OutOfPlaneSite¶
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class
simtk.openmm.openmm.OutOfPlaneSite(*args)¶ This is a VirtualSite that computes the particle location based on three other particles’ locations. If r<sub>1</sub> is the location of particle 1, r<sub>12</sub> is the vector from particle 1 to particle 2, and r<sub>13</sub> is the vector from particle 1 to particle 3, then the virtual site location is given by
r<sub>1</sub> + w<sub>12</sub>r<sub>12</sub> + w<sub>13</sub>r<sub>13</sub> + w<sub>cross</sub>(r<sub>12</sub> x r<sub>13</sub>)
The three weight factors are user-specified. This allows the virtual site location to be out of the plane of the three particles.
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__init__(self, particle1, particle2, particle3, weight12, weight13, weightCross) → OutOfPlaneSite¶ __init__(self, other) -> OutOfPlaneSite
Create a new OutOfPlaneSite virtual site.
Parameters: - particle1 (int) – the index of the first particle
- particle2 (int) – the index of the second particle
- particle3 (int) – the index of the third particle
- weight12 (double) – the weight factor for the vector from particle1 to particle2
- weight13 (double) – the weight factor for the vector from particle1 to particle3
- weightCross (double) – the weight factor for the cross product
Methods
__init__((self, particle1, particle2, ...)__init__(self, other) -> OutOfPlaneSite getNumParticles((self) -> int)Get the number of particles this virtual site depends on. getParticle((self, particle) -> int)Get the index of a particle this virtual site depends on. getWeight12((self) -> double)Get the weight factor for the vector from particle1 to particle2. getWeight13((self) -> double)Get the weight factor for the vector from particle1 to particle3. getWeightCross((self) -> double)Get the weight factor for the cross product. -
getWeight12(self) → double¶ Get the weight factor for the vector from particle1 to particle2.
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getWeight13(self) → double¶ Get the weight factor for the vector from particle1 to particle3.
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getWeightCross(self) → double¶ Get the weight factor for the cross product.
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__delattr__¶ x.__delattr__(‘name’) <==> del x.name
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__format__()¶ default object formatter
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__getattribute__¶ x.__getattribute__(‘name’) <==> x.name
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__hash__¶
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__reduce__()¶ helper for pickle
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__reduce_ex__()¶ helper for pickle
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__sizeof__() → int¶ size of object in memory, in bytes
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__str__¶
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getNumParticles(self) → int¶ Get the number of particles this virtual site depends on.
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getParticle(self, particle) → int¶ Get the index of a particle this virtual site depends on.
Parameters: particle (int) – the particle to get (between 0 and getNumParticles()) Returns: the index of the particle in the System Return type: int
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