Prevent splitting commas in SMARTS expressions

MetFragLib/src/main/java/de/ipbhalle/metfraglib/parameter/ParameterDataTypes.java

@@ -1,6 +1,8 @@
 package de.ipbhalle.metfraglib.parameter;
 
 import java.util.HashMap;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.log4j.Level;
 
@@ -264,15 +266,71 @@ public static Object getParameter(String parameter, String parameterName) throws
 				values[i] = Double.parseDouble(tmp[i]);
 			return values;
 		}
-		if(type.equals("String[]")) {
-			String[] tmp = parameter.split(",");
-			for(int i = 0; i < tmp.length; i++)
-				tmp[i] = tmp[i].trim();
-			return tmp;
+		if (type.equals("String[]")) {
+			// Special handling for SMARTS inclusion and exclusion lists
+			if (parameterName.equals(VariableNames.PRE_CANDIDATE_FILTER_SMARTS_INCLUSION_LIST_NAME)
+					|| parameterName.equals(VariableNames.PRE_CANDIDATE_FILTER_SMARTS_EXCLUSION_LIST_NAME)) {
+				return splitSmartsString(parameter);
+			} else {
+				String[] tmp = parameter.split(",");
+				for (int i = 0; i < tmp.length; i++)
+					tmp[i] = tmp[i].trim();
+				return tmp;
+			}
 		}
 		return parameter;
 	}
-
+
+	/**
+	 * Splits a string containing multiple SMARTS patterns separated by commas into an array of individual SMARTS patterns.
+	 * This method is designed to handle the complexity of SMARTS syntax, which may include commas as part of the pattern 
+	 * rather than separators.
+	 * 
+	 * Specifically, it ignores commas that are:
+	 * - Inside square brackets, which are used for atom specifications in SMARTS. 
+	 * - Surrounded by bond primitives (e.g., '-', '/', '\\', '?', '=', '#', ':', '~', '@') or the not operator '!', 
+	 *   as these commas are part of the SMARTS pattern. 
+	 *  
+	 * @param input A string containing multiple SMARTS patterns separated by commas.
+	 * @return An array of individual SMARTS patterns.
+	 */
+	public static String[] splitSmartsString(String input) {
+
+		List<String> substrings = new ArrayList<>();
+		int start = 0;
+		int squareBracketCount = 0;
+		String bondPrimitives = "-/\\?=#:~@!";
+
+		for (int i = 0; i < input.length(); i++) {
+			char c = input.charAt(i);
+			if (c == '[') {
+				squareBracketCount++;
+			} else if (c == ']') {
+				squareBracketCount--;
+			} else if (c == ',' && squareBracketCount == 0) {
+
+				// Check if the comma is surrounded by bond primitives or the not operator "!".
+				// If so, skip this comma as it's part of the SMARTS pattern, not a separator.
+				if (i > 0 && i + 1 < input.length() // Check if the comma is not at the beginning or the end of the string
+						&& bondPrimitives.indexOf(input.charAt(i - 1)) != -1
+						&& bondPrimitives.indexOf(input.charAt(i + 1)) != -1) {
+					continue;
+				}
+
+				String substring = input.substring(start, i).trim();
+				if (!substring.isEmpty()) {
+					substrings.add(substring);
+				}
+				start = i + 1;
+			}
+		}
+		String lastSubstring = input.substring(start).trim();
+		if (!lastSubstring.isEmpty()) {
+			substrings.add(lastSubstring);
+		}
+		return substrings.toArray(new String[substrings.size()]);
+	}
+
 	public static String getType(String parameterName) {
 		if(!parameterDatatypes.containsKey(parameterName)) return "";
 		return parameterDatatypes.get(parameterName);

MetFragLib/src/test/java/de/ipbhalle/metfraglib/parameter/CheckParameterDataType_Test.java

@@ -29,6 +29,29 @@ public void test() {
 		}
 	}
 
+	@Test
+	public void testSplitSmartsList() {
+		/*
+		 * check SMARTS list string splitting
+		 */
+		try {
+			String[] smartsListExpected = {
+					"C(=O)-O", // no comma in SMARTS
+					"[C,O]-c1ccccc1", // comma in a pair of square brackets 
+					"C-,=C@,!-N", // comma between bond primitives and not operator "!"
+					"[$(c1(-[O,N])ccccc1),$(c1c(-[O,N])cccc1)]-C(=O)-O", // comma in nested square brackets
+			};
+			String smartsListString = String.join(",", smartsListExpected);
+			String[] smartsListActual = (String[]) ParameterDataTypes.getParameter(smartsListString,
+					VariableNames.PRE_CANDIDATE_FILTER_SMARTS_INCLUSION_LIST_NAME);
+			assertArrayEquals("\"" + smartsListString + "\" " + VariableNames.PRE_CANDIDATE_FILTER_SMARTS_INCLUSION_LIST_NAME + " was wrongly split",
+					smartsListExpected,
+					smartsListActual);
+		} catch (ParameterNotKnownException e) {
+			fail(e.getMessage());
+		}
+	}
+
 	/**
 	 * check exception
 	 *