OEIFlavor

The OEIFlavor namespace encodes symbolic constants used as bit-masks to indicate how to write various file formats by OEChem TK.

Note

A very important introduction (with examples) as to how to manipulate these bit-masks is given Flavored Input and Output

The OEIFlavor.Generic namespace within OEIFlavor defines control bit-masks that are common to all of the input 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 TK low-level file format readers.

This namespace contains the following namespaces:

OEIFlavor::CAN

The OEIFlavor.CAN namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.CAN format file by the OEParseSmiles function.

This namespace contains the following constants:

Default

OEIFlavor::CDX

The OEIFlavor.CDX namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.CDX format file by the OEReadCDXFile low-level file reader.

This namespace contains the following constants:

Default

OEIFlavor::CIF

The OEIFlavor.CIF namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.CIF format file by the OEReadCIFFile low-level file reader.

This namespace contains the following constants, that mimic the XYZ reader.

FormalCrg

ImplicitH

BondOrder

Rings

The reader stores excluded sites and sites left after filtering. The filtering of these sites is based on the flavors listed below.

OccFilterOneHalf

If occupancy is noted in the CIF file, only the sites with occupancy larger than one half is kept. If occupancy is not defined in the CIF file, the occupancies are set to 1 to prevent filtering.

RemovePBCImages

Each site read is checked to see if it is equal to a previously read site up to periodic wrapping in fractional coordinates.

NormalizeHydPos

Hydrogen positions and bond lengths are normalized if necessary.

BondHydToClosest

Enforces that hydrogen atoms are bonded to their closest heavy atom in space.

RemoveQuestionMarkInLabel

Sites with a question mark after atom labels are assigned are filtered out. These extra sites are sometimes alternative positions of existing sites.

Default

Combination of: OEIFlavor.CIF.FormalCrg, OEIFlavor.CIF.ImplicitH, OEIFlavor.CIF.BondOrder, OEIFlavor.CIF.Rings, OEIFlavor.CIF.OccFilterOneHalf, OEIFlavor.CIF.RemovePBCImages, OEIFlavor.CIF.NormalizeHydPos, OEIFlavor.CIF.BondHydToClosest, OEIFlavor.CIF.RemoveQuestionMarkInLabel flags.

OEIFlavor::CSV

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

See also

CSV File Format

Header

Attempt to interpret the first line of the .csv file as a header line containing column names. The header line will be parsed into an OECSVHeader object and stored on the oemolistream object, retrievable by oemolstreambase.GetCSVHeader.

If this flag is not set, or the first column of the first line does not contain a valid SMILES string, the OECSVHeader will be initialized with the number of columns present in the first line of the file. The columns will then be named and parsed in the following order: SMILES, TITLE, OE_CSV_COLUMN_1, OE_CSV_COLUMN_2, …, OE_CSV_COLUMN_N.

Default

Set to include OEIFlavor.CSV.Header to automatically parse column names into molecule SD data.

DEFAULT

Synonym for OEIFlavor.CSV.Default.

OEIFlavor::CXSMILES

The OEIFlavor.CXSMILES namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEParseSmiles function.

This namespace contains the following constants:

Strict

Canon

DEFAULT

Default

Same as the OEIFlavor.CXSMILES.DEFAULT constant.

OEIFlavor::FASTA

The OEIFlavor.FASTA namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.FASTA format file by the OEReadFASTAFile low-level file reader.

This namespace contains the following constants:

Default

No special options are selected.

CustomResidues

Instructs the FASTA reader to interpret values surrounded in square brackets, [foo], as custom residues. The structure of these custom residues must first be registered with the OEAddCustomFASTAResidue function.

Warning

This is an experimental API that may change in the future.

EmbeddedSMILES

Instructs the FASTA reader to interpret values surrounded in square brackets, [CCC], as SMILES strings if a custom residue with the same name can not be found. The SMILES can optionally contain attachment points back to the peptide backbone. For example, [[R1]CSC[R15]] specifies to attach to the first and fifteenth residue in the peptide, effectively cyclizing the peptide.

Warning

This is an experimental API that may change in the future.

OEIFlavor::Generic

This namespace contains the following constants:

OEAroModelDaylight

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

OEAroModelOpenEye

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

OEAroModelTripos

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

OEAroModelMMFF

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

OEAroModelMDL

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

AroMask

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

See also

Rings

This flag indicates the rings are perceived by the OEReadMolecule 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 OEIFlavor.Generic.DEFAULT constant.

OEIFlavor::ISM

The OEIFlavor.ISM namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.ISM format file by the OEParseSmiles function.

This namespace contains the following constants:

Default

OEIFlavor::MDL

The OEIFlavor.MDL namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.MDL format file by the OEReadMDLFile low-level file reader.

