Markush DARC format (VMN)

VMN import is not supported since version 14.7.7.0.

Import from VMN format

Markush structure files complying the Markush DARC format are processed by Marvin, though with some limitations. The AMN file is looked for in the directory of the VMN file, with the same name and .amn extension (e.g. the AMN file of 46mrk001.vmn is 46mrk001.amn). The atom attributes and the AMN text notes are stored in atom properties, as described below.

Codename: vmn

Extension: .vmn

Interpretation of VMN features

  • Groups: G0 is read in as root structure while G1, G2, ... are stored in corresponding R-groups R1, R2, ... The representation of attachments is described below.

  • Undefined attachment information is stored in form of position variation (variable attachment) bonds.

  • Moieties are represented as repeating units with repetition ranges with no crossing bonds, but ignored (ungrouped) during search and enumeration.

  • Multipliers are represented asrepeating units with repetition ranges with a single crossing bond, but ignored (ungrouped) during search and enumeration.

  • Repeating units other than moieties and multipliers are described using a numerotation (numbering) attribute of three digits (e.g. 100) on the atoms of the repeating unit, with the appropriate repetition range text recorded in the corresponding AMN file (e.g. M100=1-4). Note, that there is a limitation on the number of elements in a repetition range (at most 10) and on the number of crossing bonds that can be processed (2 or 4).

  • Structure shortcuts are read in as specific built-in abbreviated groups (superatom S-groups).

  • Amino acids are read in by peptide import, which uses built-in abbreviated groups (superatom S-groups) to represent peptides.

  • Superatoms are read in as pseudo-atoms and treated as homology groups.

  • Atom attributes: we interpret the following VMN atom attributes:

    • AM - Abnormal mass is stored in the mass number of the atom

    • AV - Abnormal valence is stored in AV atom property

    • DL - Peptide attribute is interpreted by peptide import

  • Homology atom attributes: we store the following VMN homology atom attributes in Marvin atom properties:

    VMN attribute name

    Marvin atom property name

    property values

    DT - Deuterium-Tritium counts

    DTCOUNT

    D[deuterium count]T[tritium count] (e.g. D3T2)

    CR - Carbon ring attributes

    BRANCHING

    BRA, STR

    SIZE

    LO, MID, HI, LO MID, MID HI, LO HI

    SATURATION

    SAT, UNS

    RINGTYPE

    MON, FU

    data in AMN

    TEXTNOTES

    AMN text referring to the atom (e.g. N0-4,S0-4)

    For the interpretation of these attributes, refer to the Homology groups and Markush structures manual.

Structure shortcuts (abbreviated groups)

The following structure shortcuts (abbreviated groups) are supported:

C2, C3, ..., C50

ACE

BU

CN

CO1

CO2

COI

ET

IBU

IPR

MBE

NBU

NO2

NPR

OBE

PBE

PH

PO3

PO4

SBU

SO2

SO3

TBU

Amino acids (peptides)

The following standard amino acids (peptide abbreviated groups) are supported:

ALA

ARG

ASN

ASP

CYS

GLN

GLU

GLY

HIS

ILE

LEU

LYS

MET

PHE

PRO

SER

THR

TRY

TYR

VAL

The following non-standard peptides are also supported:

ABU

aminobutyric acid

ASU

aminosuberic acid

GLP

pyroglumatic acid

HCY

homocysteine

HSE

homoserine

NLE

norleucine

NVA

norvaline

ORN

ornithine

SAR

sarcosine

STA

statine

Note, that peptide connection bonds are not handled currently, therefore peptide sequences may not be correct.

For more information on peptide representation refer to the Sequences peptide DNA RNA documentation.

Superatoms (homology pseudo atoms)

Superatoms representing homology groups are read in as pseudo atoms. The following homologies are interpreted by enumeration and search:

CHK

CHE

CHY

CYC

ARY

HET

HEA

HEF

UNK

MX

AMX

A35

TRM

LAN

ACT

HAL

ACY

PRT

XX

For a detailed description of the interpretation, refer to the Homology groups and Markush structures manual.

Multiple R-group attachments

images/download/thumbnails/50434618/vmn_1.png

VMN format corrections

  • C0 is interpreted as CHK.

  • C1 is interpreted as C.

  • Deuterium/Tritium: we remove D and T ligands of the R-atoms.

  • Homology groups being in rings are transformed to XX.

  • R-group attachment bond type is transformed to parent R-atom bond type if different.

Limitations

Repeating units with repetition ranges

The number of elements in a repetition range is limited to 10 (e.g. range M100=2,5- is interpreted as M100=2,5-13). Repeating units with more than 4 crossing bonds are not processed by search and enumeration.

Superatoms (homologies) that are not supported

The following superatoms (homologies) are not supported by search and enumeration (but read in and displayed as pseudo-atoms):

POL

PEG

DYE

PRT

The detailed description of homology interpretation is described in the Homology groups and Markush structures manual.

Atom attributes that are not processed by search and enumeration

The following atom attributes are not processed by search and enumeration (but displayed in atom labels):

PA

Polymer indicator

SP

Position indicator

Export to VMN format

VMN export is not available yet.

References

  1. The Markush DARC Format, T Ferns, Internal Technical Report, Thomson Scientific, 2002

  2. Derwent World Patents Index, Markush DARC User Manual, The Thomson Corporation, 1993, 2008