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:

Amino acids (peptides)

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

The following non-standard peptides are also supported:

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:

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

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