OEOFlavor

The OEOFlavor namespace encodes symbolic constants used as bit-masks to indicate how to read various file formats by OEChem.

The OEOFlavor.Generic namespace within OEOFlavor defines control bit-masks that are common to all of the output formats. Although these generic bits are common to all file formats, they may be specified independently for each file format.

See also

The interpretation of many of these flavor values, is identical to those passed to the corresponding OEChem low-level file format writers.

This namespace contains the following namespaces:

OEOFlavor::CAN

The OEOFlavor.CAN namespace encodes symbolic constants used as bit-masks that control the processing performed by the OECreateSmiString function when writing a molecule into a OEFormat.CAN format file.

Note

If no aromaticity model is specified for the OEOFlavor.Generic namespace for this file format, then the OpenEye model is used by default to perceive aromaticity by the OEWriteMolecule high-level writer.

This namespace contains the following constants:

AtomMaps

Corresponds to the OESMILESFlag.AtomMaps constant.

AtomStereo

Corresponds to the OESMILESFlag.AtomStereo constant.

BondStereo

Corresponds to the OESMILESFlag.BondStereo constant.

Canonical

Corresponds to the OESMILESFlag.Canonical constant.

DEFAULT

Same as the OEOFlavor.CAN.Default constant.

Default

Combination of OEOFlavor.CAN.AtomMaps, OEOFlavor.CAN.Canonical and OEOFlavor.CAN.RGroups flags.

ExtBonds

Corresponds to the OESMILESFlag.ExtBonds constant.

Hydrogens

Corresponds to the OESMILESFlag.Hydrogens constant.

ImpHCount

Corresponds to the OESMILESFlag.ImpHCount constant.

Isotopes

Corresponds to the OESMILESFlag.Isotopes constant.

Kekule

Corresponds to the OESMILESFlag.Kekule constant.

RGroups

Corresponds to the OESMILESFlag.RGroups constant.

SmiMask

SuperAtoms

Corresponds to the OESMILESFlag.SuperAtoms constant.

OEOFlavor::CDX

Note

If no aromaticity model is specified for the OEOFlavor.Generic namespace for this file format, then the OpenEye model is used by default to perceive aromaticity by the OEWriteMolecule high-level writer.

This namespace contains the following constants:

Add2D

This flag indicates that 2D coordinates are generated prior to writing a molecule by the OEWriteMolecule high-level writer. If the molecule already has 2D coordinates then these coordinates are left intact. In certain cases the 2D layout may result in incorrect stereochemistry in the resulting connection table. In these cases no coordinates are generated.

UnsetBad2DStereo

This flag is used with the Add2D constant. In certain cases the 2D layout may result in incorrect stereochemistry in the output connection table format. When this flag is set the writer will output the generated coordinates and set the stereochemistry of the offending stereocenters to ‘Undefined’.

Default

Same as the OEOFlavor.CDX.Add2D constant.

OEOFlavor::CSV

This namespace contains constants for modifying the behavior of how the OEFormat.CSV file format is written.

See also

CSV File Format

Header

This flag indicates whether the first line in the .csv should contain the column names for the file. Column names are determined by the SD data present on the first molecule written to the oemolostream, regardless of whether this flag is set. The column names are retrievable through the oemolstreambase.GetCSVHeader method on the OECSVHeader object.

If this flag is not set, the first line of the output .csv file will be the first molecule record.

Default

Set to include OEOFlavor.CSV.Header to automatically write the column names as the first line in the file.

DEFAULT

Synonym for OEOFlavor.CSV.Default.

OEOFlavor::FASTA

This namespace contains the following constants:

Default

OEOFlavor::Generic

This namespace contains the following constants:

OEAroModelDaylight

This flag indicates that the Daylight aromaticity model is used to perceive aromaticity by the OEWriteMolecule high-level writer.

