OEAlignmentOptions

class OEAlignmentOptions

This class represents OEAlignmentOptions and stores the following parameters which are used when performing molecule alignment.

Property	Get method	Set method
re-generating 2D coordinates	`GetClearCoords`	`SetClearCoords`
adding depiction hydrogens	`GetAddDepictionHydrogens`	`SetAddDepictionHydrogens`
starting from the 2D coords of the reference molecule	`GetFixedCoords`	`SetFixedCoords`
max number of allowed atom pair clushes	`GetMaxAllowedAtomPairClashes`	`SetMaxAllowedAtomPairClashes`
max number of bond rotations	`GetMaxBondRotations`	`SetMaxBondRotations`
max number of pattern matches	`GetMaxPatternMatches`	`SetMaxPatternMatches`
RMSD cutoff	`GetRMSDCutoff`	`SetRMSDCutoff`
rotation around bonds	`GetRotateAroundBonds`	`SetRotateAroundBonds`
suppressing hydrogens	`GetSuppressHydrogens`	`SetSuppressHydrogens`

See also

OEPrepareAlignedDepiction function

Constructors

OEAlignmentOptions() -> OEAlignmentOptions

Default constructor that initializes an OEAlignmentOptions object with the following properties:

Property	Default value
re-generating 2D coordinates	true
adding depiction hydrogens	true
starting from the 2D coordinates of the reference molecule	false
max number of allowed atom pair clushes	0 (means an alignment is rejected if there is any atom clash)
max number of bond rotations	\(2^{16} = 65536\) (max allowed number is \(2^{31}\))
max number of pattern matches	0 (means no limit)
RMSD cutoff	0.1
rotation around bonds	true
suppressing hydrogens	true

OEAlignmentOptions(rotateBonds: bool, clearcoords: bool,
                   suppressH: bool) -> OEAlignmentOptions

Creates an OEAlignmentOptions object with the specified parameters.

rotatebonds: See the OEAlignmentOptions.SetRotateAroundBonds method.
clearcoords: See the OEAlignmentOptions.SetClearCoords method.
suppressH: See the OEAlignmentOptions.SetSuppressHydrogens method.

By default, the RMSD cutoff is 0.1 (see the OEAlignmentOptions.SetRMSDCutoff method) and maximum number of bond rotations is \(2^{16} = 65536\) (see the OEAlignmentOptions.SetMaxBondRotations method).

OEAlignmentOptions(arg2: OEAlignmentOptions) -> OEAlignmentOptions

Copy constructor.

GetAddDepictionHydrogens

GetAddDepictionHydrogens() -> bool

Returns whether the depiction hydrogens are kept/added during the molecule alignment.

See also

OEAlignmentOptions.SetAddDepictionHydrogens method

GetClearCoords

GetClearCoords() -> bool

Returns whether the 2D coordinates of the fit molecule will be re-calculated prior to the alignment process.

See also

OEDepictCoordinates function
OEAlignmentOptions.SetClearCoords method

GetFixedCoords

GetFixedCoords() -> bool

Returns whether the OEPrepareAlignedDepiction function can start the alignment process by copying over the coordinates of the reference molecule to the fit molecule.

See also

OEAlignmentOptions.SetFixedCoords method

GetMaxAllowedAtomPairClashes

GetMaxAllowedAtomPairClashes() -> int

Returns the maximum number of atom pair clashes allowed in fix coordinate mode.

See also

OEAlignmentOptions.SetMaxAllowedAtomPairClashes method

GetMaxBondRotations

GetMaxBondRotations() -> int

Returns the maximum number of bond rotations performed during the alignment process.

The default value for maximum number of bond rotations is \(2^{16} = 65536\). This means that by default only the first 16 single bonds of the fit molecule will be rotated to maximize molecule alignment. The max allowed number is \(2^{31}\) that allows the rotate 31 bonds independently to find the best alignment.

See also

OEAlignmentOptions.SetMaxBondRotations method

GetMaxPatternMatches

GetMaxPatternMatches() -> int

Returns the maximum number of matches utilized to performed molecule alignments.

See also

OEAlignmentOptions.SetMaxPatternMatches method

GetRMSDCutoff

GetRMSDCutoff() -> float

Returns the RMSD cutoff value used to identify acceptable alignments.

See also

OEAlignmentOptions.SetRMSDCutoff method

GetRotateAroundBonds

GetRotateAroundBonds() -> bool

Returns whether rotation around the bonds of the fit molecule is allowed.

See also

OEAlignmentOptions.SetRotateAroundBonds method

GetSuppressHydrogens

GetSuppressHydrogens() -> bool

Returns whether the explicit hydrogens are suppressed in the fit molecule prior to the alignment process.

