From 9d3061ca58d8b69d7dad74a68fc13fe81af0ff8e Mon Sep 17 00:00:00 2001
From: Jarrett Johnson <jarrett.johnson@schrodinger.com>
Date: Thu, 5 Sep 2024 11:20:02 -0400
Subject: [PATCH] Symbol renaming in molfile_plugin and internal linkage

Fixes #395
---
 contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h    | 10 +++++-----
 .../uiuc/plugins/molfile_plugin/src/parm7plugin.cpp    |  8 +++++---
 contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp |  2 ++
 layer0/Isosurf.cpp                                     |  6 ++++--
 layer0/Tetsurf.cpp                                     |  6 ++++--
 ov/src/OVOneToAny.cpp                                  |  2 ++
 ov/src/OVOneToOne.cpp                                  |  2 ++
 7 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h
index 21d967d79..6bd6ddb08 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h
+++ b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h
@@ -59,7 +59,7 @@
 #endif
 
 
-typedef struct parm {
+typedef struct parm7 {
   char title[85];
   char version[85];
   int   IfBox, Nmxrs, IfCap,
@@ -70,7 +70,7 @@ typedef struct parm {
         Ipatm, Natcap,Ifpert,Nbper,Ngper,Ndper,Mbper,Mgper,Mdper,
         Numextra;
   _REAL Box[3], Cutcap, Xcap, Ycap, Zcap;
-} parmstruct;
+} parm7struct;
 
 static int read_parm7_flag(FILE *file, const char *flag, const char *format) {
   char buf[1024];
@@ -359,10 +359,10 @@ static void close_parm7_file(FILE *fileptr, int popn) {
 
 static const char *parm7 = "%8d%8d%8d%8d%8d%8d%8d%8d%8d%8d\n";
 
-static parmstruct *read_parm7_header(FILE *file) {
+static parm7struct *read_parm7_header(FILE *file) {
   char sdum[512]; 
-  parmstruct *prm;
-  prm = new parmstruct;
+  parm7struct *prm;
+  prm = new parm7struct;
 
   /* READ VERSION */
   fgets(sdum, 512, file);
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp
index faf2717c6..2d46553b4 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp
+++ b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp
@@ -24,13 +24,15 @@
 #include "molfile_plugin.h"
 #include "ReadPARM7.h"
 
+namespace {
 typedef struct {
-  parmstruct *prm;
+  parm7struct *prm;
   int popn;
   FILE *fd;
   int nbonds;
   int *from, *to;
 } parmdata;
+}
 
 static void *open_parm7_read(const char *filename, const char *,int *natoms) {
   FILE *fd;
@@ -39,7 +41,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) {
     fprintf(stderr, "parm7plugin) Cannot open parm file '%s'\n", filename);
     return NULL;
   }
-  parmstruct *prm = read_parm7_header(fd);
+  parm7struct *prm = read_parm7_header(fd);
   if (!prm) {
     close_parm7_file(fd, popn);
     return NULL; 
@@ -58,7 +60,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) {
 
 static int read_parm7_structure(void *mydata, int *optflags, molfile_atom_t *atoms) {
   parmdata *p = (parmdata *)mydata;
-  const parmstruct *prm = p->prm;
+  const parm7struct *prm = p->prm;
   FILE *file = p->fd;
   char buf[85];
   char field[85];
diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp
index acabcb1b5..4996383e1 100644
--- a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp
+++ b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp
@@ -24,12 +24,14 @@
 #include "ReadPARM.h"
 #include "molfile_plugin.h"
 
+namespace {
 typedef struct {
   ReadPARM *rp;
   FILE *parm;
   int natoms;
   int *from, *to;
 } parmdata;
+}
 
 static void *open_parm_read(const char *filename, const char *, 
     int *natoms) {
diff --git a/layer0/Isosurf.cpp b/layer0/Isosurf.cpp
index 77cf42eeb..b2dfaedd7 100644
--- a/layer0/Isosurf.cpp
+++ b/layer0/Isosurf.cpp
@@ -44,11 +44,13 @@ Z* -------------------------------------------------------------------
 
 #define I4(field,P1,P2,P3,P4) ((field)->get<int>(P1,P2,P3,P4))
 
-typedef struct PointType {
+namespace {
+struct PointType {
   float Point[3];
   int NLink;
   struct PointType* Link[4];
-} PointType;
+};
+}
 
 #define EdgePtPtr(field,P2,P3,P4,P5) ((field)->ptr(P2,P3,P4,P5))
 
diff --git a/layer0/Tetsurf.cpp b/layer0/Tetsurf.cpp
index 0d78b535e..cb2f5b37b 100644
--- a/layer0/Tetsurf.cpp
+++ b/layer0/Tetsurf.cpp
@@ -38,12 +38,14 @@ Z* -------------------------------------------------------------------
 
 #define I3(field,P1,P2,P3) ((field)->get<int>(P1,P2,P3))
 
-typedef struct {
+namespace {
+struct PointType {
   float Point[3];
   float Normal[3];
   int NormalFlag;
   int Link;
-} PointType;
+};
+}
 
 typedef struct {
   PointType *p[3];
diff --git a/ov/src/OVOneToAny.cpp b/ov/src/OVOneToAny.cpp
index 1a675a51b..5dbbc498c 100644
--- a/ov/src/OVOneToAny.cpp
+++ b/ov/src/OVOneToAny.cpp
@@ -8,11 +8,13 @@
 
 /* FYI: "up" stands for UniquePair -- a precursor to OneToAny */
 
+namespace {
 typedef struct {
   int active;
   ov_word forward_value, reverse_value;
   ov_size forward_next;
 } up_element;
+}
 
 struct _OVOneToAny {
   OVHeap *heap;
diff --git a/ov/src/OVOneToOne.cpp b/ov/src/OVOneToOne.cpp
index 6dfa8f457..4e9baf9c6 100644
--- a/ov/src/OVOneToOne.cpp
+++ b/ov/src/OVOneToOne.cpp
@@ -8,11 +8,13 @@
 
 /* FYI: "up" stands for UniquePair -- a precursor to OneToOne */
 
+namespace {
 typedef struct {
   int active;
   ov_word forward_value, reverse_value;
   ov_size forward_next, reverse_next;
 } up_element;
+}
 
 struct _OVOneToOne {
   OVHeap *heap;