OEAroModelOpenEye

This flag indicates that the OpenEye aromaticity model is used to perceive aromaticity by the OEWriteMolecule high-level writer.

OEAroModelTripos

This flag indicates that the Tripos aromaticity model is used to perceive aromaticity by the OEWriteMolecule high-level writer.

OEAroModelMMFF

This flag indicates that the MMFF aromaticity model is used to perceive aromaticity by the OEWriteMolecule high-level writer.

OEAroModelMDL

This flag indicates that the MDL aromaticity model is used to perceive aromaticity by the OEWriteMolecule high-level writer.

AroMask

Combination of OEOFlavor.Generic.OEAroModelDaylight, OEOFlavor.Generic.OEAroModelOpenEye, OEOFlavor.Generic.OEAroModelTripos, OEOFlavor.Generic.OEAroModelMMFF and OEOFlavor.Generic.OEAroModelMDL flags.

Rings

This flag indicates the rings are (re)perceived by the OEWriteMolecule high-level reader by calling the OEFindRingAtomsAndBonds function.

GenericMask

Combination of OEIFlavor.Generic.AroMask and OEIFlavor.Generic.Rings flags.

SpecificMask

DEFAULT

Default

Same as the OEOFlavor.Generic.DEFAULT constant.

OEOFlavor::INCHI

The OEOFlavor.INCHI namespace encodes symbolic constants used as bit-masks that control the processing performed by the OECreateInChI function when writing a molecule into the OEFormat.INCHI format file. These constants translate into InChI library options documented in the InChI API Reference documentation.

This namespace contains the following constants:

Chiral

Corresponds to the ChiralFlagOn InChI option.

Default

Equal to OEOFlavor.INCHI.Stereo.

FixedHLayer

Corresponds to the FixedH InChI option.

Hydrogens

Corresponds to the inverse of the DoNotAddH InChI option.

ReconnectedMetals

Corresponds to the RecMet InChI option.

Stereo

Corresponds to the inverse of the SNon InChI option.

OEOFlavor::INCHIKEY

The OEOFlavor.INCHIKEY namespace encodes symbolic constants used as bit-masks that control the processing performed by the OECreateInChIKey function when writing a molecule into a OEFormat.INCHIKEY format file. These constants translate into InChI library options documented in the InChI API Reference documentation.

This namespace contains the following constants:

Chiral

Corresponds to the ChiralFlagOn InChI option.

Default

Equal to OEOFlavor.INCHI.Stereo.

FixedHLayer

Corresponds to the FixedH InChI option.

Hydrogens

Corresponds to the inverse of the DoNotAddH InChI option.

ReconnectedMetals

Corresponds to the RecMet InChI option.

Stereo

Corresponds to the inverse of the SNon InChI option.

OEOFlavor::ISM

The OEOFlavor.ISM namespace encodes symbolic constants used as bit-masks that control the processing performed by the OECreateSmiString function when writing a molecule into a OEFormat.ISM format file.

Note

If no aromaticity model is specified for the OEOFlavor.Generic namespace for this file format, then the OpenEye model is used by default to perceive aromaticity by the OEWriteMolecule high-level writer.

This namespace contains the following constants:

AtomMaps

Corresponds to the OESMILESFlag.AtomMaps constant.

AtomStereo

Corresponds to the OESMILESFlag.AtomStereo constant.

BondStereo

Corresponds to the OESMILESFlag.BondStereo constant.

Canonical

Corresponds to the OESMILESFlag.Canonical constant.

DEFAULT

Same as the OEOFlavor.ISM.Default constant.

Default

Combination of OEOFlavor.ISM.AtomMaps, OEOFlavor.ISM.AtomStereo, OEOFlavor.ISM.BondStereo, OEOFlavor.ISM.Canonical, OEOFlavor.ISM.Isotopes and OEOFlavor.ISM.RGroups flags.

ExtBonds

Corresponds to the OESMILESFlag.ExtBonds constant.

