PlantAI-dev/tools/pymol-open-source/contrib/uiuc/plugins/molfile_plugin/post.patch

diff --git a/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c b/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c
index e4285af..468411e 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c
+++ b/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c
@@ -218,7 +218,7 @@ typedef struct {
 /* Use block-based I/O by default when writing structures larger */
 /* than JSBLOCKIO_THRESH atoms, or when directed by the user and */
 /* not otherwise prohibited...                                   */
-static int js_blockio_check_and_set(jshandle *js) {
+static void js_blockio_check_and_set(jshandle *js) {
   if ((getenv("VMDJSNOBLOCKIO") == NULL) && 
       ((js->natoms > JSBLOCKIO_THRESH) || getenv("VMDJSBLOCKIO"))) {
     js->optflags |= JSOPT_TS_BLOCKIO;
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c b/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
index 5cca862..5f1e9f0 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
+++ b/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
@@ -1280,7 +1280,7 @@ static int read_wave_coeffs(FILE *file, qm_wavefunction_t *wave) {
       
       // DEBUG
       //printf("moldenplugin) %d,%d: %d %f\n", i, AOid-1, AOid, wave_coeffs[i*wave->num_coeffs+AOid-1]);
-      nr2 = sscanf(buffer, "%s", &keystring);
+      nr2 = sscanf(buffer, "%s", keystring);
       if(!strcmp(keystring,"Ene=")||nr2==-1) 
         break;
 
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/ply.h b/contrib/uiuc/plugins/molfile_plugin/src/ply.h
index 127844c..784378f 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/ply.h
+++ b/contrib/uiuc/plugins/molfile_plugin/src/ply.h
@@ -66,7 +66,7 @@ extern "C" {
 
 typedef struct PlyProperty {    /* description of a property */
 
-  char *name;                   /* property name */
+  const char *name;             /* property name */
   int external_type;            /* file's data type */
   int internal_type;            /* program's data type */
   int offset;                   /* offset bytes of prop in a struct */
@@ -222,7 +222,6 @@ void set_prop_rules_ply (PlyFile *, PlyRuleList *);
 PlyRuleList *append_prop_rule (PlyRuleList *, char *, char *);
 int matches_rule_name (char *);
 
-int equal_strings(char *, char *);
 char *recreate_command_line (int, char *argv[]);
 
 
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h b/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h
index 272d31a..31a7d5f 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h
+++ b/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h
@@ -37,12 +37,12 @@ WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
 #include <string.h>
 #include <ply.h>
 
-char *type_names[] = {  /* names of scalar types */
+const char *type_names[] = {  /* names of scalar types */
 "invalid",
 "int8", "int16", "int32", "uint8", "uint16", "uint32", "float32", "float64",
 };
 
-char *old_type_names[] = {  /* old names of types for backward compatability */
+const char *old_type_names[] = {  /* old names of types for backward compatability */
 "invalid",
 "char", "short", "int", "uchar", "ushort", "uint", "float", "double",
 };
@@ -60,13 +60,14 @@ int ply_type_size[] = {
 #define NAMED_PROP       1
 
 /* returns 1 if strings are equal, 0 if not */
-int equal_strings(char *, char *);
+static
+int equal_strings(const char *, const char *);
 
 /* find an element in a plyfile's list */
-PlyElement *find_element(PlyFile *, char *);
+PlyElement *find_element(PlyFile *, const char *);
 
 /* find a property in an element's list */
-PlyProperty *find_property(PlyElement *, char *, int *);
+PlyProperty *find_property(PlyElement *, const char *, int *);
 
 /* write to a file the word describing a PLY file data type */
 void write_scalar_type (FILE *, int);
@@ -105,7 +106,7 @@ void ascii_get_element(PlyFile *, char *);
 void binary_get_element(PlyFile *, char *);
 
 /* memory allocation */
-static char *my_alloc(int, int, char *);
+static char *my_alloc(int, int, const char *);
 
 
 /*************/
@@ -188,9 +189,7 @@ PlyFile *open_for_writing_ply(
   int file_type
 )
 {
-  int i;
   PlyFile *plyfile;
-  PlyElement *elem;
   char *name;
   FILE *fp;
 
@@ -333,9 +332,7 @@ void element_count_ply(
   int nelems
 )
 {
-  int i;
   PlyElement *elem;
-  PlyProperty *prop;
 
