Fix sdf parser and add sulfur and nitrogen atoms

elementdata.c

@@ -6,7 +6,7 @@
 #include <string.h>
 
 #define MAX_ELEMENTS 120
-#define MAX_LINE_LENGTH 2048
+#define MAX_CSV_LINE_LENGTH 2048
 
 typedef struct {
     char name[50];
@@ -100,7 +100,7 @@ Element* parseCSV(const char* filename, int* element_count) {
         return NULL;
     }
 
-    char line[MAX_LINE_LENGTH];
+    char line[MAX_CSV_LINE_LENGTH];
     fgets(line, sizeof(line), file); // Skip the header line
 
     *element_count = 0;
@@ -156,14 +156,31 @@ Element* parseCSV(const char* filename, int* element_count) {
     return elements;
 }
 
-int main() {
+
+int testParser() {
     int element_count;
     Element* elements = parseCSV("resources/periodictable.csv", &element_count);
     if (elements) {
         for (int i = 0; i < element_count; i++) {
-            printf("Element: %s (%s), Atomic Mass: %.2f, Atomic Radius: %.2f\n", elements[i].name, elements[i].symbol, elements[i].atomic_mass, elements[i].electron_affinity);
+            printf("Element: %s (%s)\n", elements[i].name, elements[i].symbol);
+            printf("Atomic Mass: %.2f\n", elements[i].atomic_mass);
+            printf("Category: %s\n", elements[i].category);
+            printf("Atomic Number: %d\n", elements[i].number);
+            printf("Period: %d\n", elements[i].period);
+            printf("Group: %d\n", elements[i].group);
+            printf("Phase: %s\n", elements[i].phase);
+            printf("Summary: %s\n", elements[i].summary);
+            printf("Shells: %s\n", elements[i].shells);
+            printf("Electron Configuration: %s\n", elements[i].electron_configuration);
+            printf("Electron Configuration Semantic: %s\n", elements[i].electron_configuration_semantic);
+            printf("Electron Affinity: %.2f\n", elements[i].electron_affinity);
+            printf("Electronegativity Pauling: %.2f\n", elements[i].electronegativity_pauling);
+            printf("Ionization Energies: %s\n", elements[i].ionization_energies);
+            printf("CPK Hex Color: %s\n", elements[i].cpk_hex);
+            printf("Block: %s\n", elements[i].block);
         }
         free(elements);
     }
     return 0;
 }
+

main.c

@@ -1,4 +1,5 @@
 #include "debug.h"
+#include "elementdata.c"
 #include "raylib.h"
 #include "sdfparse.c"
 #include <complex.h>
@@ -25,6 +26,9 @@ int main(int argc, char *argv[]) {
   Molecule mol = parseSDF("./resources/sildenafil.sdf");
   // normalizeCoordinates(&mol, screenWidth, screenHeight);
 
+  int element_count;
+  Element* elements = parseCSV("resources/periodictable.csv", &element_count);
+
   D printf("Number of atoms: %d\n", mol.num_atoms);
   for (int i = 0; i < mol.num_atoms; i++) {
     D printf("Atom %d: %s (%.4f, %.4f, %.4f) - neighbours: %d\n", i + 1,
@@ -133,7 +137,8 @@ int main(int argc, char *argv[]) {
   // De-Initialization
   //--------------------------------------------------------------------------------------
 
-  // TODO: Unload all loaded data (textures, fonts, audio) here!
+  free(elements);
+
 
   CloseWindow(); // Close window and OpenGL context
   //--------------------------------------------------------------------------------------
@@ -144,22 +149,27 @@ int main(int argc, char *argv[]) {
 void drawAtom(Atom atom) {
   Color color;
   float radius;
+  int scalingFactor = 100;
 
+// radius is empirical from https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page) 
   if (strcmp(atom.atom_type, "C") == 0) {
     color = BLACK;
-    radius = 70.0f / 100;
+    radius = 70.0f / scalingFactor;
   } else if (strcmp(atom.atom_type, "O") == 0) {
     color = RED;
-    radius = 60.0f / 100;
+    radius = 60.0f / scalingFactor;
   } else if (strcmp(atom.atom_type, "H") == 0) {
     color = LIGHTGRAY;
-    radius = 25.0f / 100;
+    radius = 25.0f / scalingFactor;
   } else if (strcmp(atom.atom_type, "S") == 0) {
     color = YELLOW;
-    radius = 100.0f / 100;
+    radius = 100.0f / scalingFactor;
+  } else if (strcmp(atom.atom_type, "N") == 0) {
+    color = BLUE;
+    radius = 65.0f / scalingFactor;
   } else {
     color = GRAY;
-    radius = 25.0f / 100;
+    radius = 25.0f / scalingFactor;
   }
 
   DrawSphereWires((Vector3){atom.x, atom.y, atom.z}, radius, 25, 25, color);

sdfparse.c

@@ -39,11 +39,13 @@ Molecule parseSDF(const char *filename) {
   char line[MAX_LINE_LENGTH];
   while (fgets(line, MAX_LINE_LENGTH, file) != NULL) {
     // break if you reach M  END
-    if (strncmp(line, "M  END", 6) == 0)
+    if (strncmp(line, "M  END", 6) == 0) {
+      D printf("Reached END\n");
       break;
+    }
 
-    // Ignore the line with bond and atom count, molfile version etc.
-    if (isdigit(line[0]) && isdigit(line[2]))
+    // continue of line contains V2000 or V3000
+    if (strstr(line, "V2000") || strstr(line, "V3000"))
       continue;
 
     // Parse the atoms and their coordinates