Hydrogens

Corresponds to the OESMILESFlag.Hydrogens constant.

ImpHCount

Corresponds to the OESMILESFlag.ImpHCount constant.

Isotopes

Corresponds to the OESMILESFlag.Isotopes constant.

Kekule

Corresponds to the OESMILESFlag.Kekule constant.

RGroups

Corresponds to the OESMILESFlag.RGroups constant.

SmiMask

SuperAtoms

Corresponds to the OESMILESFlag.SuperAtoms constant.

OEOFlavor::MDL

The OEOFlavor.MDL namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEWriteMDLFile and the OEWriteMolecule functions when writing a molecule into a OEFormat.MDL format file.

This namespace contains the following constants:

Add2D

This flag indicates that if a molecule has no coordinates, then 2D coordinates are generated prior to writing a molecule by the OEWriteMolecule high-level writer. If the molecule already has 2D or 3D coordinates then these coordinates are left intact. In certain cases the 2D layout may result in incorrect stereochemistry in the resulting connection table. In these cases no coordinates are generated.

UnsetBad2DStereo

This flag is used with the Add2D constant. In certain cases the 2D layout may result in incorrect stereochemistry in the output connection table format. When this flag is set the writer will output the generated coordinates and set the stereochemistry of the offending stereocenters to ‘Undefined’.

MCHG

The OEOFlavor.MDL.MCHG flag is used to instruct the MDL mol file writer to write M CHG and M RAD lines for charged/radical atoms in the output connection table, even if the charge and radical values of every atom are within the ranges representable by the MDL atom block. By default, M CHG and M RAD lines are only used for connection tables that ‘overflow’ the allowed atom block limits.

MISO

The OEOFlavor.MDL.MISO flag is used to instruct the OEChem MDL mol file writer to write M ISO lines for isotopes in the output connection table, even if the isotopic masses of every atom are within the range representable by the MDL atom block. By default, M ISO lines are only used for connection tables that ‘overflow’ the allowed atom block limits.

MRGP

The OEOFlavor.MDL.MRGP flag is used to instruct the OEChem MDL mol file writer to write out M RGP entries for each R-group atom, i.e. atom with element zero and a non-zero atom map index. These atoms are always written with atomic symbol R#.

MV30

Force every molecule to be written in V3000 format. By default, only molecules with more than 999 atoms or enhanced stereo groups will be written in V3000 format.

MDLParity

If this flag is set and OEMDLHasParity returns false ,then OEMDLPerceiveParity function is called to perceive the MDL atom stereo parity fields.

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWriteMDLFile.

NoParity

If this flag is set, then the MDL atom stereo parity fields are left intact.

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWriteMDLFile.

CurrentParity

If this flag is set, then OEMDLClearParity function is called to set all MDL atom stereo parity fields to zero.

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWriteMDLFile.

MMask

PMask

Combination of OEOFlavor.MDL.MDLParity, OEOFlavor.MDL.NoParity and OEOFlavor.MDL.CurrentParity flags. The flag controls the processing of the MDL stereo parity bit field of each atom.

DEFAULT

Combination of OEOFlavor.MDL.Add2D, OEOFlavor.MDL.MDLParity, OEOFlavor.MDL.MRGP, OEOFlavor.MDL.MISO and OEOFlavor.MDL.MCHG flags.

Default

Same as the OEOFlavor.MDL.DEFAULT constant.

OEOFlavor::MF

The OEOFlavor.MF namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEWriteMolecule functions when writing a molecule into a OEFormat.MF format file.

This namespace contains the following constants:

Title

If this flag is set, then the molecule’s title (returned by OEMolBase.GetTitle method) is written to the output file.

DEFAULT

Same as the OEOFlavor.MF.Title constant.

Default

Same as the OEOFlavor.MF.DEFAULT constant.

