MDL Molfiles, RGfiles, SDfiles, Rxnfiles, RDfiles

Codenames: mol, mol:V3, mol:V3ec, mol:V3ea, rgf, sdf, rxn, rxn:V3, rdf, file extensions: .mol, .sdf, .rxn, .rdf

MDL Molfiles, RGfiles, SDfiles, Rxnfiles, RDfiles formats

Extended molfiles (V3.0)
Reaction files (V2.0)
Extended reaction files (V3.0)

Molfile compression
Special information

Implicit hydrogens on aromatic nitrogen
Multipage molecular document
Coordination compounds and markush structures
Charge displayed on S-group bracket

Import options
Export options
Reference

MDL Molfiles, RGfiles, SDfiles, Rxnfiles, RDfiles formats

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 LOG - Rgroup logic
- M LIN - link nodes
- M SUB - substitution count query property (s)
- M UNS - unsaturated atom query property (u)
- M RBC - ring bond count query property (rb)
- 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 SDT - Data sgroup field description
- M SDD - Data sgroup display information
- M SCD - Data sgroup data
- M SED - Data sgroup data end of line
- M SNC - Sgroup component numbers
- M CRS - Sgroup correspondence
- M SDI - display coordinates in each S-group bracket
- M SBT - the displayed S-group bracket style
- M MRV SMA - SMARTS H, X, R, r, a, A properties (Marvin extension)
- A - Atom alias
- V - Atom value

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
- SUBST - Substitution count query property (s)
- UNSAT - Unsaturated atom query property (u)
- RBCNT - Ring bond count query property
  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
LINKNODE - 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
- FIELDNAME - data Sgroup field name
- FIELDINFO - data Sgroup field information (type and units)
- FIELDDISP - data Sgroup field display information
- QUERYTYPE - data Sgroup program query code
- QUERYOP - data Sgroup query operator
- FIELDDATA - data Sgroup field value
- BRKXYZ - display coordinates in each S-group bracket
- BRKTYP - the displayed S-group bracket style
- COMPNO - Sgroup component numbers
- CBONDS - Sgroup's crossing bonds
- XBHEAD, XBCORR - Sgroup correspondence
- SUBTYPE - Sgroup subtype
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.

Special data types in SDfile and RDfile fields

Data fields store strings normally, but other data types are also supported in Marvin, in a non-standard way. If the data starts with the "MProp:scalar:" or "MProp:array:" string, then it can have a special type:

MProp:scalar:boolean:true and MProp:scalar:boolean:false — boolean values (java.lang.Boolean class),
MProp:scalar:integer:n — integer value (java.lang.Integer class),
MProp:array:m:integer: n₀ ... n_m-1 — m-element integer array (int[] in java),
MProp:scalar:double:x — double precision floating point value (java.lang.Double class),
MProp:scalar:MDocument:... — an MDocument object,
MProp:scalar:Molecule:... — a Molecule object (in SDfiles only; RDfiles store molecule properties in a different, standard way).

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

Special information

Implicit hydrogens on aromatic nitrogen

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.

Multipage molecular document

To save information about multipage molecular document, properties are stored as attached data. The field names and values are the following:

MRV_PAGE_SELECTED - the selected page in multipage molecular document. Its value is a non-negative integer.
MRV_PAGE_COLUMN_COUNT - number of columns in multipage molecular document. Its value is a non-negative integer.
MRV_PAGE_ROW_COUNT - number of rows in multipage molecular document. Its value is a non-negative integer.
MRV_PAGE_WIDTH - width of a page in multipage molecular document. Its value is a floating point number.
MRV_PAGE_HEIGHT - height of a page in multipage molecular document. Its value is a floating point number.
MRV_PAGE_LEFT_MARGIN - left margin of a page in multipage molecular document. Its value is a floating point number.
MRV_PAGE_RIGHT_MARGIN - right of a page in multipage molecular document. Its value is a floating point number.
MRV_PAGE_TOP_MARGIN - top margin of a page in multipage molecular document. Its value is a floating point number.
MRV_PAGE_BOTTOM_MARGIN - bottom margin of a page in multipage molecular document. Its value is a floating point number.

Coordination compounds and markush structures

To save information about coordination compounds and markush structures, properties are stored as attached data. The field names and values are the following:

MRV_MULTICENTER_ATOM_INDEX - index of the multi-center atom. Its value is a positive integer.
MRV_COORDINATE_BOND_TYPE - index of the coordinate atom. Its value is a positive integer.

Charge displayed on S-group bracket

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:

MRV_CHARGE_ON_GROUP - the charge displayed on the bracket. Its value is an integer.

Import options

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.

Export options

... 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"

Reference

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

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"

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