Codenames: mol, mol:V3, mol:V3ec, mol:V3ea, rgf, sdf, rxn, rxn:V3, rdf, file extensions: .mol, .sdf, .rxn, .rdf
Marvin imports and exports MDL Molfiles, RGfiles, SDfiles, REACCS Rxnfiles and RDfiles. The following features are supported in V2.0 molfiles:
M ALS
- atom list and exclusive listM APO
- Rgroup attachment pointM CHG
- chargeM RAD
- radicalM ISO
- isotope mass numbersM RGP
- Rgroup labels on root structureM LOG
- Rgroup logicM LIN
- link nodesM SUB
- substitution count query property (s)M UNS
- unsaturated atom query property (u)M RBC
- ring bond count query property (rb)M STY
- Sgroup typeM SST
- Sgroup subtypeM SCN
- Sgroup connectivity (head-to-head, head-to-tail
or either/unknown)M SAL
- atoms that define the SgroupM SPA
- multiple group parent atom list (paradigmatic
repeating unit atoms)M SBL
- Sgroup's crossing bondsM SMT
- Sgroup labelM SPL
- Sgroup parent listM SDS EXP
- Sgroup expansionM SDT
- Data sgroup field descriptionM SDD
- Data sgroup display informationM SCD
- Data sgroup dataM SED
- Data sgroup data end of lineM SNC
- Sgroup component numbersM CRS
- Sgroup correspondenceM SDI
- Sgroup display information - export onlyM MRV SMA
- SMARTS H, X, R, r, a, A properties
(Marvin extension)A
- Atom aliasV
- Atom valueCHG
- chargeRAD
- radicalCFG
- parityVAL
- valenceMASS
- isotope mass numberHCOUNT
- number of implicit hydrogensSTBOX
- stereo care boxINVRET
- inversion/retention flagATTCHPT
- R-group attachment pointRGROUPS
- R-groups that comprise this R# atomSUBST
- Substitution count query property (s)UNSAT
- Unsaturated atom query property (u)RBCNT
- Ring bond count query propertyCFG
- bond stereo configuration: up or downTOPO
- bond topology: ring or chainSTBOX
- stereo care boxLINKNODE
- Link nodes.ATOMS
- atoms that define the SgroupPATOMS
- multiple group parent atom list (paradigmatic
repeating unit atoms)XBONDS
- crossing bondsMULT
- multiple group multiplierCONNECT
- connectivity
(head-to-head, head-to-tail or either/unknown)LABEL
- display labelPARENT
- parent SgroupESTATE
- expanded stateFIELDNAME
- data Sgroup field nameFIELDINFO
- data Sgroup field information (type and units)FIELDDISP
- data Sgroup field display informationQUERYTYPE
- data Sgroup program query codeQUERYOP
- data Sgroup query operatorFIELDDATA
- data Sgroup field valueBRKXYZ
- Sgroup display information - export onlyCOMPNO
- Sgroup component numbersCBONDS
- Sgroup's crossing bondsXBHEAD, XBCORR
- Sgroup correspondenceSUBTYPE
- Sgroup subtypeMDLV30/STEABS
- ABSOLUTE stereochemical groupMDLV30/STEREL
- OR stereochemical groupMDLV30/STERAC
- AND stereochemical groupMDLV30/HILITE
- Highlighted atoms and bonds, currently
as represented as atom/bond set 1.
(This feature is experimental and import only!)RLOGIC
entriesReaction files (V2.0). A reaction file consists of a REACTANT block, a PRODUCT block, and (optionally) an AGENT block. Reaction files containing reaction agents are non-standard.
A reaction agent is a molecule structure that does not take part in the chemical reaction, but is added to the reaction equation for informative purpose only. Agents are normally displayed graphically above the reaction arrow, added to the reaction file after the reactants and the products. The number of agents is displayed in the file header (after the number of reactants and the number of products) if it is non-zero. Reaction files containing agents are non-standard.
Extended reaction files (V3.0). This format is used automatically if a reaction includes Rgroups and/or the number of atoms or bonds exceeds 999. An extended reaction file consists of a REACTANT block, a PRODUCT block, (optionally) an AGENT block, and (optionally) RGROUP blocks.
In SDfiles read by marvin, the name field is special, it overrides the molecule name specified in the molfile part.