OEOFlavor::MMOD

This namespace contains following constants:

AtomTypes

DEFAULT

Default

Same as the OEOFlavor.MMOD.DEFAULT constant.

OEOFlavor::MOL2

Note

Except for MOL2 Flavor Forcefield, if no aromaticity model is specified for the OEOFlavor.Generic namespace for this file format, then the Tripos model is used by default to perceive aromaticity by the OEWriteMolecule high-level writer.

This namespace contains the following constant:

AtomNames

AtomTypeNames

BondTypeNames

ChargePrecision

This flavour allows for increased precision of partial charges by writing them out to 5 decimal places.

Forcefield

Combination of OEOFlavor.MOL2.GeneralFFFormat, OEOFlavor.MOL2.ChargePrecision, and OEOFlavor.MOL2.BondTypeNames flags

This variant of MOL2 reflects a common use of MOL2 format to embody information for a general forcefield. It combines the OEOFlavor.MOL2.GeneralFFFormat so that atom names, atom types, and atom ordering are written out “as is” based on the input molecule, and OEOFlavor.MOL2.ChargePrecision, which writes out atomic partial charges to 5 decimal places. Mol2 OEOFlavor.MOL2.BondTypeNames are retained from the Tripos standard at this point because they are generally reasonable and historically they don’t conflict with the other needs of general forcefield format.

GeneralFFFormat

This variant of MOL2 is commonly used for carrying information for force fields more general than the Tripos forcefield (the MOL2 standard). Here the atom names, atom types, and atom ordering are retained from the input molecule, rather than being changed to comply with the Tripos MOL2 standard. If an atom does not have a user-defined atom name and atom type for all atoms, warnings will be given and no molecule will be written.

Hydrogens

OrderAtoms

Substructure

NameMask

AllMask

DEFAULT

Default

Same as the OEOFlavor.MOL2.DEFAULT constant.

OEOFlavor::MOL2H

Note

If no aromaticity model is specified for the OEOFlavor.Generic namespace for this file format, then the Tripos model is used by default to perceive aromaticity by the OEWriteMolecule high-level writer.

This namespace contains the following constants:

AtomTypeNames

BondTypeNames

AtomNames

OrderAtoms

Hydrogens

Substructure

NameMask

AllMask

DEFAULT

Default

Same as the OEOFlavor.MOL2H.DEFAULT constant.

OEOFlavor::MOPAC

This namespace contains the following constants:

XYZ

CHARGES

AllMask

DEFAULT

Default

Same as the OEOFlavor.MOPAC.DEFAULT constant.

OEOFlavor::OEB

This namespace contains the following constants:

Default

OEOFlavor::PDB

The OEOFlavor.PDB namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEWritePDBFile and the OEWriteMolecule functions when writing a molecule into a OEFormat.PDB format file.

This namespace contains the following constants:

BONDS

Controls whether the OEChem PDB file writer includes CONECT records to describe the connectivity of the molecule. If this flag is given without OEOFlavor.PDB.ORDERS all bonds are written as ‘single’ bonds. OEOFlavor.PDB.BONDS is off by default.

ORDERS

Controls whether the PDB file writer should use repeated CONECT records to represent multiple bond orders (i.e. double and triple bonds). If this flag is given without OEOFlavor.PDB.BONDS only double and triple bonds are written to the file. OEOFlavor.PDB.ORDERS is off by default.

BOTH

Controls whether CONECT records are written bi-directionally. Conventionally, PDB files list connect records both from source atom to destination atom, and again from destination to source. This duplication doubles the number/size of CONECT records with redundant information, as most readers (if they honor CONECT records at all) can work with uni-directional CONECT records. By default, OEChem’s PDB writer only output uni-directional CONECT records where the source atom’s serial number is always less than the destination atom’s. The OEOFlavor.PDB.BOTH can be used to request full bi-directional PDB files.

