OE2DMolDisplaySetup

This namespace encodes symbolic constants used as bit-masks to indicate which molecule depiction parameters are being created when invoking the OEConfigure2DMolDisplayOptions function.

See also

• OE2DMolDisplayOptions class

All

The combination of following constants:

• OE2DMolDisplaySetup::AromaticStyle

• OE2DMolDisplaySetup::AtomColorStyle

• OE2DMolDisplaySetup::AtomPropDisplay

• OE2DMolDisplaySetup::AtomStereoStyle

• OE2DMolDisplaySetup::BondColorStyle

• OE2DMolDisplaySetup::BondPropDisplay

• OE2DMolDisplaySetup::BondStereoStyle

• OE2DMolDisplaySetup::DefaultLineWidth

• OE2DMolDisplaySetup::HydrogenStyle

• OE2DMolDisplaySetup::ProtectiveGroupStyle

• OE2DMolDisplaySetup::Scale

• OE2DMolDisplaySetup::SuperAtomStyle

AromaticStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the aromatic ring style.

Contents of parameter -aromstyle
    Aliases : -astl
    Type : string
    Allow list : false
    Default : Kekule
    Simple : true
    Required : false
    Legal values : Kekule Circle Dash
    Brief : Aromatic ring display style
    Detail

        API : OE2DMolDisplayOptions::SetAromaticStyle method and OEAromaticStyle namespace

See also

• OEAromaticStyle namespace

• OE2DMolDisplayOptions::SetAromaticStyle method

AtomColorStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the atom color style.

Contents of parameter -atomcolor
    Aliases : -acolor
    Type : string
    Allow list : false
    Default : WhiteCPK
    Simple : true
    Required : false
    Legal values : WhiteCPK BlackCPK WhiteMonochrome BlackMonochrome cow cob bow wob
    Brief : Atom coloring style
    Detail

       API : OE2DMolDisplayOptions::SetAtomColorStyle method and OEAtomColorStyle namespace

       cow          - (color on white) same as WhiteCPK
       cob          - (color on black) same as BlackCPK
       bow          - (black on white) same as WhiteMonochrome
       wob          - (white on black) same as BlackMonochrome

See also

• OEAtomColorStyle namespace

• OE2DMolDisplayOptions::SetAtomColorStyle method

AtomPropDisplay

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the atom property display.

Contents of parameter -atomprop
    Aliases : -aprop
    Type : string
    Allow list : false
    Default : Hidden
    Simple : true
    Required : false
    Legal values : Hidden AtomIdx MapIdx
    Brief : Atom property display
    Detail

        API : OE2DMolDisplayOptions::SetAtomPropertyFunctor method, OEDisplayNoAtomProp, OEDisplayAtomIdx, and OEDisplayAtomMapIdx functors

See also

• OEDisplayAtomIdx class

• OEDisplayAtomMapIdx class

• OEDisplayNoAtomProp class

• OE2DMolDisplayOptions::SetBondPropertyFunctor method

AtomStereoStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the atom stereo display style.

Contents of parameter -atomstereostyle

    Aliases : -atomsstl
    Type : string
    Allow list : false
    Default : AtomStereo|MDLStereoCenter|FancyStyle
    Simple : true
    Required : false
    Brief : Atom stereo display style
    Detail

        API : OE2DMolDisplayOptions::SetAtomStereoStyle method and OEAtomStereoStyle namespace

        Primitive expressions :
        Hidden       - no atom stereo information is displayed
        AtomStereo   - display wedge/hash bonds
        CIPAtomStereo - display S/R CIP stereo labels
        MDLStereoCenter - display ABS/AND/OR stereo labels
        StandardStyle - standard hash/wedge style
        FancyStyle   - fancy hash/wedge style

        Combined expressions :
        Created by combining primitive tokens with |

See also

• OEAtomStereoStyle namespace

• OE2DMolDisplayOptions::SetAtomStereoStyle method

BondColorStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the bond color style.

Contents of parameter -bondcolor
    Aliases : -bcolor
    Type : string
    Allow list : false
    Default : ByElement
    Simple : true
    Required : false
    Legal values : ByElement Monochrome
    Brief : Bond coloring style
    Detail

       API : OE2DMolDisplayOptions::SetBondColorStyle method and OEBondColorStyle namespace

See also

• OEBondColorStyle namespace

• OE2DMolDisplayOptions::SetBondColorStyle method

BondPropDisplay

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the bond property display.

