Markush DARC format - VMN

{warning} 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.

Code : 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)

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

Multiple R-group attachments

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

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