CHARGE

Controls whether the PDB file writer takes the value for the PDB file’s B-factor field from the atom’s partial charge property. A number of applications, including Delphi, (ab)use the PDB file format specification to store atomic partial charges in the b-factor field rather instead of crystallographically determined anisotropic temperature factors. OEOFlavor.PDB.CHARGE is off by default.

RADIUS

Controls whether the PDB file writer takes the value for the PDB file’s occupancy field from the atom’s radius property. A number of applications, including Delphi, (ab)use the PDB file format specification to store radii in the occupancy field rather instead of crystallographically determined anisotropic occupancies. OEOFlavor.PDB.RADIUS is off by default.

TER

Controls whether the PDB file writer terminates each connection table with a TER record rather than an END record. Some dubious molecular graphics software, such as Grasp, requires that multiple compounds be separated by the chain/fragment separator TER, rather than the molecule separator END. OEOFlavor.PDB.TER is off by default.

DELPHI

Combination of OEOFlavor.PDB.CHARGE and OEOFlavor.PDB.RADIUS flags.

ELEMENT

Controls whether the PDB writer writes the chemical symbol right-justified in columns 77-78, as specified by version 2.2 of the PDB format specification. This is a new feature as of OEChem 1.3.5. OEOFlavor.PDB.ELEMENT is on by default.

FORMALCHARGE

Controls whether the PDB file write writes the formal charge right-justified (e.g. 2+, 2-) in columns 79-80, as specified by version 2.2 of the PDB format specification. This is a new feature as of OEChem 1.3.5. This flag is off by default. Enabling OEOFlavor.PDB.FORMALCHARGE also enables OEOFlavor.PDB.ELEMENT.

HETBONDS

BasicMask

OEResidues

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWritePDBFile.

NoResidues

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWritePDBFile.

CurrentResidues

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWritePDBFile.

OrderAtoms

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWritePDBFile.

AllMask

DEFAULT

Combination of OEOFlavor.PDB.OrderAtoms, OEOFlavor.PDB.OEResidues, OEOFlavor.PDB.HETBONDS, OEOFlavor.PDB.ELEMENT and OEOFlavor.PDB.BOTH flags.

Default

Same as the OEOFlavor.PDB.DEFAULT constant.

OEOFlavor::SDF

The OEOFlavor.SDF namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEWriteMDLFile and the OEWriteMolecule functions when writing a molecule into a OEFormat.SDF format file.

This namespace contains the following constants:

Add2D

This flag indicates that if a molecule has no coordinates, then 2D coordinates are generated prior to writing a molecule by the OEWriteMolecule high-level writer. If the molecule already has 2D or 3D coordinates then these coordinates are left intact. In certain cases the 2D layout may result in incorrect stereochemistry in the resulting connection table. In these cases no coordinates are generated.

UnsetBad2DStereo

This flag is used with the Add2D constant. In certain cases the 2D layout may result in incorrect stereochemistry in the output connection table format. When this flag is set the writer will output the generated coordinates and set the stereochemistry of the offending stereocenters to ‘Undefined’.

MCHG

MISO

MRGP

MV30

MDLParity

If this flag is set and OEMDLHasParity returns false ,then OEMDLPerceiveParity function is called to perceive the MDL atom stereo parity fields.

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWriteMDLFile.

NoParity

If this flag is set, then the MDL atom stereo parity fields are left intact.

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWriteMDLFile.

CurrentParity

If this flag is set, then OEMDLClearParity function is called to set all MDL atom stereo parity fields to zero.

Note

This flag is only interpreted by the high-level file writers (OEWriteMolecule) and not in OEWriteMDLFile.

MMask

PMask

Combination of OEOFlavor.SDF.MDLParity, OEOFlavor.SDF.NoParity and OEOFlavor.SDF.CurrentParity flags. The flag controls the processing of the MDL stereo parity bit field of each atom.

