MDL Molfiles, RGfiles, SDfiles, Rxnfiles, RDfiles

Code names: 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:

Atom block:
- x, y, z coordinates
- atom type:
  - ₁H, ₂He, ₃Li, ..., ₁₀₃Lr,
  - atom list and exclusive list L,
  - "any" atoms A, Q, *,
  - lonely pair LP
- charge
- stereo care box
- valence
- atom-atom mapping (for reactions)
- inversion/retention flag (for reactions)
Bond block:
- bond type: 1, 2, 3, aromatic, "any", "single or double", "single or aromatic", "double or aromatic"
- bond stereo information: up or down
- bond topology: ring or chain
Properties block:
- M ALS - atom list and exclusive list
- M APO - Rgroup attachment point
- M CHG - charge
- M RAD - radical
- M ISO - isotope mass numbers
- M RGP - Rgroup labels on root structure
- M LIN - link nodes
- M STY - Sgroup type
- M SST - Sgroup subtype
- M SCN - Sgroup connectivity (head-to-head, head-to-tail or either/unknown)
- M SAL - atoms that define the Sgroup
- M SPA - multiple group parent atom list (paradigmatic repeating unit atoms)
- M SBL - Sgroup's crossing bonds
- M SMT - Sgroup label
- M SPL - Sgroup parent list
- M SDS EXP - Sgroup expansion
- M MRV SMA - SMARTS H, X, R, r, a, A properties (Marvin extension)

Extended molfiles (V3.0). If the number of atoms or bonds in a molecule exceeds 999, then the extended format is used. In an extended molfile, the following properties are supported:

Atom block:
- x, y, z coordinates
- atom type:
  - ₁H, ₂He, ₃Li, ..., ₁₀₃Lr,
  - "any" atoms A, Q, *,
  - lonely pair LP
- atom-atom mapping (for reactions)
- inversion/retention flag (INVRET)
- CHG - charge
- RAD - radical
- CFG - parity
- VAL - valence
- MASS - isotope mass number
- HCOUNT - number of implicit hydrogens
- STBOX - stereo care box
- INVRET - inversion/retention flag
- ATTCHPT - R-group attachment point
- RGROUPS - R-groups that comprise this R# atom
  Restriction: only one R-group can comprise an atom in Marvin
Bond block:
- bond type: 1, 2, 3, aromatic, "any", "single or double", "single or aromatic", "double or aromatic"
- CFG - bond stereo configuration: up or down
- TOPO - bond topology: ring or chain
- STBOX - stereo care box
Link nodes.
Sgroup block:
- ATOMS - atoms that define the Sgroup
- PATOMS - multiple group parent atom list (paradigmatic repeating unit atoms)
- XBONDS - crossing bonds
- MULT - multiple group multiplier
- CONNECT - connectivity (head-to-head, head-to-tail or either/unknown)
- LABEL - display label
- PARENT - parent Sgroup
- ESTATE - expanded state
Collection block:
Enhanced stereo features, see also the V3ec and V3ea export options.
- MDLV30/STEABS - ABSOLUTE stereochemical group
- MDLV30/STEREL - OR stereochemical group
- MDLV30/STERAC - AND stereochemical group
Atom highlighting.
- MDLV30/HILITE - Highlighted atoms and bonds, currently as represented as atom/bond set 1. (This feature is experimental and import only!)
Rgroup blocks with RLOGIC entries

Reaction 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.

Molfile compression

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

Import options

Xsg Expand all S-groups.

Usg Ungroup all S-groups.

bXXX Set C-C bond length. 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 nonzero. If XXX = 0, then coordinates are not rescaled. 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).
Default: C-C bond length is calculated by averaging in 2D V2 molfiles, Å units are used in any other case.

Export options

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"

a or +a     Aromatize. Example: "mol:a"

a_... or +a_...   Aromatize using the specified algorithm.
ChemAxon: a_cx or a_chemaxon (default),
Daylight: a_day or a_daylight.
Example: "mol:a_day"

-a Dearomatize. Example: "mol:-a"

H or +H Add explicit Hydrogen atoms. Example: "mol:H"

-H Remove explicit Hydrogen atoms. Example: "mol:-H"

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"

Reference

http://www.mdl.com/downloads/public/ctfile/ctfile.pdf

Xsg	Expand all S-groups.
Usg	Ungroup all S-groups.
bXXX	Set C-C bond length. 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 nonzero. If XXX = 0, then coordinates are not rescaled. 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). Default: C-C bond length is calculated by averaging in 2D V2 molfiles, Å units are used in any other case.

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"
a or +a	Aromatize. Example: "mol:a"
a_... or +a_...	Aromatize using the specified algorithm. ChemAxon: a_cx or a_chemaxon (default), Daylight: a_day or a_daylight. Example: "mol:a_day"
-a	Dearomatize. Example: "mol:-a"
H or +H	Add explicit Hydrogen atoms. Example: "mol:H"
-H	Remove explicit Hydrogen atoms. Example: "mol:-H"
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"