Fixing pdb2cif, and sequence checking

src/pdb/pdb2cif.cpp

@@ -6440,9 +6440,9 @@ file read(std::istream &is)
 		// Well, not quite, Unfortunately... People insisted that
 		// Well, not quite, Unfortunately... People insisted that
 		// having only ATOM records also makes up a valid PDB file...
 		// having only ATOM records also makes up a valid PDB file...
 		// Since mmCIF files cannot validly start with a letter character
 		// Since mmCIF files cannot validly start with a letter character
-		// the test has changed into the following:
+		// apart from the letter 'd', the test has changed into the following:
 
 
-		if (std::isalpha(ch))
+		if (std::isalpha(ch) and std::toupper(ch) != 'D')
 			read_pdb_file(is, result);
 			read_pdb_file(is, result);
 		else
 		else
 		{
 		{

src/pdb/validate-pdbx.cpp

@@ -248,13 +248,12 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 					for (auto comp_id : comp_ids)
 					for (auto comp_id : comp_ids)
 					{
 					{
 						std::string letter;
 						std::string letter;
-						if (compound_factory::kBaseMap.contains(comp_id))
-							letter = compound_factory::kBaseMap.at(comp_id);
-						else if (compound_factory::kAAMap.contains(comp_id))
-							letter = compound_factory::kAAMap.at(comp_id);
-						else
+
+						if (can)
 						{
 						{
-							if (can)
+							if (compound_factory::kBaseMap.contains(comp_id))
+								letter = compound_factory::kBaseMap.at(comp_id);
+							else
 							{
 							{
 								auto c = cf.create(comp_id);
 								auto c = cf.create(comp_id);
 								if (c and c->one_letter_code())
 								if (c and c->one_letter_code())
@@ -262,6 +261,13 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 								else
 								else
 									letter = "X";
 									letter = "X";
 							}
 							}
+						}
+						else
+						{
+							if (compound_factory::kAAMap.contains(comp_id))
+								letter = compound_factory::kAAMap.at(comp_id);
+							else if (comp_id.length() == 1 and compound_factory::kBaseMap.contains(comp_id))
+								letter = compound_factory::kBaseMap.at(comp_id);
 							else
 							else
 								letter = '(' + comp_id + ')';
 								letter = '(' + comp_id + ')';
 						}
 						}