   /* look for appropriate element */
   elem = find_element (plyfile, elem_name);
@@ -613,7 +610,6 @@ PlyFile *ply_read(FILE *fp, int *nelems, char ***elem_names)
   PlyFile *plyfile;
   int nwords;
   char **words;
-  int found_format = 0;
   char **elist;
   PlyElement *elem;
   char *orig_line;
@@ -656,7 +652,6 @@ PlyFile *ply_read(FILE *fp, int *nelems, char ***elem_names)
       else
         return (NULL);
       plyfile->version = atof (words[2]);
-      found_format = 1;
     }
     else if (equal_strings (words[0], "element"))
       add_element (plyfile, words, nwords);
@@ -1302,10 +1297,9 @@ void get_info_ply(PlyFile *ply, float *version, int *file_type)
 Compare two strings.  Returns 1 if they are the same, 0 if not.
 ******************************************************************************/
 
-int equal_strings(char *s1, char *s2)
+static
+int equal_strings(const char *s1, const char *s2)
 {
-  int i;
-
   while (*s1 && *s2)
     if (*s1++ != *s2++)
       return (0);
@@ -1361,7 +1355,7 @@ Exit:
   returns the element, or NULL if not found
 ******************************************************************************/
 
-PlyElement *find_element(PlyFile *plyfile, char *element)
+PlyElement *find_element(PlyFile *plyfile, const char *element)
 {
   int i;
 
@@ -1385,7 +1379,7 @@ Exit:
   returns a pointer to the property, or NULL if not found
 ******************************************************************************/
 
-PlyProperty *find_property(PlyElement *elem, char *prop_name, int *index)
+PlyProperty *find_property(PlyElement *elem, const char *prop_name, int *index)
 {
   int i;
 
@@ -1416,7 +1410,6 @@ void ascii_get_element(PlyFile *plyfile, char *elem_ptr)
   char **words;
   int nwords;
   int which_word;
-  FILE *fp = plyfile->fp;
   char *elem_data,*item;
   char *item_ptr;
   int item_size;
@@ -1697,7 +1690,6 @@ Exit:
 char **get_words(FILE *fp, int *nwords, char **orig_line)
 {
 #define BIG_STRING 4096
-  int i,j;
   static char str[BIG_STRING];
   static char str_copy[BIG_STRING];
   char **words;
@@ -2310,8 +2302,6 @@ Entry:
 
 void add_property (PlyFile *plyfile, char **words, int nwords)
 {
-  int prop_type;
-  int count_type;
   PlyProperty *prop;
   PlyElement *elem;
 
@@ -2421,7 +2411,7 @@ Entry:
   fname - file name from which memory was requested
 ******************************************************************************/
 
-static char *my_alloc(int size, int lnum, char *fname)
+static char *my_alloc(int size, int lnum, const char *fname)
 {
   char *ptr;
 
@@ -2759,9 +2749,7 @@ void describe_element_ply(
   int nelems
 )
 {
-  int i;
   PlyElement *elem;
-  PlyProperty *prop;
 
   /* look for appropriate element */
   elem = find_element (plyfile, elem_name);
@@ -2916,7 +2904,7 @@ void describe_other_elements_ply (
 
 typedef struct RuleName {
   int code;
-  char *name;
+  const char *name;
 } RuleName;
 
 RuleName rule_name_list[] = {
@@ -3043,10 +3031,6 @@ Entry:
 
 void start_props_ply (PlyFile *ply, PlyPropRules *rules)
 {
-  int i;
-  int count;
-  PlyElement *elem = rules->elem;
-
   /* save pointer to the rules in the PLY object */
   ply->current_rules = rules;
 
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp
index a0f6c8e..e79fb98 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp
+++ b/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp
@@ -44,10 +44,6 @@ typedef struct Face {
   void *other_props;       /* other properties */
 } Face;
 
-char *elem_names[] = { /* list of the elements in the object */
-  "vertex", "face"
-};
-
 PlyProperty vert_props[] = { /* list of property information for a vertex */
   {"x", Float32, Float32, offsetof(Vertex,x), 0, 0, 0, 0},
   {"y", Float32, Float32, offsetof(Vertex,y), 0, 0, 0, 0},
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp
index a8acdcb1d..008ad6c28 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp
+++ b/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp
@@ -109,6 +109,8 @@ static void *open_file_read(const char *filepath, const char *filetype,
   msms->vfd = vfd;
   msms->graphics = NULL;
   *natoms = 0;
+  free(facefilepath);
+  free(vertfilepath);
   return msms;
 }
 
