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The
MakeLine
module provides functions to generate the coordinates
of lines.
The
MakeLine
module is located in Yup.Tools. Thus, the required
import statement is some variant of:
from
Yup.Tools.MakeLine import
*.
Currently,
there is a function to generate a line with a
specified distribution of spacing between the
points, angles spanned by three successive points
and torsion angle spanned by four successive
points. There a another function that can generate
a line with a desired average span, angle and
torsion distribution with specified standard
deviations.
The
fixedline()
function creates a line with a specified
distribution of spacings, angles and
torsions.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
fixedline
|
4
|
tuple
of tuple
|
|
Argument
|
Type
|
Preset
Value
|
|
spacings
|
list
of floats
|
-
|
|
angles
|
list
of floats
|
-
|
|
torsions
|
list
of floats
|
-
|
|
recenter
|
integer
|
0
|
The
spacings argument must contain a list of
distances between successive points in the
line.
The
angles argument must contain a list of
angles [radians] between a succession of three points in the
line. The angle for three atoms 1-2-3 is between
the line segments 1-2 and 2-3. Thus, it is 0
radian (0 degrees) for a straight line segment. The first angle in the list will not be used.
The
torsions argument contains a list of
torsional angles [radians] between a succession of four
points in the line. This can be applied only if the
four atoms are not in a plane. The first and second torsion angles will not be used.
Although the leading angles and torsions are not used, the three lists must be of equal
length. Angular measures must be given in radians.
The
recenter argument is set to 0 (the default)
if the generated coordinates are not modified in
any way. Set to any value other than zero, to
recenter the coordinates on the origin.
The
returned tuple contains the coordinate tuples (of
three floats) of the generated line. There will be one more point than the number of spacings
provided.
The
randomline()
function returns the coordinates of a randomly
generated line.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
randomline
|
8
|
tuple
of tuple
|
|
Argument
|
Type
|
Preset
Value
|
|
numpoints
|
integer
|
-
|
|
spacing
|
float
|
-
|
|
ds
|
float
|
0.0
|
|
angle
|
float
|
0.0
|
|
da
|
float
|
0.0
|
|
torsion
|
float
|
0.0
|
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dt
|
float
|
0.0
|
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recenter
|
integer
|
0
|
The
numpoints argument specifies the number of
points in the desired line. The number of line
segments is one less than this number.
This
spacing argument specifies the average
spacing between successive points.
The
ds argument specifies the standard deviation
in the spacings between successive
points.
The
angle argument specifies the average angle
spanned by three successive points of the line. A
straight line segment has an angle of 0.0
degrees.
The
da argument specifies the standard deviation
in the angle spanned by three successive points of
the generated line.
The
torsion argument specifies the average
torsional angle spanned by four successive points
of the line.
The
dt argument specifies the standard deviation
of the torsional angles spanned by four successive
points of the generated line.
The
recenter argument specifies whether the
generated coordinates are to be recentered at the
origin or not.
This
function first generates the spacings, angles and
torsion to the specified statistics, then calls
fixedline() to actually generate the
coordinates.
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