#31, cleaned and reordered #includes

ofdock_taskpar_xl/host/inc/calcenergy.h

 #ifndef CALCENERGY_H_
 #define CALCENERGY_H_
-
-#include <math.h>
-#include <stdio.h>
-
-#include "defines.h"
+
+#include "ext_headers.h"
 #include "miscellaneous.h"
 #include "processligand.h"
 #include "getparameters.h"
@@ -50,10 +47,9 @@ typedef struct
 	float  		qasp;
 } Dockparameters;
 
-#include "xcl2.hpp"
+// Aligning struc explictly to XILINX_MEMALIGN to avoid additional memcpy() calls
 #define XILINX_MEMALIGN 4096
 
-// Aligning struc to XILINX_MEMALIGN to avoid additional memcpy() calls
 typedef struct
 {
        	float 		atom_charges_const	     [MAX_NUM_OF_ATOMS]                    	__attribute__ ((aligned (XILINX_MEMALIGN)));

ofdock_taskpar_xl/host/inc/ext_headers.h

+#ifndef EXT_HEADERS_H_
+#define EXT_HEADERS_H_
+
+#include "defines.h"
+
+#include <math.h>	// calcenergy.h, getparameters.h, miscellaneous.h, processgrid.h, processresult.h
+#include <stdio.h>	// calcenergy.h, getparameters.h, miscellaneous.h, processgrid.h, processresult.h, performdocking.h
+#include "xcl2.hpp"	// calcenergy.h, performdocking.h
+#include <string.h>	// getparameters.h, processgrid.h, processresult.h
+#include <time.h>	// miscellaneous.h, performdocking.h, main.cpp
+#include <stdlib.h>	// miscellaneous.h, performdocking.h, processgrid.h
+#include <ctype.h>	// miscellaneous.h
+#include <vector>	// performdocking.h, processgrid.h
+#include <assert.h>	// performdocking.h
+#include <cstring>	// performdocking.h
+#include <libgen.h>	// processgrid.h
+#include <sys/time.h>	// main.cpp
+
+#endif /* EXT_HEADERS_H_ */

ofdock_taskpar_xl/host/inc/getparameters.h

 #ifndef GETPARAMETERS_H_
 #define GETPARAMETERS_H_
 
-#include <math.h>
-#include <string.h>
-#include <stdio.h>
-
-#include "defines.h"
+#include "ext_headers.h"
 #include "processligand.h"
 #include "processgrid.h"
 #include "miscellaneous.h"
@@ -73,5 +69,3 @@ void gen_initpop_and_reflig(Dockpars*       mypars,
 			    const Gridinfo* mygrid);
 
 #endif /* GETPARAMETERS_H_ */
-
-

ofdock_taskpar_xl/host/inc/miscellaneous.h

 #ifndef MISCELLANEOUS_H_
 #define MISCELLANEOUS_H_
 
-#include <time.h>
-#include <stdio.h>
-#include <math.h>
-#include <stdlib.h>
-#include <ctype.h>
+#include "ext_headers.h"
 
 #define PI 3.1415926535
 

ofdock_taskpar_xl/host/inc/performdocking.h

 #ifndef PERFORMDOCKING_H_
 #define PERFORMDOCKING_H_
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <time.h>
-//#include <math.h>
-
+#include "ext_headers.h"
 #include "processgrid.h"
 #include "miscellaneous.h"
 #include "processligand.h"
@@ -13,8 +9,6 @@
 #include "calcenergy.h"	
 #include "processresult.h"
 
-#include "xcl2.hpp"
-#include <vector>
 using std::vector;
 
 #define ELAPSEDSECS(stop,start) ((float) stop-start)/((float) CLOCKS_PER_SEC)
@@ -33,4 +27,4 @@ double check_progress(int* evals_of_runs,
 		      int max_num_of_gens,
 		      int num_of_runs);
 
-#endif /* PERFORMDOCKING_H_ */
+#endif /* PERFORMDOCKING_H_ */

ofdock_taskpar_xl/host/inc/processgrid.h

 #ifndef PROCESSGRID_H_
 #define PROCESSGRID_H_
 
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
-
-#include <libgen.h>
+#include "ext_headers.h"
 
 // libgen.h contains basename() and dir() from a fullpath name
 // Specific: to open correctly grid map field fiels and associated files
@@ -16,7 +11,6 @@
 #include "miscellaneous.h"
 
 // Added for allocating fgrids
-#include <vector>
 using std::vector;
 
 #define getvalue_4Darr(mempoi, grinf, t, z, y, x)                  *(mempoi + (grinf).size_xyz[0] * (y + (grinf).size_xyz[1] * (z + (grinf).size_xyz[2]*t)) + x)

ofdock_taskpar_xl/host/inc/processligand.h

 #ifndef PROCESSLIGAND_H_
 #define PROCESSLIGAND_H_
 
-#include "defines.h"
+#include "ext_headers.h"
 #include "processgrid.h"
 #include "miscellaneous.h"
 

ofdock_taskpar_xl/host/inc/processresult.h

 #ifndef PROCESSRESULT_H_
 #define PROCESSRESULT_H_
 
-#include <stdio.h>
-#include <string.h>
-#include <math.h>
-
-#include "defines.h"
+#include "ext_headers.h"
 #include "processligand.h"
 #include "getparameters.h"
 

ofdock_taskpar_xl/host/src/main.cpp

-//#include <stdio.h>
-//#include <stdlib.h>
-#include <time.h>
-
+#include "ext_headers.h"
 #include "processgrid.h"
-//include "processresult.h"
 #include "processligand.h"
 #include "getparameters.h"
 #include "performdocking.h"
 
-
 // ------------------------
 // Correct time measurement
 // Moved to performdocking.cpp to skip measuring build time
-#include <sys/time.h>
 // ------------------------
 
 int main(int argc, char* argv[])

ofdock_taskpar_xl/host/src/performdocking.cpp

@@ -2,18 +2,9 @@
 //// Correct time measurement
 //// Moved from main.cpp to performdocking.cpp
 //// to skip measuring build time
-//#include <sys/time.h>
 //// ------------------------
 #include "performdocking.h"
 
-
-#include <assert.h>
-//#include <stdio.h>
-//#include <stdlib.h>
-//#include <math.h>
-#include <cstring>
-
-
 //// --------------------------------
 //// Device memory buffers
 //// --------------------------------