See also

OEAlignmentOptions.SetSuppressHydrogens method

SetAddDepictionHydrogens

SetAddDepictionHydrogens(a: bool) -> None

Sets whether depiction hydrogens are kept/added during alignment.

See also

OEAddDepictionHydrogens function
OEPrepareDepictionOptions.GetAddDepictionHydrogens method

SetClearCoords

SetClearCoords(c: bool) -> None

Sets whether the 2D coordinates of the fit molecule will be re-calculated prior to the alignment process by calling the OEPrepareDepiction function.

See also

OEDepictCoordinates function
OEAlignmentOptions.GetClearCoords method

SetFixedCoords

SetFixedCoords(f: bool) -> None

Sets whether the OEPrepareAlignedDepiction function can start the alignment process by copying over the coordinates of the reference molecule to the fit molecule based on the provided match.

If the alignment process based of ‘fixed’ coordinates can not be performed or it is unsuccessful i.e. no alignment is found without atom clashes than the OEPrepareAlignedDepiction function falls back to maximizing the overlap between the fit and the reference 2D molecules by rotating around single bonds. See also OEAlignmentOptions.SetMaxAllowedAtomPairClashes method that can be used to allow some atom clashes.

The alignment process based on ‘fixed’ coordinates currently can only be performed if:

neither the reference nor the fit molecule have more than one component
there is no partial ring match i.e. if a ring atom of the fit molecule is matched for alignment than all of the atom of the same ring systems have to be matched for alignment

See also

OEAlignmentOptions.GetFixedCoords method

SetMaxAllowedAtomPairClashes

SetMaxAllowedAtomPairClashes(m: int) -> None

Sets the number of atom pair clashes allowed after the ‘fixed’ coordinates alignment process (see OEAlignmentOptions.SetFixedCoords method). The default value is 0, i.e. no atom clashes are allowed. If the number of clashes exceeds this limit the alignment is rejected and process falls back to maximizing the overlap between the fit and the reference 2D molecules by rotating around single bonds.

See also

OEAlignmentOptions.SetMaxAllowedAtomPairClashes method

SetMaxBondRotations

SetMaxBondRotations(m: int) -> None

Sets the maximum number of bond rotations performed during the alignment process.

maxrotations: The zero value means that there is no limit. Upon reaching this limit, the alignment process terminates and returns the best alignment identified up to that point.

Hint

The default value for maximum number of bond rotations is \(2^{16} = 65536\). This means that by default only the first 16 single bonds of the fit molecule will be rotated to maximize molecule alignment.

It is recommended to use this parameter in the following cases:

if the fit molecule being aligned has a large number of rotatable bonds
if the match that determines the atoms of the fit molecule that will be aligned to the atoms of the reference molecule has a large number of rotatable bonds

See also

OEAlignmentOptions.GetMaxBondRotations method

SetMaxPatternMatches

SetMaxPatternMatches(m: int) -> None

Sets the maximum number of matches utilized to perform molecule alignments.

maxmatches: The zero value means that there is no limit. If the molecule alignment is based on more than one matches, then upon reaching this limit, the alignment process terminates and returns the best alignment identified up to that point.

Hint

It is recommended to use this parameter in the following cases:

if the alignment is based on substructure or maximum common substructure matches and the reference or/and fit molecules are highly symmetrical i.e. a large number of matches returned by the substructure or maximum common substructure search algorithms, respectively.

See also

OEAlignmentOptions.GetMaxPatternMatches method

SetRMSDCutoff

SetRMSDCutoff(r: float) -> None

Sets the RMSD cutoff value used to identify acceptable alignments.

rmsdcutoff: This number has to be non-negative number. The alignment procedure terminates when the rmsdcutoff between the fit and the reference molecule is below this limit and there is no internal clash detected between the atoms of the fit molecule.

See also

OEAlignmentOptions.GetRMSDCutoff method

SetRotateAroundBonds

SetRotateAroundBonds(r: bool) -> None

Sets whether rotation around the bonds of the fit molecule is allowed.

rotatebonds: If ‘true’, then bond of the fit molecule will be rotated to find the best alignment between molecules. If ‘false’, then only 2D rotation and translation of the fit molecule is allowed (i.e. no rotations around bonds) in order to align it to the reference molecule

See also

OEAlignmentOptions.GetRotateAroundBonds method

SetSuppressHydrogens

SetSuppressHydrogens(s: bool) -> None

Sets whether the explicit hydrogens are suppressed in the fit molecule prior to the alignment process. Only hydrogens that are necessary to faithfully represent tetrahedral stereochemistry will be kept.

See also

OEAddDepictionHydrogens function
OEHasDepictionHydrogens function
OEAlignmentOptions.GetSuppressHydrogens method