![]() ![]() ![]() Journal of Chemical Information and Modeling. ![]() "Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited". M V30 COUNTS na nb nsg n3d chiral M V30 COUNTS This is only used when the regno exceeds 999999 (the limit of the format in the molfile header line). Optionally, the counts line can specify molregno. It also specifies whether or not the CHIRAL flag is set. It specifies the number of atoms, bonds, 3D objects, and Sgroups. 3., 1992Ī counts line is required, and must be first. Unlike the V2000 molfile, the V3000 extended Rgroup molfile has the same header format as a non-Rgroup molfile. Thus “3D” really means 3D, although “2D” will be interpreted as 3D if any non-zero Z-coordinates are found. The “dimensional code” is maintained more explicitly.(All current readers will disregard the count and stop at M END.) The number of appendix lines is always written as 999, regardless of how many there actually are.There are two other changes to the header in addition to the version: Note that the “no structure” is flagged with the “V3000” instead of the “V2000” version stamp. The following figure shows both an alanine structure and the extended molfile corresponding to it. The extended (V3000) molfile consists of a regular molfile “no structure” followed by a single molfile appendix that contains the body of the connection table (Ctab). Where the values are described in the following table:ġ= Single, 2 = Double, 3 = Triple, 4 = Aromatic,5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = AnyĠ= Use x-, y-, z-coords from atom block to determine cis or trans 3=Cis or trans (either) double bondĠ = unmarked, 1 = a center, -1 = not a center, Additional: 2 = no change, 4 = bond made/broken, 8 = bond order changesĥ = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1) are also possibleĮxtended Connection Table (V3000) The Bond Block is made up of bond lines, one line per bond, with the following format: (NOTE: some programs don't like a blank line before M END)Ĭounts line block specification Value (1 line for each bond): 1st atom, 2nd atom, type, etc. (1 line for each atom): x, y, z (in angstroms), element, etc. (Name of source program and a file timestamp)Ĭomment line (can be blank but line must exist) Title line (can be blank but line must exist) The contents of a Molfile of L-Alanine L-Alanine ![]()
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