This namespace contains the following constants:

Default

FixBondMarks

This input flavor requests that the reader make an attempt to repair stereocenters that throw warnings due to issues identified by OEMDLStereoFromBondStereo. With this input flavor enabled, the warnings will continue to be issued to allow user inspection and verification of the modified bond marks. However, once the corrected structure(s) have been rewritten with any format that captures bond stereomark information, a re-read of the structure(s) should emit fewer stereocenter correction warnings. This input flavor is not enabled for the default OEFormat.MDL setting.

SuppressEmptyMolSkip

This input flavor suppresses the default action of skipping empty molecules in the input stream. This may be important in order to recover SDData stored on empty molecule records.

SuppressImp2ExpENHSTE

This input flavor suppresses any enhanced stereogroup implicit to explicit conversions for an input V3000 format molfile.

ForceImp2ExpENHSTE

This input flavor performs implicit to explicit enhanced stereogroup conversions for an input V2000 or V3000 format molfile.

OEIFlavor::MMCIF

The OEIFlavor.MMCIF namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.MMCIF format file by the OEReadCIFFile low-level file reader.

This namespace contains the following constants.

NoAltLoc

This flavor is obsolete. The MMCIF reader does not by default read alternate locations any longer

ALTLOC

This flavor is required when OEAltLocationFactory is to be used so that all the atoms with alternate location codes are retained.

DEFAULT

Same as the OEIFlavor.MMCIF.DEFAULT constant.

SpruceDefault

Combination of OEIFlavor.MMCIF.DEFAULT, OEIFlavor.MMCIF.ALTLOC, flags.

OEIFlavor::MMOD

The OEIFlavor.MMOD namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.MMOD format file by the OEReadMacroModelFile low-level file reader.

This namespace contains the following constants:

FormalCrg

This flag indicates that high-level molecular file reader calls the OEAssignFormalCharges function to assign formal charges.

Default

OEIFlavor::MOL2

The OEIFlavor.MOL2 namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecular file reader OEReadMolecule after reading OEFormat.MOL2 format file by the OEReadMol2File low-level file reader.

This namespace contains the following constants:

M2H

Forcefield

This specifies a commonly used variant of MOL2, wherein the chemical element for an atom is inferred from the atom name, but not using the second character if it is capitalized. For example:

  • CA specifies carbon (not calcium)

  • Ca specifies calcium

  • NA specifies nitrogen (not sodium)

  • Na specifies sodium

  • HA specifies hydrogen (not hahnium)

Exceptions were made for atom names beginning with FE, ZN, MG, MN, CL, and BR: these specify chemical elements Fe, Zn, Mg, Mn, Cl, and Br, respectively.

AllMask

DEFAULT

Default

OEIFlavor::MOL2H

This namespace contains the following constants:

M2H

AllMask

DEFAULT

Default

OEIFlavor::OEB

This namespace contains the following constants:

Default

OEIFlavor::OEZ

This namespace contains the following constants:

Default

OEIFlavor::PDB

This namespace contains the following constants:

TER

Controls whether the PDB file reader should separate consecutive molecules at TER records. OEIFlavor.PDB.TER is off by default.

END

Controls whether the PDB file reader should separate consecutive molecules at END records. OEIFlavor.PDB.END is on by default.

ENDM

Controls whether the PDB file reader should separate consecutive molecules at ENDM records.

OEIFlavor.PDB.ENDM is on by default.

TerMask

Combination of OEIFlavor.PDB.TER and OEIFlavor.PDB.END and OEIFlavor.PDB.ENDM flags.

Note

By default, only OEIFlavor.PDB.END and OEIFlavor.PDB.ENDM are on (and OEIFlavor.PDB.TER is off), meaning that different chains are read into the a single molecule, but different NMR models and concatenated PDB files are treated as sequential molecules.

If OEIFlavor.PDB.END, OEIFlavor.PDB.ENDM and OEIFlavor.PDB.TER are all turned off, all of the ATOM and HETATM records in a single PDB file will be read into a single OEMolBase.

ALL

It used to indicate that all of the atom records in the input file should be read into the OEMolBase. By default, the OEReadPDBFile function ignores/omits ATOM and HETATM records that represent pseudo or dummy atoms and/or alternate conformations. Without OEIFlavor.PDB.ALL, the PDB file reader ignores all atoms whose alternate location indicator is other than ' ', A or 1, all atoms with atom names beginning " Q", all atoms with residue name "DUM", and all atoms with coordinates 9999.000, 9999.000, 9999.000 (as used by XPLOR/CNS to represent dummy atoms).

ALTLOC

Combination of OEIFlavor.Generic.Default, OEIFlavor.PDB.Default, and OEIFlavor.PDB.ALL flags. This flavor is required when OEAltLocationFactory is to be used so that all the atoms with alternate location codes are retained.

DATA

Controls whether the PDB file reader preserves the PDB file’s header data as OEMolBase’s generic data. This option currently preserves the following records:

Note

Modifying or reordering the molecule may invalidate the atom serial numbers used in some of the PDB records.

CHARGE

It is used to indicate that the contents of the b-factor column in the input PDB file contains a partial charge, and should be stored in the ‘partial charge’ property of an atom, instead of the ‘b-factor’ property. This value can then be retrieved using the OEAtomBase.GetPartialCharge method.

RADIUS

It is used to indicate that the contents of the occupancy column in the input PDB file contains a radius, and should be stored in the ‘radius’ property of an atom instead of the ‘occupancy’ property. This value can then be retrieved using the OEAtomBase.GetRadius method.

DELPHI

Combinations of OEIFlavor.PDB.CHARGE and OEIFlavor.PDB.RADIUS flags.

FORMALCHARGE

Controls whether the PDB reader should read the formal charge of the atom from column 79 and 80. Note, this flavor is not turned on default because the subsequent perception steps would not take this formal charge into account when filling valences with bonds and hydrogens.

SecStruct

This controls whether protein secondary structure is perceived after a file is read in. It is on by default. If this flavor is off, secondary structure information specified in the input PDB file (through SHEET and HELIX records) is retained.

BasicMask

FormalCrg

Note

This flag is only relevant in the high-level file reader (OEReadMolecule) and not in OEReadPDBFile.

ImplicitH

Note

This flag is only relevant in the high-level file reader (OEReadMolecule) and not in OEReadPDBFile.

BondOrder

Note

This flag is only relevant in the high-level file reader (OEReadMolecule) and not in OEReadPDBFile.

Rings

Note

This flag is only relevant in the high-level file reader (OEReadMolecule) and not in OEReadPDBFile.

Connect

Note

This flag is only relevant in the high-level file reader (OEReadMolecule) and not in OEReadPDBFile.

ExtraMask

Note

This flag is only relevant in the high-level file reader (OEReadMolecule) and not in OEReadPDBFile.

AllMask

SpruceDefault

Combination of OEIFlavor.PDB.DEFAULT, OEIFlavor.PDB.ALTLOC, flags.

OEIFlavor::RDF

The OEIFlavor.RDF namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.RDF format file by the OEReadMDLFile low-level file reader.

Default

FixBondMarks

This input flavor requests that the reader make an attempt to repair stereocenters that throw warnings due to issues identified by OEMDLStereoFromBondStereo. With this input flavor enabled, the warnings will continue to be issued to allow user inspection and verification of the modified bond marks. However, once the corrected structure(s) have been rewritten with any format that captures bond stereomark information, a re-read of the structure(s) should emit fewer stereocenter correction warnings. This input flavor is not enabled for the default OEFormat.RDF setting.

SuppressEmptyMolSkip

This input flavor suppresses the default action of skipping empty molecules in the input stream. This may be important in order to recover SDData stored on empty molecule records.

SuppressImp2ExpENHSTE

This input flavor suppresses any enhanced stereogroup implicit to explicit conversions for an input V3000 format RDFile.

ForceImp2ExpENHSTE

This input flavor performs implicit to explicit enhanced stereogroup conversions for an input RDFile.

OEIFlavor::SDF

The OEIFlavor.SDF namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.SDF format file by the OEReadMDLFile low-level file reader.

This namespace contains the following constants:

Default

FixBondMarks

This input flavor requests that the reader make an attempt to repair stereocenters that throw warnings due to issues identified by OEMDLStereoFromBondStereo. With this input flavor enabled, the warnings will continue to be issued to allow user inspection and verification of the modified bond marks. However, once the corrected structure(s) have been rewritten with any format that captures bond stereomark information, a re-read of the structure(s) should emit fewer stereocenter correction warnings. This input flavor is not enabled for the default OEFormat.SDF setting.

SuppressEmptyMolSkip

This input flavor suppresses the default action of skipping empty molecules in the input stream. This may be important in order to recover SDData stored on empty molecule records.

SuppressImp2ExpENHSTE

This input flavor suppresses any enhanced stereogroup implicit to explicit conversions for an input V3000 format SDFile.

ForceImp2ExpENHSTE

This input flavor performs implicit to explicit enhanced stereogroup conversions for an input V2000 or V3000 format SDFile.

OEIFlavor::SKC

The OEIFlavor.SKC namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.SKC format file by the OEReadSketchFile low-level file reader.

This namespace contains the following constants:

Default

OEIFlavor::SMI

The OEIFlavor.SMI namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEParseSmiles function.

This namespace contains the following constants:

Strict

Canon

DEFAULT

Default

Same as the OEIFlavor.SMI.DEFAULT constant.

OEIFlavor::USM

The OEIFlavor.USM namespace encodes symbolic constants used as bit-masks that control the processing performed by the OEParseSmiles function.

This namespace contains constants.

Default

OEIFlavor::XYZ

The OEIFlavor.XYZ namespace encodes symbolic constants used as bit-masks that control the processing performed by the high-level molecule file reader OEReadMolecule after reading OEFormat.XYZ format file by the OEReadXYZFile low-level file reader.

This namespace contains the following constants:

FormalCrg

ImplicitH

BondOrder

Rings

Connect

ExtraMask

Default