Contents of parameter -bondprop
    Aliases : -bprop
    Type : string
    Allow list : false
    Default : Hidden
    Simple : true
    Required : false
    Legal values : Hidden BondIdx
    Brief : Bond property display
    Detail

       API : OE2DMolDisplayOptions::SetBondPropertyFunctor method, OEDisplayNoBondProp and OEDisplayBondIdx functors

See also

• OEDisplayBondIdx class

• OEDisplayNoBondProp class

• OE2DMolDisplayOptions::SetBondPropertyFunctor method

BondStereoStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the bond stereo display style.

Contents of parameter -bondstereostyle
    Aliases : -bondsstl
    Type : string
    Allow list : false
    Default : BondStereo
    Simple : true
    Required : false
    Brief : Bond stereo display style
    Detail

        API : OE2DMolDisplayOptions::SetBondStereoStyle method and OEBondStereoStyle namespace

        Primitive expressions :
        Hidden
        BondStereo
        CIPBondStereo

        Combined expressions :
        Created by combining primitive tokens with |

See also

• OEBondStereoStyle namespace

• OE2DMolDisplayOptions::SetBondStereoStyle method

DefaultLineWidth

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the default bond line width.

Contents of parameter -linewidth
    Aliases : -linew
    Type : int
    Allow list : false
    Default : 2
    Simple : true
    Required : false
    Legal ranges :
        8 to 1
    Brief : Default bond line width
    Detail

       API : OE2DMolDisplayOptions::SetDefaultBondPen method and OEPen class

See also

• OE2DMolDisplayOptions::SetDefaultBondPen method

• OEPen class

HydrogenStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the hydrogen display style.

Contents of parameter -hydrstyle
    Aliases : -hstl
    Type : string
    Allow list : false
    Default : ImplicitHetero|ExplicitAll
    Simple : true
    Required : false
    Brief : Hydrogen display style
    Detail

        API : OE2DMolDisplayOptions::SetHydrogenStyle method and OEHydrogenStyle namespace

        Primitive expressions :
        Hidden
        ImplicitHetero
        ImplicitTerminal
        ImplicitAll
        ExplicitHetero
        ExplicitTerminal
        ExplicitAll

        Combined expressions :
        Created by combining primitive tokens with |

See also

• OEHydrogenStyle namespace

• OE2DMolDisplayOptions::SetHydrogenStyle method

ProtectiveGroupStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the protective group display style.

Contents of parameter -protgroupdisp
    Aliases : -pgroup
    Type : string
    Allow list : false
    Default : Off
    Simple : true
    Required : false
    Brief : Protective group display style
    Detail

        API : OE2DMolDisplayOptions::SetProtectiveGroupStyle method and OEProtectiveGroupStyle namespace

