stick_round_nub, UTF-8, display_scale_factor, ...

* stick_round_nub for COLLADA export * UTF-8 in feedback * display_scale_factor (ported from Incentive PyMOL) * dx map import: support "type float" and skewed delta
schrodinger · Feb 28, 2018 · 4bbe425 · 4bbe425
1 parent e2df29a
commit 4bbe425
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Showing 109 changed files with 1,535 additions and 1,183 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -2,6 +2,16 @@
 CHANGE LOG
 =========================================================================
 
+2018-02-28 Thomas Holder <[email protected]>
+
+	* stick_round_nub for COLLADA export
+
+	* UTF-8 in feedback
+
+	* display_scale_factor (ported from Incentive PyMOL)
+
+	* dx map import: support "type float" and skewed delta
+
 2018-02-07 Thomas Holder <[email protected]>
 
 	* new selection keywords: polymer.protein polymer.nucleic

diff --git a/layer0/Base.h b/layer0/Base.h
@@ -21,14 +21,6 @@ Z* -------------------------------------------------------------------
 #include"os_limits.h"
 #include"os_types.h"
 
-#ifndef true
-#define true 1
-#endif
-
-#ifndef false
-#define false 0
-#endif
-
 #ifndef NULL
 #define NULL ((void*)0)
 #endif
@@ -37,13 +29,9 @@ Z* -------------------------------------------------------------------
 #define PI 3.14159265358979323846
 #endif
 
-#ifndef uchar
-#define uchar unsigned char
-#endif
+typedef unsigned char uchar;
 
-#ifndef uint
-#define uint unsigned int
-#endif
+typedef unsigned int uint;
 
 #define MAX_VDW 2.5F            /* this has to go */
 
@@ -60,7 +48,7 @@ Z* -------------------------------------------------------------------
 #endif
 
 typedef struct {
-  int index;                    /* atom index.
+  unsigned int index;           /* atom index.
                                    NOTE: that first record contains the list count...not pick info */
   int bond;                     /* bond index, 
                                    >=0 for bond
@@ -125,7 +113,7 @@ typedef struct _CRay CRay;
 /* likewise */
 
 #ifndef CGO_DEFINED
-typedef struct _CGO CGO;
+class CGO;
 #define CGO_DEFINED
 #endif
 

diff --git a/layer0/Crystal.cpp b/layer0/Crystal.cpp
@@ -31,9 +31,6 @@ Z* -------------------------------------------------------------------
 
 PyObject *CrystalAsPyList(CCrystal * I)
 {
-#ifdef _PYMOL_NOPY
-  return NULL;
-#else
   PyObject *result = NULL;
 
   if(I) {
@@ -42,14 +39,10 @@ PyObject *CrystalAsPyList(CCrystal * I)
     PyList_SetItem(result, 1, PConvFloatArrayToPyList(I->Angle, 3));
   }
   return (PConvAutoNone(result));
-#endif
 }
 
 int CrystalFromPyList(CCrystal * I, PyObject * list)
 {
-#ifdef _PYMOL_NOPY
-  return 0;
-#else
   int ok = true, rok = true;
   int ll = 0;
   if(ok)
@@ -70,8 +63,6 @@ int CrystalFromPyList(CCrystal * I, PyObject * list)
      Always check ll when adding new PyList_GetItem's */
 
   return (rok);
-#endif
-
 }
 
 void CrystalFree(CCrystal * I)

diff --git a/layer0/Crystal.h b/layer0/Crystal.h
@@ -18,7 +18,7 @@ Z* -------------------------------------------------------------------
 #define _H_Crystal
 
 #include"Vector.h"
-#include"CGOStruct.h"
+#include"Base.h"
 #include"os_python.h"
 
 typedef struct {

diff --git a/layer0/Err.cpp b/layer0/Err.cpp
@@ -31,15 +31,11 @@ void ErrFatal(const PyMOLGlobals *, const char *where, const char *what)
 
 int ErrMessage(PyMOLGlobals * G, const char *where, const char *what)
 {
-  char buffer[1024];
-  if(Feedback(G, FB_Executive, FB_Errors)) {
-
     /* unclassified errors are assigned to the Executive catch-all */
 