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c b/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c
index 7d74ba305..d981df93f 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c
+++ b/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c
@@ -139,7 +139,7 @@ static int read_vaspoutcar_structure(void *mydata, int *optflags, molfile_atom_t
    * that contains the name of the element (H, He, C etc.).
    * Otherwise try to find similar mass in periodic table.
    */
-  if (strstr(potcarfile, "OUTCAR")) {
+  if (strstr(data->filename, "OUTCAR")) {
     strcpy(potcarfile, data->filename);
     strcpy(strstr(potcarfile, "OUTCAR"), "POTCAR");
     potcar = fopen(potcarfile, "r");
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c b/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c
index 5bff3c70b..42f02409e 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c
+++ b/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c
@@ -75,13 +75,14 @@ static void *open_vaspposcar_read(const char *filename, const char *filetype, in
   /* Read the number of atoms per atom type */
   data->numatoms = 0;
   for (i = 0; i < MAXATOMTYPES; ++i) {
-    char const *tmplineptr = strdup(lineptr);
+    char const *tmplineptr = lineptr;
     char const *token = (i == 0 ? strtok(lineptr, " ") : strtok(NULL, " "));
     int const n = (token ? atoi(token) : -1);
 
     /* if fails to read number of atoms, then assume VASP5 */
     if (i == 0 && n <= 0) {
       data->version = 5;
+      free(data->titleline);
       data->titleline =  strdup(tmplineptr);
       fgets(lineptr, LINESIZE, data->file);
       break;
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c b/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c
index a01ea4241..9243b4f25 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c
+++ b/contrib/uiuc/plugins/molfile_plugin/src/corplugin.c
@@ -127,7 +127,7 @@ static FILE *open_cor_file(const char *fname, int *natom, int *iofoext) {
       return NULL;
     }
 
-    if (sscanf(inbuf, "%10c", header) != 1) {
+    if (sscanf(inbuf, "%10s", header) != 1) {
       fclose(f);
       printf("corplugin) Error opening file: improperly formatted line.\n");
       return NULL;
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
index 8308fd90f..e55e6f0db 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
+++ b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
@@ -799,6 +799,7 @@ namespace {
 
   class AtomArray : public Array {
     int i_name, i_resname, i_resid, i_x, i_y, i_z, i_vx, i_vy, i_vz, 
+        i_inscode,
         i_anum, i_chain, i_segid, i_charge;
     std::vector<molfile_atom_t> &atoms;
     std::vector<pos_t> &pos;
@@ -811,6 +812,7 @@ namespace {
       i_name(-1), i_resname(-1), i_resid(-1), 
       i_x(-1), i_y(-1), i_z(-1), 
       i_vx(-1), i_vy(-1), i_vz(-1),
+      i_inscode(-1),
       i_anum(-1), i_chain(-1), i_segid(-1),
       i_charge(0),
       atoms( h->ctmap[m_ct].particles ),
@@ -840,6 +842,7 @@ namespace {
         else if (attr=="m_chain_name")       i_chain=i;
         else if (attr=="m_pdb_segment_name") i_segid=i;
         else if (attr=="m_formal_charge")  { i_charge=i; h->optflags |= MOLFILE_CHARGE; }
+        else if (attr=="m_insertion_code") { i_inscode=i; }
       }
     }
 
@@ -852,6 +855,7 @@ namespace {
       if (i_resid>=0)   get_int(row[i_resid], a.resid);
       if (i_segid>=0)   GET_STR(row[i_segid], a.segid);
       if (i_chain>=0)   GET_STR(row[i_chain], a.chain);
+      if (i_inscode>=0) GET_STR(row[i_inscode], a.insertion);
 
 #if defined(DESRES_CTNUMBER)
       a.ctnumber = m_ct;
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp
index 5d95c4344..f6a8f02bf 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp
+++ b/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp
@@ -231,7 +231,9 @@ static void *open_cube_read(const char *filepath, const char *filetype,
   // the cellvectors (and the coordinates) in such a way,
   // that the a-vector is collinear with the x-axis and
   // the b-vector is in the xy-plane. 
+#if 0
   cube_buildrotmat(cube, voltmpl.origin, a, b);
+#endif
   // print warning, if the rotation will be significant:
   if ((fabs((double) a[1]) + fabs((double) a[2]) + fabs((double) b[2]))
       > 0.001) {