private IRenderingElement generateMixtureSgroup(Sgroup sgroup) {
// draw the brackets
// TODO - mixtures normally have attached Sgroup data
// TODO - e.g. COMPONENT_FRACTION, ACTIVITY_TYPE, WEIGHT_PERCENT
List<SgroupBracket> brackets = sgroup.getValue(SgroupKey.CtabBracket);
if (brackets != null) {
SgroupType type = sgroup.getType();
String subscript = "?";
switch (type) {
case CtabComponent:
Integer compNum = sgroup.getValue(SgroupKey.CtabComponentNumber);
if (compNum != null) subscript = "c" + Integer.toString(compNum);
else subscript = "c";
break;
case CtabMixture:
subscript = "mix";
break;
case CtabFormulation:
subscript = "f";
break;
}
return generateSgroupBrackets(sgroup, brackets, subscript, null);
} else {
return new ElementGroup();
}
}
/**
* If the molecule has display shortcuts (abbreviations or multiple group sgroups) certain parts
* of the structure are hidden from display. This method marks the parts to hide and in the case
* of abbreviations, remaps atom symbols. Appart from additional property flags, the molecule is
* unchanged by this method.
*
* @param container molecule input
* @param symbolRemap a map that will hold symbol remapping
*/
static void prepareDisplayShortcuts(IAtomContainer container, Map<IAtom, String> symbolRemap) {
List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);
if (sgroups == null || sgroups.isEmpty()) return;
// select abbreviations that should be contracted
for (Sgroup sgroup : sgroups) {
if (sgroup.getType() == SgroupType.CtabAbbreviation) {
Boolean expansion = sgroup.getValue(SgroupKey.CtabExpansion);
// abbreviation is displayed as expanded
if (expansion != null && expansion == Boolean.TRUE) continue;
// no or empty label, skip it
if (sgroup.getSubscript() == null || sgroup.getSubscript().isEmpty()) continue;
contractAbbreviation(container, symbolRemap, sgroup);
} else if (sgroup.getType() == SgroupType.CtabMultipleGroup) {
hideMultipleParts(container, sgroup);
}
}
}
/**
* Generates polymer Sgroup elements.
*
* @param sgroup the Sgroup
* @return the rendered elements (empty if no brackets defined)
*/
private IRenderingElement generatePolymerSgroup(Sgroup sgroup) {
// draw the brackets
List<SgroupBracket> brackets = sgroup.getValue(SgroupKey.CtabBracket);
if (brackets != null) {
SgroupType type = sgroup.getType();
String subscript = sgroup.getValue(SgroupKey.CtabSubScript);
String connectivity = sgroup.getValue(SgroupKey.CtabConnectivity);
switch (type) {
case CtabCopolymer:
subscript = "co";
String subtype = sgroup.getValue(SgroupKey.CtabSubType);
if ("RAN".equals(subtype)) subscript = "ran";
else if ("BLK".equals(subtype)) subscript = "blk";
else if ("ALT".equals(subtype)) subscript = "alt";
break;
case CtabCrossLink:
subscript = "xl";
break;
case CtabAnyPolymer:
subscript = "any";
break;
case CtabGraft:
subscript = "grf";
break;
case CtabMer:
subscript = "mer";
break;
case CtabMonomer:
subscript = "mon";
break;
case CtabModified:
subscript = "mod";
break;
case CtabStructureRepeatUnit:
if (subscript == null) subscript = "n";
if (connectivity == null) connectivity = "eu";
break;
}
return generateSgroupBrackets(sgroup, brackets, subscript, connectivity);
} else {
return new ElementGroup();
}
}
/**
* Generate the Sgroup elements for the provided atom contains.
*
* @param container molecule
* @return Sgroup rendering elements
*/
IRenderingElement generateSgroups(IAtomContainer container) {
ElementGroup result = new ElementGroup();
List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);
if (sgroups == null || sgroups.isEmpty()) return result;
for (Sgroup sgroup : sgroups) {
switch (sgroup.getType()) {
case CtabAbbreviation:
result.add(generateAbbreviationSgroup(sgroup));
break;
case CtabMultipleGroup:
result.add(generateMultipleSgroup(sgroup));
break;
case CtabAnyPolymer:
case CtabMonomer:
case CtabCrossLink:
case CtabCopolymer:
case CtabStructureRepeatUnit:
case CtabMer:
case CtabGraft:
case CtabModified:
result.add(generatePolymerSgroup(sgroup));
break;
case CtabComponent:
case CtabMixture:
case CtabFormulation:
result.add(generateMixtureSgroup(sgroup));
break;
case CtabGeneric:
// not strictly a polymer but okay to draw as one
result.add(generatePolymerSgroup(sgroup));
break;
}
}
return result;
}