accept corrupt remark 3 fields, improve cif-grep

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@182 a1961a4f-ab94-4bcc-80e8-33b5a54de466

src/PDB2Cif.cpp

@@ -3569,6 +3569,7 @@ void PDBFileParser::ConstructEntities()
 				{ "gene_src_tissue_fraction", cmp.mSource["TISSUE_FRACTION"] },
 				{ "pdbx_gene_src_cell_line", cmp.mSource["CELL_LINE"] },
 				{ "pdbx_gene_src_organelle", cmp.mSource["ORGANELLE"] },
+				{ "pdbx_gene_src_cell", cmp.mSource["CELL"] },
 				{ "pdbx_gene_src_cellular_location", cmp.mSource["CELLULAR_LOCATION"] },
 				{ "host_org_common_name", cmp.mSource["EXPRESSION_SYSTEM_COMMON"] },
 				{ "pdbx_gene_src_scientific_name", cmp.mSource["ORGANISM_SCIENTIFIC"] },
@@ -3577,6 +3578,7 @@ void PDBFileParser::ConstructEntities()
 				{ "pdbx_host_org_ncbi_taxonomy_id", cmp.mSource["EXPRESSION_SYSTEM_TAXID"] },
 				{ "pdbx_host_org_strain", cmp.mSource["EXPRESSION_SYSTEM_STRAIN"] },
 				{ "pdbx_host_org_variant", cmp.mSource["EXPRESSION_SYSTEM_VARIANT"] },
+				{ "pdbx_host_org_cell_line", cmp.mSource["EXPRESSION_SYSTEM_CELL_LINE"] },
 				{ "pdbx_host_org_cellular_location", cmp.mSource["EXPRESSION_SYSTEM_CELLULAR_LOCATION"] },
 				{ "pdbx_host_org_vector_type", cmp.mSource["EXPRESSION_SYSTEM_VECTOR_TYPE"] },
 				{ "pdbx_host_org_vector", cmp.mSource["EXPRESSION_SYSTEM_VECTOR"] },

src/PDB2CifRemark3.cpp

@@ -1020,7 +1020,7 @@ void Remark3Parser::storeCapture(const char* category, initializer_list<const ch
 		string value = mM[capture].str();
 		ba::trim(value);
 
-		if (iequals(value, "NULL") or iequals(value, "NONE"))
+		if (iequals(value, "NULL") or iequals(value, "NONE") or iequals(value, "******"))
 			continue;
 
 		if (VERBOSE >= 3)
@@ -1120,7 +1120,7 @@ void Remark3Parser::storeRefineLsRestr(const char* type, initializer_list<const
 
 		string value = mM[capture].str();
 		ba::trim(value);
-		if (value.empty() or iequals(value, "NULL"))
+		if (value.empty() or iequals(value, "NULL") or iequals(value, "******"))
 			continue;
 
 		if (not r)
@@ -1151,7 +1151,7 @@ void Remark3Parser::updateRefineLsRestr(const char* type, initializer_list<const
 
 				string value = mM[capture].str();
 				ba::trim(value);
-				if (iequals(value, "NULL"))
+				if (iequals(value, "NULL") or iequals(value, "******"))
 					value.clear();
 
 				r[item] = value;