        Primitive expressions :
        Off            -  no protective group detection
        All            -  detect all protective groups
        Ac             -  R-C(=O)C
        Ad             -  R-C12CC3CC(C1)CC(C3)C2
        Alloc          -  R-C(=O)OCC=C
        Bn,Bzl,Benzyl  -  R-Cc1ccccc1
        BOC            -  R-C(=O)OC(C)(C)(C)
        Bom            -  R-COCc1ccccc1
        Bpoc           -  R-C(=O)OC(C)(C)c1ccc(cc1)c2ccccc2
        Bs             -  R-S(=O)(=O)c1ccc(cc1)Br
        Bt             -  R-n1c2ccccc2nn1
        Btm            -  R-CSc1ccccc1
        Bz, Benzoyl    -  R-C(=O)c1ccccc1
        Bzh            -  R-C(c1ccccc1)c2ccccc2
        BzOM           -  R-COc1ccccc1
        cHx            -  R-C1CCCCC1
        Dan, Dansyl    -  R-S(=O)(=O)c1cccc2c1cccc2N(C)C
        DCB            -  R-Cc1c(cccc1Cl)Cl
        DDE            -  R-C(=C1C(=O)CC(CC1=O)(C)C)C
        DDIV           -  R-C(=C1C(=O)CC(CC1=O)(C)C)CC(C)C
        DEIPS          -  R-[Si](CC)(CC)C(C)C
        DMAB           -  R-Cc1ccc(cc1)NC(=C2C(=O)CC(CC2=O)(C)C)CC(C)C
        DMIPS          -  R-[Si](C)(C)C(C)C
        DMPM           -  R-Cc1ccc(c(c1)OC)OC
        DMPS           -  R-[Si](C)(C)c1ccccc1
        DMTr           -  R-C(c1ccccc1)(c2ccc(cc2)OC)c3ccc(cc3)OC
        DNBZ           -  R-C(=O)c1cc(cc(c1)[N+](=O)[O-])[N+](=O)[O-]
        DNP            -  R-c1ccc(cc1[N+](=O)[O-])[N+](=O)[O-]
        DOC            -  R-C(=O)OC(C(C)C)C(C)C
        DPIPS          -  R-[Si](c1ccccc1)(c2ccccc2)OC(C)C
        Dpp            -  R-P(=O)(c1ccccc1)c2ccccc2
        DTBMS          -  R-[Si](C)(C(C)(C)C)C(C)(C)C
        EE             -  R-C(C)OCC
        ESC            -  R-C(=O)OCCS(=O)(=O)CC
        Fmoc           -  R-C(=O)OCC3c1ccccc1c2ccccc23
        FourOMeBz      -  R-C(=O)c1ccc(cc1)OC
        FPMP           -  R-C1(CCN(CC1)c2ccccc2F)OC
        Im             -  R-n1ccnc1
        Lev            -  R-C(=O)CCC(=O)C
        MDIPS          -  R-[Si](C)(C(C)C)C(C)C
        MDPS           -  R-[Si](C)(c1ccccc1)c2ccccc2
        MEM            -  R-COCCOC
        Mes            -  R-c1c(cc(cc1C)C)C
        MMTR           -  R-C(c1ccccc1)(c2ccccc2)c3ccc(cc3)OC
        MOM            -  R-COC
        Moz            -  R-C(=O)OCc1ccc(cc1)OC
        MPC            -  R-C(=O)OC(C)(C)c1ccc(cc1)C
        MPM            -  R-c1ccccc1OC
        MS             -  R-S(=O)(=O)C
        MTHP           -  R-C1(CCOCC1)OC
        MTM            -  R-CSC
        MTr            -  R-S(=O)(=O)c1c(cc(c(c1C)C)OC)C
        NPE            -  R-CCc1ccc(cc1)[N+](=O)[O-]
        NPEOC          -  R-C(=O)OCCc1ccc(cc1)[N+](=O)[O-]
        NPES           -  R-S(=O)(=O)CCc1ccc(cc1)[N+](=O)[O-]
        Np             -  R-c1ccc(cc1)[N+](=O)[O-]
        NPS            -  R-Sc1ccccc1[N+](=O)[O-]
        NVOC           -  R-C(=O)OCc1cc(c(cc1[N+](=O)[O-])OC)OC
        OBzl           -  R-OCc1ccccc1
        ONOS           -  R-S(=O)(=O)c1ccccc1[N+](=O)[O-]
        OtBu           -  R-OC(C)(C)C
        OTf            -  R-S(=O)(=O)(C(F)(F)F)
        PAC            -  R-CC(=O)c1ccccc1
        PBF            -  R-S(=O)(=O)c1c(c(c2c(c1C)CC(O2)(C)C)C)C
        PCB            -  R-c1ccc(cc1)Cl
        PHF            -  R-C1(c2ccccc2-c3c1cccc3)c4ccccc4
        Pht            -  R-C(=O)c1ccccc1C=O
        Piv            -  R-C(=O)C(C)(C)C
        PMB            -  R-Cc1ccc(cc1)OC
        PMBM           -  R-COCc1ccc(cc1)OC
        Poc            -  R-C(=O)OC1CCCC1
        PPi            -  R-P(=O)([O-])OP(=O)([O-])[O-]
        SEM            -  R-COCC[Si](C)(C)C
        SES            -  R-S(=O)(=O)CC[Si](C)(C)C
        StBu           -  R-SC(C)(C)C
        TBDPS          -  R-[Si](C(C)(C)(C))(c1ccccc1)(c1ccccc1)
        TBMPS          -  R-[Si](c1ccccc1)(C(C)(C)C)C(C)(C)C
        TBS, TBDMS     -  R-[Si](C)(C)C(C)(C)C
        TCP            -  R-c1cc(c(cc1Cl)Cl)Cl
        Teoc           -  R-C(=O)OCC[Si](C)(C)C
        TES            -  R-[Si](CC)(CC)CC
        TFA            -  R-C(=O)C(F)(F)F
        Thexyl         -  R-C(C)(C)C(C)C
        THF            -  R-C1CCCO1
        THP            -  R-C1CCCCO1
        TIPS           -  R-[Si](C(C)C)(C(C)C)C(C)C
        TMOB           -  R-Cc1c(cc(cc1OC)OC)OC
        TMS            -  R-[Si](C)(C)C
        transCinnamyl  -  R-C/C=C/c1ccccc1
        Trisyl         -  R-S(=O)(=O)c1c(cc(cc1C(C)C)C(C)C)C(C)C
        Troc           -  R-C(=O)OCC(Cl)(Cl)Cl
        TRT            -  R-C(c1ccccc1)(c2ccccc2)c3ccccc3
        TS, Tos        -  R-S(=O)(=O)c1ccc(cc1)C
        Xyl            -  R-c1c(cccc1C)C
        Z, Cbz         -  R-C(=O)OCc1ccccc1

