OEPlaceHydrogensOptions

class OEPlaceHydrogensOptions : public OESystem::OEOptions

The OEPlaceHydrogensOptions class encapsulates properties and resources that determine how OEPlaceHydrogens functions.

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Constructors

OEPlaceHydrogensOptions(compatibleAlts: bool = False) -> OEPlaceHydrogensOptions
OEPlaceHydrogensOptions(rhs: OEPlaceHydrogensOptions) -> OEPlaceHydrogensOptions

Constructor and copy constructor. The optional parameter compatibleAlts controls how alternate location codes are interpreted by OEPlaceHydrogens.

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GetAddMetadata

GetAddMetadata() -> bool

Returns true if metadata describing the results will be added to the molecule. The metadata is the string generated by the OEPlaceHydrogensDetails.Describe method and can be accessed by the OEGetPlaceHydrogensMetadata function.

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GetAltsMustBeCompatible

GetAltsMustBeCompatible() -> bool

Returns true if alternate location codes are required to be compatible (either identical or blank) when atoms interact. If true, incompatible atoms do not interact.

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GetBadClashOverlapDistance

GetBadClashOverlapDistance() -> float

Returns the amount of excess van der Waals overlap considered to be a “bad” clash.

GetBypassPredicate

GetBypassPredicate() -> OEUnaryAtomPred

Returns a new copy of the predicate that OEPlaceHydrogens will use to exclude from analysis all movers having a matching atom.

(Default: OEIsFalseAtom)

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GetFlipBias

GetFlipBias() -> float

Returns the score bias against flipping a mover. The score bias is determined by the scoring system but can be controlled indirectly with the SetFlipBiasScale method.

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GetFlipBiasScale

GetFlipBiasScale() -> float

Returns the scaling factor for the score bias against flipping a mover. The actual score bias is determined by the scoring system.

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GetFlipPredicate

GetFlipPredicate() -> OEUnaryAtomPred

Returns a new copy of the predicate that OEPlaceHydrogens will use to restrain to the flipped state all flippable movers having a matching atom.

(Default: OEIsFalseAtom)

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GetMaxSubstateCutoff

GetMaxSubstateCutoff() -> float

Max number of substates processed in a single step of the state optimizer.

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GetNoFlipPredicate

GetNoFlipPredicate() -> OEUnaryAtomPred

Returns a new copy of the predicate that OEPlaceHydrogens will use to restrain to the original (unflipped) state all flippable movers having a matching atom.

(Default: OEIsFalseAtom)

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GetStandardizeBondLen

GetStandardizeBondLen() -> bool

Returns whether the length of bonds to hydrogen atoms are adjusted to standard size.

GetWaterProcessing

GetWaterProcessing() -> int

Returns a constant indicating how waters (and analogs) are processed.

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SetAddMetadata

SetAddMetadata() -> None

Controls whether metadata describing the results should be added to the molecule. The metadata is the string generated by the OEPlaceHydrogensDetails.Describe method and can be accessed by the OEGetPlaceHydrogensMetadata function.

(Default: true)

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SetAltsMustBeCompatible

SetAltsMustBeCompatible() -> None

Set if alternate location codes are required to be compatible (either identical or blank) for atoms to interact. If set to true, incompatible atoms will not interact.

The appropriate setting will depend on how alternate locations are prepared in the input molecule. If an OEAltLocationFactory was used to select the highest occupancy alternate locations, only one location remains for each atom so compatible should be false, it could prevent legitimate interactions. The same is true if alt information was stripped and only codes A and blank remain (the default behavior when a .pdb file is read with the default flavor).

If all location codes are retained on input with the ALTLOC flavor and not modified, then compatible should be true. This is not perfect, but generally works OK. But it is generally recommended that you read .pdb files using the ALTLOC flavor, process it with the OEAltLocationFactory, and leave compatible set to false when calling OEPlaceHydrogens.

(Default: false)

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SetBadClashOverlapDistance

SetBadClashOverlapDistance(value: float) -> bool

Sets the amount of excess van der Waals overlap considered to be a “bad” clash. (Default: 0.4 Å)

SetBypassPredicate

SetBypassPredicate(value: OEUnaryAtomPred) -> bool

Stores a predicate that OEPlaceHydrogens will use to exclude from analysis all movers having a matching atom. Useful for groups where a specific orientation has already been established.

Note

For any given mover, this predicate takes precedence over both the flip and the noFlip predicates.

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SetFlipBiasScale

SetFlipBiasScale(value: float) -> bool

Sets a scaling factor for the score bias against flipping a mover. The actual score bias is determined by the scoring system. Setting the bias to 0.0 will turn off any bias towards the input structure. (Default: 1.0)

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SetFlipPredicate

SetFlipPredicate(value: OEUnaryAtomPred) -> bool

Stores a predicate that OEPlaceHydrogens will use to restrain to the flipped state all flippable movers having a matching atom.

Note

For any given mover, if either the bypass predicate or the noFlip predicate matches, this predicate will be ignored.

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SetMaxSubstateCutoff

SetMaxSubstateCutoff(value: float) -> bool

Set the maximum number of substates processed in a single step of the state optimizer. (Default: 1.0e8)

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SetNoFlipPredicate

SetNoFlipPredicate(value: OEUnaryAtomPred) -> bool

Stores a predicate that OEPlaceHydrogens will use to restrain to the original (unflipped) state all flippable movers having a matching atom. Useful in preventing a group from being automatically flipped.

Note

For any given mover, if the bypass predicate matches, this predicate will be ignored. In addition, this predicate takes precedence over the flip predicate.

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SetStandardizeBondLen

SetStandardizeBondLen() -> None

Sets whether the length of bonds to hydrogen atoms are adjusted to standard size. (Default: true)

SetWaterProcessing

SetWaterProcessing(value: int) -> bool

Sets how waters (and analogs) are processed. (Default: OEPlaceHydrogensWaterProcessing_Default)

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