future, the transformation matrix obtained from this function will still be correct. Page Index Distance The Distance() function takes two AV arguments, and returns the distance (Angstroms) between the atoms represented by the AVs. Function Name Number of Arguments Return Type Return Value Distance 2 Python float the distance in Angstroms Keyword Argument Value Preset Value - required the first AtomVector - - required the second AtomVector - The AVs may be of any dimensions but both AVs must be of the same dimension. Each AV should be for only one atom (it may be an Extract for example). The calculation of the distance will use only the coordinates of the first atom of each AV. Page Index Angle The Angle() function takes three AV arguments, and the angle (degrees) formed by the atoms represented by the AVs will be returned. The second AV is that of the vertex atom. Function Name Number of Arguments Return Type Return Value Angle 3 Python float the angle in degrees Keyword Argument Value Preset Value - required the first AtomVector - - required the second AtomVector (vertex atom) - - required the third AtomVector - The AVs may be of any dimensions but all AVs must be of the same dimension. Each AV should be for only one atom (it may be an Extract). The calculation of the angle will use only the coordinates of the first atom of each AV. Page Index Torsion The Torsion() function takes four AV arguments, and the torsion angle (degrees) formed by the atoms represented by the AVs will be returned. The torsional angle is about a line through the atoms represented by the second and third AVs. Function Name Number of Arguments Return Type Return Value Torsion 4 Python float the torsion angle in degrees Keyword Argument Value Preset Value - required the first AtomVector - - required the second AtomVector - - required the third AtomVector - - required the fourth AtomVector - All the AVs must have exactly three dimensions. Each AV should be for only one atom (it may be an Extract). The calculation of the torsional angle will use only the coordinates of the first atom of each AV. Page Index Intro New Print Compare Operators Data Methods Functions Subscript Files