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 (
Structure shortcuts are read in as specific built-in abbreviated groups (superatom S-groups).
Superatoms are read in as pseudo-atoms and treated as homology groups.
Atom attributes: we interpret the following VMN atom attributes:
|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|
|data in AMN||TEXTNOTES||AMN text referring to the atom (e.g. N0-4,S0-4)|
The following structure shortcuts (abbreviated groups) are supported:
|C2, C3, ..., C50|
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 representing homology groups are read in as pseudo atoms. The following homologies are interpreted by enumeration and search:
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.
The following superatoms (homologies) are not supported by search and enumeration (but read in and displayed as pseudo-atoms):
The following atom attributes are not processed by search and enumeration (but displayed in atom labels):
VMN export is not available yet.