DEFAULT

Combination of OEOFlavor.SDF.Add2D, OEOFlavor.SDF.MDLParity, OEOFlavor.SDF.MRGP, OEOFlavor.SDF.MISO and OEOFlavor.SDF.MCHG flags.

Default

Same as the OEOFlavor.SDF.DEFAULT constant.

OEOFlavor::SLN

Note

If no aromaticity model is specified for the OEOFlavor.Generic namespace for this file format, then the Tripos model is used by default to perceive aromaticity by the OEWriteMolecule high-level writer.

This namespace contains the following constants:

Default

OEOFlavor::SMI

The OEOFlavor.SMI namespace encodes symbolic constants used as bit-masks that control the processing performed by the OECreateSmiString function when writing a molecule into a OEFormat.SMI format file.

Note

If no aromaticity model is specified for the OEOFlavor.Generic namespace for this file format, then the OpenEye model is used by default to perceive aromaticity by the OEWriteMolecule high-level writer.

This namespace contains the following constants:

AtomMaps

Corresponds to the OESMILESFlag.AtomMaps constant.

AtomStereo

Corresponds to the OESMILESFlag.AtomStereo constant.

BondStereo

Corresponds to the OESMILESFlag.BondStereo constant.

Canonical

Corresponds to the OESMILESFlag.Canonical constant.

DEFAULT

Same as the OEOFlavor.SMI.Default constant.

Default

Combination of OEOFlavor.ISM.AtomMaps, OEOFlavor.ISM.AtomStereo, OEOFlavor.ISM.BondStereo, OEOFlavor.ISM.Canonical, OEOFlavor.ISM.Isotopes and OEOFlavor.ISM.RGroups flags.

ExtBonds

Corresponds to the OESMILESFlag.ExtBonds constant.

Hydrogens

Corresponds to the OESMILESFlag.Hydrogens constant.

ImpHCount

Corresponds to the OESMILESFlag.ImpHCount constant.

Isotopes

Corresponds to the OESMILESFlag.Isotopes constant.

Kekule

Corresponds to the OESMILESFlag.Kekule constant.

RGroups

Corresponds to the OESMILESFlag.RGroups constant.

SmiMask

SuperAtoms

Corresponds to the OESMILESFlag.SuperAtoms constant.

OEOFlavor::USM

This namespace contains constants.

AtomMaps

Corresponds to the OESMILESFlag.AtomMaps constant.

AtomStereo

Corresponds to the OESMILESFlag.AtomStereo constant.

BondStereo

Corresponds to the OESMILESFlag.BondStereo constant.

Canonical

Corresponds to the OESMILESFlag.Canonical constant.

DEFAULT

Same as the OEOFlavor.USM.Default constant.

Default

Combination of OEOFlavor.ISM.AtomMaps, OEOFlavor.ISM.RGroups flags.

ExtBonds

Corresponds to the OESMILESFlag.ExtBonds constant.

Hydrogens

Corresponds to the OESMILESFlag.Hydrogens constant.

ImpHCount

Corresponds to the OESMILESFlag.ImpHCount constant.

Isotopes

Corresponds to the OESMILESFlag.Isotopes constant.

Kekule

Corresponds to the OESMILESFlag.Kekule constant.

RGroups

Corresponds to the OESMILESFlag.RGroups constant.

SmiMask

SuperAtoms

Corresponds to the OESMILESFlag.SuperAtoms constant.

OEOFlavor::XYZ

The OEOFlavor.XYZ namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEWriteXYZFile function when writing a molecule into a OEFormat.XYZ format file.

This namespace contains the following constants:

Charges

Specifies that the partial charge for each atom should be appended as an additional column.

Symbols

Write the atomic symbol instead of the atomic number.

SinglePrecision

Forces coordinates to be written in single precision with only 5 significant digits.

DoublePrecision

Forces coordinates to be written in double precision with only 18 significant digits.

Default

Equivalent to Charges | Symbols. By default, what precision, single or double precision will be introspected from the molecule type.