Scale

Contents of parameter -scale
    Aliases : -s
    Type : float
    Allow list : false
    Default : 0.0
    Simple : true
    Required : false
    Legal ranges :
       500.0 to 0.0
    Brief :  Scaling of the depicted molecule
    Detail

        API : OE2DMolDisplayOptions::SetScale method

        0.0 value means that the molecule is scaled to
        auto-fit the (width/height) dimensions of the image

See also

• OE2DMolDisplayOptions::SetScale method

• Controlling the Size of Depicted Molecules section

SuperAtomStyle

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the super atom display style.

Contents of parameter -superdisp
Aliases : -super
Type : string
Allow list : false
Default : Off
Simple : true
Required : false
Brief : Super atom display style
Detail

   API : OE2DMolDisplayOptions::SetSuperAtomStyle method and OESuperAtomStyle namespace

   Primitive expressions :
   Off          -  no super atom detection
   COOH         -  R-C(=O)OH
   COO_         -  R-C(=O)[O-]
   CHO          -  R-C(=O)H
   NC           -  R-C#[NX1]
   CN           -  R-[N+]#[C-]
   N2           -  R=[N+]=[N-]
   N3           -  R-N=[N+]=[N-]
   NCO          -  R-N=C=O
   NO2          -  R-N(=O)(=0) or R-[N+]([O-])(=0)
   CNO          -  R-C#[N+]-[O-]
   ONO          -  R-O-N=0
   SO3H         -  R-S(=O)(=O)(-OH)
   SO3_         -  R-S(=O)(=O)(-[O-])
   PO3H2        -  R-P(=O)(-OH)(-OH)
   CF3          -  R-C(-F)(-F)(-F)
   CCl3         -  R-C(-Cl)(-Cl)(-Cl)
   Me           -  R-CH3
   Et           -  R-CH2-CH3
   Pr           -  R-CH2-CH2-CH3
   Bu           -  R-CH2-CH2-CH2-CH3
   iBu          -  R-CH2-CH(-CH3)(-CH3)
   sBu          -  R-CH(-CH2-CH3)(-CH3)
   tBu          -  R-C(-CH3)(-CH3)(-CH3)
   OMe          -  R-O-CH3
   OEt          -  R-O-CH2-CH3
   OPr          -  R-O-CH2-CH2-CH3
   OBu          -  R-O-CH2-CH2-CH2-CH3
   All          -  Detect all super atoms

   Combined expressions :
   Created by combining primitive tokens with |

See also

• OESuperAtomStyle namespace

• OE2DMolDisplayOptions::SetSuperAtomStyle method

TitleLocation

Passing this constant to the OEConfigure2DMolDisplayOptions function result in generating the following default interface to configure the location of the molecule title.

Contents of parameter -titleloc
    Aliases : -tloc
    Type : string
    Allow list : false
    Default : Top
    Simple : true
    Required : false
    Legal values : Hidden Top Bottom
    Brief : Location of the molecule title
    Detail

       API : OE2DMolDisplayOptions::SetTitleLocation method and OETitleLocation namespace

See also

• OETitleLocation namespace

• OE2DMolDisplayOptions::SetTitleLocation method