@Test public void testParseToCML() { NameToStructure nts = NameToStructure.getInstance(); String cml = nts.parseToCML("ethane"); assertEquals("Parsing 'ethane'", "<cml xmlns=\"http: "convention=\"conventions:molecular\" " + "xmlns:conventions=\"http: "xmlns:cmlDict=\"http: "xmlns:nameDict=\"http: "<molecule id=\"m1\">" + "<name dictRef=\"nameDict:unknown\">ethane</name><atomArray>" + "<atom id=\"a1\" elementType=\"C\"><label value=\"1\" dictRef=\"cmlDict:locant\"/><label value=\"alpha\" dictRef=\"cmlDict:locant\"/></atom>" + "<atom id=\"a2\" elementType=\"C\"><label value=\"2\" dictRef=\"cmlDict:locant\"/><label value=\"beta\" dictRef=\"cmlDict:locant\"/></atom>" + "<atom id=\"a3\" elementType=\"H\"/>" + "<atom id=\"a4\" elementType=\"H\"/>" + "<atom id=\"a5\" elementType=\"H\"/>" + "<atom id=\"a6\" elementType=\"H\"/>" + "<atom id=\"a7\" elementType=\"H\"/>" + "<atom id=\"a8\" elementType=\"H\"/>" + "</atomArray><bondArray>" + "<bond id=\"a1_a2\" atomRefs2=\"a1 a2\" order=\"S\"/>" + "<bond id=\"a1_a3\" atomRefs2=\"a1 a3\" order=\"S\"/>" + "<bond id=\"a1_a4\" atomRefs2=\"a1 a4\" order=\"S\"/>" + "<bond id=\"a1_a5\" atomRefs2=\"a1 a5\" order=\"S\"/>" + "<bond id=\"a2_a6\" atomRefs2=\"a2 a6\" order=\"S\"/>" + "<bond id=\"a2_a7\" atomRefs2=\"a2 a7\" order=\"S\"/>" + "<bond id=\"a2_a8\" atomRefs2=\"a2 a8\" order=\"S\"/>" + "</bondArray></molecule></cml>", cml); assertNull("Won't parse helloworld", nts.parseToCML("helloworld")); }
public String parseToCML(String name) { OpsinResult result = parseChemicalName(name); String cml = result.getCml(); if(cml != null && LOG.isDebugEnabled()){ LOG.debug(cml); } return cml; }
NameToStructure { public String parseToCML(String name) { OpsinResult result = parseChemicalName(name); String cml = result.getCml(); if(cml != null && LOG.isDebugEnabled()){ LOG.debug(cml); } return cml; } }
NameToStructure { public String parseToCML(String name) { OpsinResult result = parseChemicalName(name); String cml = result.getCml(); if(cml != null && LOG.isDebugEnabled()){ LOG.debug(cml); } return cml; } private  NameToStructure(); }
NameToStructure { public String parseToCML(String name) { OpsinResult result = parseChemicalName(name); String cml = result.getCml(); if(cml != null && LOG.isDebugEnabled()){ LOG.debug(cml); } return cml; } private  NameToStructure(); static synchronized NameToStructure getInstance(); static String getVersion(); String parseToCML(String name); String parseToSmiles(String name); OpsinResult parseChemicalName(String name); OpsinResult parseChemicalName(String name, NameToStructureConfig n2sConfig); static ParseRules getOpsinParser(); static void main(String [] args); }
NameToStructure { public String parseToCML(String name) { OpsinResult result = parseChemicalName(name); String cml = result.getCml(); if(cml != null && LOG.isDebugEnabled()){ LOG.debug(cml); } return cml; } private  NameToStructure(); static synchronized NameToStructure getInstance(); static String getVersion(); String parseToCML(String name); String parseToSmiles(String name); OpsinResult parseChemicalName(String name); OpsinResult parseChemicalName(String name, NameToStructureConfig n2sConfig); static ParseRules getOpsinParser(); static void main(String [] args);  }