dev[fix]: remove all alloc replace to malloc

.gitignore

@@ -21,4 +21,5 @@ __version__.py
 pydockrmsd.egg-info/
 core
 dockrmsd.c
-DockRMSD
+DockRMSD
+a.out

pydockrmsd/DockRMSD_sources/DockRMSD.c

@@ -1,6 +1,3 @@
-#ifndef _GNU_SOURCE
-#define _GNU_SOURCE 1
-#endif
 #include <float.h>
 #include <stdio.h>   /* needed for vsnprintf */
 #include <stdlib.h>  /* needed for malloc-free */
@@ -679,7 +676,7 @@ DockRMSD assignAtoms(char **tempatom, char ***tempbond,
                      DockRMSD rmsd)
 {
     int **allcands = (int **)malloc(sizeof(int *) * atomcount); // List of all atoms in the template that could feasibly be each query atom
-    int *candcounts = (int *)alloca(atomcount * sizeof(int *)); // Number of atoms in the template that could feasibly be each query atom
+    int *candcounts = (int *)malloc(atomcount * sizeof(int)); // Number of atoms in the template that could feasibly be each query atom
     // Iterate through each query atom and determine which template atoms correspond to the query
     for (int i = 0; i < atomcount; i++)
     {
@@ -852,6 +849,7 @@ DockRMSD assignAtoms(char **tempatom, char ***tempbond,
     rmsd.optimal_mapping = optimal_mapping;
     for (int i = 0; i < atomcount; i++)
         free(allcands[i]);
+    free(candcounts);
     free(allcands);
     free(assign);
     free(bestassign);