A special feature of Marvin RGfiles is that they can contain a reaction as the root structure. This feature is non-standard, such mixed RG/Rxnfiles can only be imported by Marvin.
MarvinSketch and MarvinView can handle compressed molfiles that are typically five times smaller than their original, uncompressed version. This reduces the download time of HTML pages containing molecule applets.
Compressed molfiles can be created by choosing
Edit/Source, then
Format/Compressed Molfile in
MarvinSketch or MarvinView.
If you cannot find the Edit menu, then click on the upper left arrow in
MarvinSketch, right click or double click the compound in MarvinView.
Codenames: csmol, csrgf, cssdf, csrxn, csrdf, file extensions: .csmol, .cssdf, .csrxn, .csrdf
The mol family of formats cannot store the implicit hydrogens of atoms, so it is calculated from the bond orders. This is always correct when the molecule is in Kekule format, but causes problems when nitrogen-containing aromatic rings are saved with aromatic bond types.
To counteract the information loss, implicit hydrogen count is stored in these formats as attached data on the nitrogen. The associated data sgroup has field name of MRV_IMPLICIT_H and value IMPL_H<n> where n is the number of implicit hydrogens. These special data attachments are then converted back to implicit hydrogens upon import. When the file is read in ISIS/Draw, the lost hydrogen will not reappear, but the attached data will be visible as a warning.
To save information about multipage molecular document, properties are stored as attached data. The field names and values are the following:
To save information about coordination compounds and markush structures, properties are stored as attached data. The field names and values are the following:
To save information about charge location in S-groups in case of generic, monomer, mer and component S-group types, properties are stored as attached data. The field name and value are:
Xsg Expand all S-groups. Usg Ungroup all S-groups. bXXX Set the C-C bond length used in the molfile. The molecule file is supposed to store coordinates in 1.54Å/XXX units. Marvin uses Å units internally, thus coordinates are rescaled by factor 1.54/XXX at import if XXX is a nonzero number. If XXX = 0, then coordinates are not rescaled (default for 3D V2 molfiles and for V3 molfiles). If XXX = A, then coordinates are rescaled to transform the molfile's average C-C bond length to 1.54 Å (default for 2D V2 molfiles). Examples: "caffeine.mol{b0}" or "caffeine.mol{b1.54}" (bond lengths are in angstroms), "caffeine.mol{b0.825}" (bond lengths are in ISISDraw's units), "caffeine-V3.mol{bA}" (forces average bond length calculation for V3 molfile). nomolp Read molecule type data fields ( $DTYPE $MFMT
and$RFMT
in RDfiles) as strings instead of Molecule objects.skipMMRV Neglect ChemAxon/Marvin specific lines in the properties block. Such lines are in the following format: M MRV
... They should be skipped if the file is converted with non-ChemAxon software, which preserved them but made them invalid, e.g. by changing the total number of atoms and bonds.
... Basic options for aromatization and H atom adding/removal. V2 or V3 Force writing V2 or V3 (extended) molfiles. The default format is V2 for simple molecules, V3 if the number of atoms or bonds exceeds 999 and in case of reactions with Rgroups. Example: "mol:V3" P Write floating point numbers with maximum precision. Only meaningful for V3 molfiles. Example: "mol:V3P" bXXX Set C-C bond length. If XXX is nonzero, then the exported atom coordinates are scaled in such a way that the average C-C bond length will be the specified number. If XXX = 0, then coordinates are not rescaled.
Examples: "mol:b0" or "mol:b1.54" (bond lengths are in angstroms), "mol:b1.54a" (set bond length, aromatize).
Default: 0.825 in V2 format for 2D molecules, 1.54 (Å units) in any other case.ec Convert to enhanced stereo representation, considering the chiral flag. Only meaningful with option V3. (Chiral centers are grouped into ABS or an AND stereo group, depending on the chiral flag. When the input molecule contained any enhanced stereo labels, the unlabeled stereo centers always will form a new AND group.) Example: "mol:V3ec" ea Convert to enhanced stereo representation, assuming absolute stereochemistry. Only meaningful with option V3. (Chiral centers are grouped into the ABS group. In case the input molecule already contains enhanced stereo labels, the behaviour is similar to the one described at option ec above.) Example: "mol:V3ec"