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| ImplicitSolventRecipe (const ImplicitSolventKit< T > &isk, const NeckGeneralizedBornKit< T > &ngbk) |
| The constructor takes two abstracts / kits, from the AtomGraph and from an instantiation of the "neck" GB coefficient tables struct. The results are combined into a single struct, which is essentially a combined abstract but called a "recipe" to denote its status as a fusion of multiple abstracts.
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const int | natom |
| Number of atoms in the system.
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const ImplicitSolventModel | igb |
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const int | table_size |
| Size of the neck Generalized Born tables (if applicable)
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const T | dielectric |
| The dielectric constant to use in solvent screening.
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const T | kappa |
| Inverse of the Debye-Huckel length (based on the dielectic)
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const T | gb_offset |
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const T | gb_neckscale |
| Neck function scaling parameter for neck GB.
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const T | gb_neckcut |
| Cutoff for the "neck" GB function.
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const int * | neck_gb_idx |
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const T * | pb_radii |
| Poisson-Boltzmann (or Generalized Born) baseline radii.
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const T * | gb_screen |
| Generalized Born screening factors.
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const T * | gb_alpha |
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const T * | gb_beta |
| Generalized Born beta parameters.
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const T * | gb_gamma |
| Generalized Born gamma parameters.
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const T * | neck_max_sep |
| Neck GB maximum separations table.
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const T * | neck_max_val |
| Neck GB maximum values table.
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◆ ImplicitSolventRecipe()
The constructor takes two abstracts / kits, from the AtomGraph and from an instantiation of the "neck" GB coefficient tables struct. The results are combined into a single struct, which is essentially a combined abstract but called a "recipe" to denote its status as a fusion of multiple abstracts.
- Parameters
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◆ gb_alpha
Generalized Born alpha parameters (obtained from the designated model and atomic numbers / elements of each atom)
◆ gb_offset
Offset for baseline Generalized Born radii (default 0.9, larger for neck GB model II)
◆ igb
◆ neck_gb_idx
Neck GB indices for each atom (if applicable–not for all GB models)
The documentation for this struct was generated from the following file: