8.9 OEOFlavor

The OEOFlavor namespace is used to encode bitmasks representing the flavor, of minor file format variations, to the molecular file formats that may be written by OEChem. The Generic namespace within OEOFlavor specify control bits that are common to all of the output formats. Although these code Generic bits are common to all file formats, they may be specified independently for each file format.

The values are set and retrieved using the oemolstreambase::SetFormat and oemolstreambase::GetFormat methods of an oemolostream.

The interpretation of many of these flavor values, is identical to those passed to the corresponding OEChem low-level file format writer. Readers should also consult the flavor documentation for the appropriate low-level file format writer.

namespace OEOFlavor {
  namespace Generic   {
    const unsigned int OEAroModelDaylight = 0x8000;
    const unsigned int OEAroModelOpenEye  = 0x4000;
    const unsigned int OEAroModelTripos   = 0x2000;
    const unsigned int OEAroModelMMFF     = 0x1000;
    const unsigned int OEAroModelMDL      = 0x0800;
    const unsigned int AroMask            = 0xF800;

    const unsigned int Rings              = 0x0400;
    const unsigned int GenericMask        = 0xFC00;
    const unsigned int DEFAULT            = 0x4400;
    const unsigned int Default            = DEFAULT;
  }
  namespace SMI       {
    const unsigned int Isotopes   = 0x01;
    const unsigned int Hydrogens  = 0x02;
    const unsigned int RGroups    = 0x04;
    const unsigned int AtomStereo = 0x08;
    const unsigned int BondStereo = 0x10;
    const unsigned int AtomMaps   = 0x20;
    const unsigned int Canonical  = 0x40;
    const unsigned int Kekule     = 0x80;
    const unsigned int SmiMask    = 0xff;

    const unsigned int DEFAULT    = 0x24;
    const unsigned int Default    = DEFAULT;
  }
  namespace MDL       {
    const unsigned int MCHG          = 0x01;
    const unsigned int MISO          = 0x02;
    const unsigned int MRGP          = 0x04;
    const unsigned int MDLParity     = 0x08;
    const unsigned int NoParity      = 0x10;
    const unsigned int CurrentParity = 0x20;
    const unsigned int MMask         = 0x07;
    const unsigned int PMask         = 0x38;
    const unsigned int DEFAULT       = 0x0f;
    const unsigned int Default = DEFAULT;
  }
  namespace PDB       {
    const unsigned int BONDS           = 0x01;
    const unsigned int ORDERS          = 0x02;
    const unsigned int BOTH            = 0x04;
    const unsigned int CHARGE          = 0x08;
    const unsigned int BasicMask       = 0x0f;

    const unsigned int OEResidues      = 0x10;
    const unsigned int NoResidues      = 0x20;
    const unsigned int CurrentResidues = 0x40;
    const unsigned int OrderAtoms      = 0x80;
    const unsigned int AllMask         = 0xff;
    const unsigned int DEFAULT         = 0x90;
    const unsigned int Default = DEFAULT;
  }
  namespace MOL2      {
    const unsigned int AtomTypeNames = 0x01;
    const unsigned int BondTypeNames = 0x02;
    const unsigned int AtomNames     = 0x04;
    const unsigned int NameMask      = 0x07;
    const unsigned int DEFAULT       = 0x07;
    const unsigned int Default = DEFAULT;
  }
  namespace BIN       {
    const unsigned int Default = 0x0;
  }
  namespace TDT       {
    const unsigned int Default = 0x0;
  }
  namespace ISM       {
    const unsigned int Isotopes   = 0x01;
    const unsigned int Hydrogens  = 0x02;
    const unsigned int RGroups    = 0x04;
    const unsigned int AtomStereo = 0x08;
    const unsigned int BondStereo = 0x10;
    const unsigned int AtomMaps   = 0x20;
    const unsigned int Canonical  = 0x40;
    const unsigned int Kekule     = 0x80;
    const unsigned int SmiMask    = 0xff;

    const unsigned int DEFAULT    = 0x7d;
    const unsigned int Default    = DEFAULT;
  }
  namespace MOL2H     {
    const unsigned int AtomTypeNames = 0x01;
    const unsigned int BondTypeNames = 0x02;
    const unsigned int AtomNames     = 0x04;
    const unsigned int NameMask      = 0x07;
    const unsigned int DEFAULT       = 0x07;
    const unsigned int Default = DEFAULT;
  }
  namespace SDF       {
    const unsigned int MCHG          = 0x01;
    const unsigned int MISO          = 0x02;
    const unsigned int MRGP          = 0x04;
    const unsigned int MDLParity     = 0x08;
    const unsigned int NoParity      = 0x10;
    const unsigned int CurrentParity = 0x20;
    const unsigned int MMask         = 0x07;
    const unsigned int PMask         = 0x38;
    const unsigned int DEFAULT       = 0x0f;
    const unsigned int Default       = DEFAULT;
  }
  namespace CAN       {
    const unsigned int Isotopes   = 0x01;
    const unsigned int Hydrogens  = 0x02;
    const unsigned int RGroups    = 0x04;
    const unsigned int AtomStereo = 0x08;
    const unsigned int BondStereo = 0x10;
    const unsigned int AtomMaps   = 0x20;
    const unsigned int Canonical  = 0x40;
    const unsigned int Kekule     = 0x80;
    const unsigned int SmiMask    = 0xff;

    const unsigned int DEFAULT    = 0x64;
    const unsigned int Default    = DEFAULT;
  }
  namespace MF        {
    const unsigned int Title   = 0x1;
    const unsigned int DEFAULT = 0x1;
    const unsigned int Default = DEFAULT;
  }
  namespace XYZ       {
    const unsigned int Default = 0x0;
  }
  namespace FASTA     {
    const unsigned int Default = 0x0;
  }
  namespace MOPAC     {
    const unsigned int XYZ     = 0x01;
    const unsigned int CHARGES = 0x02;
    const unsigned int DEFAULT = 0x02;
    const unsigned int Default = DEFAULT;
  }
  namespace OEB       {
    const unsigned int Default = 0x0;
  }
  namespace MMOD      {
    const unsigned int AtomTypes = 0x1;
    const unsigned int DEFAULT   = 0x1;
    const unsigned int Default   = DEFAULT;
  }
  namespace SLN       {
    const unsigned int Default = 0x0;
  }
}

Subsections

				OEChem - API Manual Version 1.3.1

				OEChem - API Manual Version 1.3.1