| AngleBend |
Angle bending energy term class.
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| BadAtomTypeException |
The BadAtomTypeException is thrown when there is a bad atom type in a
molecule.
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| BadRingAromException |
The BadRingAromException is thrown when there is a problem with the MMFF
ring aromaticity assignment.
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| BondStretch |
Bond stretching energy term class.
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| Electrostatic |
Nonbonded electrostatic energy term class.
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| EnergyTerm |
Interface class for energy terms.
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| MMFFMolecule |
MMFF molecule is a wrapper class for the ExtendedMolecule.
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| OutOfPlane |
Out of plane energy term class.
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| RingBoolean |
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| Sdf.OnMolecule |
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| Searchable |
Interface that must be implemented for array objects that can be
searched by the binary search function.
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| Separation |
The Separation class is an efficient storage of an adjacency matrix
representing how many degrees of separation there are between any two
atoms.
|
| Separation.Relation |
Relation class shows the relationship between two atoms A1 and A2.
|
| SortedPair |
SortedPair class is used in the Separation table.
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| StretchBend |
Stretch bending energy term class.
|
| Tables |
A collection of tables with the official parameters of the
MMFF94/MMFF94s force field variants.
|
| TorsionAngle |
Torsional Angle energy term class.
|
| VanDerWaals |
Nonbonded van der Waals energy term class.
|
| Vector3 |
The Vector3 class provides common vector operations used throughout the
MMFF codebase.
|