MDL Query Depiction¶

In order to depict an MDL query the query molecule has to be imported by calling the OEReadMDLQueryFile function. The rest of the process is identical to depicting a molecule. First the OEPrepareDepiction function has to be called to generate the 2D atom coordinates, then the image can be created by rendering the molecule (OERenderMolecule).

Listing 1: Example of MDL query depiction

        if (argv.length != 2) {
            oechem.OEThrow.Usage("DepictMDLQuery <mdlquery> <imagefile>");
        }
        oemolistream ifs = new oemolistream(argv[0]);
        OEGraphMol qmol = new OEGraphMol();
        oechem.OEReadMDLQueryFile(ifs, qmol);
        ifs.close();
        oedepict.OEPrepareDepiction(qmol);
        oedepict.OERenderMolecule(argv[1], qmol);

Atom Query Features¶

The depiction of the following MDL atom query features is supported:

The 8th column in the atom block in the V2K format file (or HCOUNT= in the V3K format file) is used to define the number of allowed hydrogens for an atom. (See examples in Table: Example of depicting hydrogen count)
- (H0) means no hydrogen atoms allowed unless explicitly drawn.
- (Hn) means atom must have n or more implicit hydrogen(s)
Examples of depicting hydrogen count¶

query
Query atom types:
- A = any atom type except hydrogen
- Q = any atom type except hydrogen and carbon
- L = atom list
The M ALS line in the property block in the V2K format file ( or [aaa,bbb,..] in the V3K format) is used to list alternative atom types for an atom. (See examples in Table: Examples of depicting query atom types)

Examples of depicting query atom types¶

query

target

target

target
M CHG line in the property block in the V2K format file (or CHG= in the V3K format) is used to define atom formal charges. (See examples in Table: Example of depicting formal charge)

Examples of depicting formal charge¶

query

target

target
M RBC line in the property block in the V2K format file (or RBCNT= in the V3K format) is used to limit the number of allowed ring bonds attached to an atom. (See examples in Table: Example of depicting ring count)
- (r0) means no ring bond allowed
- (r*) means as drawn
- (rn) means n number of ring bonds allowed
Examples of depicting ring count¶

query

target

target
M SUB line in the property block in the V2K format file (or SUBST= in the V3K format) is used to set the number of allowed substitutions of an atom. (See examples in Table: Examples of depicting substitution count)
- (s0) means no substitution allowed
- (s*) means as drawn
- (sn) means n number of substitution(s) allowed
Examples of depicting substitution count¶

query

target

target
M UNS line in the property block in the V2K format file (or UNSAT= in the V3K format) is used to specify whether or not an atom is unsaturated, i.e., having at least one multiple bond. (See examples in Table: Examples of depicting unsaturated property)

Examples of depicting unsaturated property¶

query

target

target

Bond Query Features¶

The depiction of the following MDL bond query features is supported:

Alternative bond types in the bond block (4 = aromatic, 5 = single or double, 6 = single or aromatic, 7 = double or aromatic, 8 = any bond). (See examples in Table: Examples of depicting query bond types)

Examples of depicting query bond types¶

query

target

target

target
See also
- OEBondDisplayType namespace
The 6th column in the atom block in the V2K format file ( or TOPO= in the V3K format) describes bond topology. (See examples in Table: Examples of depicting bond topology)
- (rn) means that it can only mapped to ring bond
- (ch) means that it can only mapped to chain bond
Examples of depicting bond topology¶

query

target

target
Double bond stereochemistry is considered if both ends of the bond are marked with stereo care flags in the atom block in the V2K format file ( or STBOX= in the V3K format). (See examples in Table: Examples of depicting bond stereo care)

Examples of depicting bond stereo care¶

query

target

target

R-group Depiction¶

OEDepict TK can also depict R-group information by interpreting the M RGP line in the property block of an MDL file (See examples in Table: Examples of depicting R-groups)

**Examples of depicting R-groups**¶

**Examples of depicting query atom types**¶
query	target	target	target

**Examples of depicting ring count**¶
query	target	target

**Examples of depicting substitution count**¶
query	target	target

**Examples of depicting query bond types**¶
query	target	target	target