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Bond geometry utilities
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Imported modules
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from chimera import distance, cross, Point, Vector, Xform_zAlign, Xform_lookAt, Xform_yRotation
from math import pi, sin, cos
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Functions
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anglePos
bondPositions
linearPos
planarPos
rightAngle
singlePos
tetraPos
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anglePos
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anglePos (
atomPos,
bondPos,
bondLength,
degrees,
coplanar=None,
)
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Exceptions
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ValueError, "More than 2 coplanar positions specified!"
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bondPositions
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bondPositions (
bondee,
geom,
bondLen,
bonded,
coPlanar=None,
toward=None,
away=None,
toward2=None,
away2=None,
)
Return a list of possible bond partner positions for bondee that
satisfy geometry geom and are of length bondLen. bonded are
positions of already-bonded substituents to bondee.
bondee is a Point and bonded is a list of Points. The return
value is a list of Points.
For planar geometries, coPlanar can be a list of one or two
points that the bond positions should be coplanar with.
For rotamers, if toward is specified then one bond position of
the rotamer will be as close as possible to the toward point.
Conversely, if away is specified, then all bond positions will
be as far as possible from the away point. toward has
precedence over away. If this doesn't completely determine
the bond positions (i.e. no initial bonded substituents), then
toward2 and away2 will be considered in a similar manner to
determine the remaining positions.
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Exceptions
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ValueError, "Cannot specify both toward and away," " or both toward2 and away2"
ValueError, "Unknown geometry type '%s'" % geom
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linearPos
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linearPos (
bondee,
bonded,
bondLen,
toward=None,
away=None,
)
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planarPos
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planarPos (
bondee,
bonded,
bondLen,
coPlanar=None,
toward=None,
away=None,
toward2=None,
away2=None,
)
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rightAngle
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rightAngle ( orig )
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singlePos
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singlePos (
bondee,
bondLen,
toward=None,
away=None,
)
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tetraPos
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tetraPos (
bondee,
bonded,
bondLen,
toward=None,
away=None,
toward2=None,
away2=None,
)
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