-    sprintf(buffer, "%s-Error: %s\n", where, what);
-    OrthoAddOutput(G, buffer);
-    OrthoRestorePrompt(G);
-  }
+  PRINTFB(G, FB_Executive, FB_Errors)
+    "%s-Error: %s\n", where, what
+    ENDFB(G);
   return (0);
 }
 

diff --git a/layer0/Feedback.cpp b/layer0/Feedback.cpp
@@ -144,10 +144,15 @@ void FeedbackEnable(PyMOLGlobals * G, unsigned int sysmod, unsigned char mask)
 void FeedbackAutoAdd(PyMOLGlobals * G, unsigned int sysmod, unsigned char mask, const char *str)
 {
   if(Feedback(G, sysmod, mask))
-    OrthoAddOutput(G, str);
+    FeedbackAddColored(G, str, mask);
 }
 
 void FeedbackAdd(PyMOLGlobals * G, const char *str)
 {
   OrthoAddOutput(G, str);
 }
+
+void FeedbackAddColored(PyMOLGlobals * G, const char *str, unsigned char mask)
+{
+  FeedbackAdd(G, str);
+}
diff --git a/layer0/Feedback.h b/layer0/Feedback.h
@@ -229,6 +229,7 @@ void FeedbackPop(PyMOLGlobals * G);
 void FeedbackAutoAdd(PyMOLGlobals * G, unsigned int sysmod, unsigned char mask,
                      const char *str);
 void FeedbackAdd(PyMOLGlobals * G, const char *str);
+void FeedbackAddColored(PyMOLGlobals * G, const char *str, unsigned char mask);
 
 void FeedbackSetMask(PyMOLGlobals * G, unsigned int sysmod, unsigned char mask);
 void FeedbackDisable(PyMOLGlobals * G, unsigned int sysmod, unsigned char mask);

diff --git a/layer0/File.cpp b/layer0/File.cpp
@@ -4,6 +4,11 @@
  * Basic file IO.
  */
 
+#ifdef _WIN32
+#include <vector>
+#include <Windows.h>
+#endif
+
 #include <stdio.h>
 #include <stdlib.h>
 
@@ -44,13 +49,33 @@ static char * fgetcontents(FILE *fp, long *size) {
   return contents;
 }
 
+#ifdef _WIN32
+FILE * pymol_fopen(const char * filename, const char * mode) {
+  FILE *fp = fopen(filename, mode);
+
+  if (!fp) {
+    size_t len_filename = strlen(filename);
+    std::vector<wchar_t> wfilename(len_filename + 1);
+    std::vector<wchar_t> wmode(mode, mode + strlen(mode) + 1);
+
+    if (!MultiByteToWideChar(CP_UTF8, MB_ERR_INVALID_CHARS,
+          filename, len_filename, wfilename.data(), wfilename.size()))
+      return NULL;
+
+    fp = _wfopen(wfilename.data(), wmode.data());
+  }
+
+  return fp;
+}
+#endif
+
 /*
  * Allocate memory and read the entire file for the given filename.
  * The file size is stored into the size pointer if not NULL.
  */
 char * FileGetContents(const char *filename, long *size) {
   char *contents;
-  FILE *fp = fopen(filename, "rb");
+  FILE *fp = pymol_fopen(filename, "rb");
 
   if (!fp)
     return NULL;

diff --git a/layer0/File.h b/layer0/File.h
@@ -7,6 +7,12 @@
 #ifndef _H_File
 #define _H_File
 
+#ifdef _WIN32
+FILE * pymol_fopen(const char * filename, const char * mode);
+#else
+#define pymol_fopen fopen
+#endif
+
 char * FileGetContents(const char *filename, long *size);
 
 #endif
diff --git a/layer0/Matrix.cpp b/layer0/Matrix.cpp
@@ -1176,7 +1176,7 @@ float MatrixFitRMSTTTf(PyMOLGlobals * G, int n, const float *v1, const float *v2
 
       /* Primary iteration scheme to determine rotation matrix for molecule 2 */
       double sg, bb, cc;
-      int iters, ix, iy, iz, unchanged = 0;
+      int iters, iy, iz, unchanged = 0;
       double sig, gam;
       double tmp;
       double save[3][3];
@@ -1196,7 +1196,6 @@ float MatrixFitRMSTTTf(PyMOLGlobals * G, int n, const float *v1, const float *v2
         /* IX, IY, and IZ rotate 1-2-3, 2-3-1, 3-1-2, etc. */
         iz = (iters + 1) % 3;
         iy = (iz + 1) % 3;
-        ix = (iy + 1) % 3;
         sig = aa[iz][iy] - aa[iy][iz];
         gam = aa[iy][iy] + aa[iz][iz];