message: tweaks to sdf output
diff: @@ -68,7 +68,7 @@ export class SdfEncoder implements Encoder<string> {
  // use separate builder because we still need to write Counts and Bonds line
  const ctab = StringBuilder.create();
  const bonds = StringBuilder.create();
  - const charges = StringBuilder.create();
  + // const charges = StringBuilder.create();
  // write Atom block and gather data for Bonds and Charges
  const { instance, source } = getCategoryInstanceData(category, context);
  @@ -99,7 +99,8 @@ export class SdfEncoder implements Encoder<string> {
  StringBuilder.writeIntegerPadLeft(bonds, i2 + 1, 3);
  StringBuilder.writeIntegerPadLeft(bonds, order, 3);
  StringBuilder.writeSafe(bonds, ' 0 0 0 0\n');
  - // TODO 2nd value: Single bonds: 0 = not stereo, 1 = Up, 4 = Either, 6 = Down, Double bonds: 0 = Use x-, y-, z-coords from atom block to determine cis or trans, 3 = Cis or trans (either) double bond
  + // TODO 3rd value: charge - 0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1, 4 = doublet radical, 5 = -1, 6 = -2, 7 = -3
  + // TODO optional 2nd value: Single bonds: 0 = not stereo, 1 = Up, 4 = Either, 6 = Down, Double bonds: 0 = Use x-, y-, z-coords from atom block to determine cis or trans, 3 = Cis or trans (either) double bond
  bondCount++;
  }
  });
  @@ -108,13 +109,13 @@ export class SdfEncoder implements Encoder<string> {
  // write counts line
  StringBuilder.writeIntegerPadLeft(this.builder, atoms.length, 3);
  StringBuilder.writeIntegerPadLeft(this.builder, bondCount, 3);
  - StringBuilder.write(this.builder, ' 0 0 0 0 0 0 0999 V2000\n');
  - // TODO 2nd value: chiral flag: 0=not chiral, 1=chiral
  + StringBuilder.write(this.builder, ' 0 0 0 0 0 0 0 0 0\n');
  + // TODO optional 2nd value: chiral flag: 0=not chiral, 1=chiral
  StringBuilder.writeSafe(this.builder, StringBuilder.getString(ctab));
  StringBuilder.writeSafe(this.builder, StringBuilder.getString(bonds));
  - StringBuilder.writeSafe(this.builder, StringBuilder.getString(charges));
  - // TODO charges?
  + // StringBuilder.writeSafe(this.builder, StringBuilder.getString(charges));
  + // TODO optional charges
  StringBuilder.writeSafe(this.builder, 'M END\n');
  }
  