[patch] CCP4 patches to sci-libs/mmdb.

mmdb-1.21-ccp4-6.1.3.patch (text/plain), 5.84 KB, created by Johan Hattne on 2010-04-15 05:35:55 UTC

diff -Naur src/file_.cpp ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/file_.cpp
--- src/file_.cpp	2009-05-06 08:46:03.000000000 -0500
+++ ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/file_.cpp	2009-07-01 05:58:09.000000000 -0500
@@ -347,10 +347,10 @@
           if (i>0)  sleep ( 1 );
 #endif
           if (TextMode)  {
-            if (ReadOnly)  hFile = fopen ( FName,"r"   );
+            if (ReadOnly)  hFile = fopen ( FName,"rt"   );
                      else  hFile = fopen ( FName,"r+t" );
           } else  {
-            if (ReadOnly)  hFile = fopen ( FName,"r"   );
+            if (ReadOnly)  hFile = fopen ( FName,"rb"   );
                      else  hFile = fopen ( FName,"r+b" );
           }
 #ifndef _MVS
diff -Naur src/machine_.h ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/machine_.h
--- src/machine_.h	2009-05-06 08:46:07.000000000 -0500
+++ ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/machine_.h	2008-09-03 03:51:26.000000000 -0500
@@ -127,8 +127,12 @@
 # define CALL_LIKE_VMS  1
 
 // MVS stands for Microsoft Visual Studio
-#elif defined(_MVS) 
+#elif defined(_MSC_VER)
+# if (_MSC_VER) >= 800
+# define CALL_LIKE_MVS  2
+# else
 # define CALL_LIKE_MVS  1
+# endif
 
 #elif defined(F2C) || defined(G77)
 # define CALL_LIKE_SUN  8
@@ -400,6 +404,36 @@
 
 #elif defined(CALL_LIKE_MVS)
 
+# if ( CALL_LIKE_MVS == 2 )
+
+  typedef pstr fpstr;
+
+# define FTN_STR(s)  s
+# define FTN_LEN(s)  s##_len
+
+# define char_struct(s)           \
+    pstr  s;                      \
+    int   s##_len;
+# define fill_char_struct(s,str)  \
+    s  = str;                     \
+    s##_len = strlen(str);
+
+# ifdef __cplusplus
+#   define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
+    extern "C" void NAME p_sun
+# else
+#   define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
+    void NAME p_sun
+# endif
+
+# define FORTRAN_EXTERN(NAME,name,p_sun,p_stardent,p_mvs) \
+    extern "C" void NAME p_sun
+
+# define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
+    NAME p_sun
+
+# else 
+
   typedef pstr fpstr;
 
 # define FTN_STR(s)  s
@@ -425,7 +459,7 @@
 
 # define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
     NAME p_mvs
-
+# endif
 #else
 
 # error  Unknown machine!!!
diff -Naur src/mmdb_chain.cpp ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_chain.cpp
--- src/mmdb_chain.cpp	2009-05-06 08:46:03.000000000 -0500
+++ ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_chain.cpp	2009-08-21 08:35:09.000000000 -0500
@@ -672,7 +672,8 @@
     i  = 0;
     sN = 1;
     while (i<numRes)  {
-      PutInteger ( &(S[8]),sN,2 );
+      //PutInteger ( &(S[8]),sN,2 );
+      PutInteger ( &(S[7]),sN,3 );
       k = 19;
       while ((i<numRes) && (k<70))  {
         if (resName[i][0])
diff -Naur src/mmdb_rwbrook.cpp ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_rwbrook.cpp
--- src/mmdb_rwbrook.cpp	2009-05-06 08:46:03.000000000 -0500
+++ ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_rwbrook.cpp	2008-11-27 08:14:25.000000000 -0600
@@ -1478,7 +1478,6 @@
 SegID    sgID;
 Element  element;
 PCAtom   atom;
-pstr     p;
 char     charge[10];
 
   strcpy ( LastFunc,"MMDB_F_Atom" );
@@ -1552,10 +1551,9 @@
     } else
       charge [0] = char(0);
 
-/*
     if (FTN_STR(ID)[0]==' ')  {
       atomName[0] = char(0);
-      if ((FTN_STR(AtNam)[1]=='H') ||
+      if ((FTN_STR(AtNam)[1]=='H') && (FTN_STR(AtNam)[0]!='H') ||
           ((FTN_STR(AtNam)[1]=='D') && (FTN_STR(ID)[2]=='D')))  {
         i = 0;
         while ((i<nHydAtomNames) && 
@@ -1563,12 +1561,16 @@
         if (i<nHydAtomNames)
           GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
       }
-      if (!atomName[0])  {
+
+      if ((FTN_STR(AtNam)[0]=='A') || ((FTN_STR(AtNam)[0]=='N') && (FTN_STR(ID)[1]!='N'))) {
+        GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
+      } else if ((FTN_STR(ID)[1]=='N') && ( (FTN_STR(AtNam)[0]=='N') && (FTN_STR(AtNam)[1]=='N') )) {
+        GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
+      } else if (!atomName[0])  {
         atomName[0] = ' ';
         GetStrTer ( &(atomName[1]),FTN_STR(AtNam),3,4,FTN_LEN(AtNam) );
       }
     } else
-*/
       GetStrTer ( atomName,FTN_STR(AtNam),4,5,4 );
 
 
diff -Naur src/mmdb_sbase0.cpp ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_sbase0.cpp
--- src/mmdb_sbase0.cpp	2009-05-06 08:46:03.000000000 -0500
+++ ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_sbase0.cpp	2009-07-01 05:52:19.000000000 -0500
@@ -1320,7 +1320,11 @@
     dirpath = new char[i+10];
     strcpy ( dirpath,path );
     if (i>0)  {
+#if defined(_MSC_VER) || defined (WIN32)
+      if (dirpath[i-1]!='\\')  strcat ( dirpath,"\\" );
+#else
       if (dirpath[i-1]!='/')  strcat ( dirpath,"/" );
+#endif
     }
   }
 
diff -Naur src/mmdb_selmngr.cpp ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_selmngr.cpp
--- src/mmdb_selmngr.cpp	2009-05-06 08:46:03.000000000 -0500
+++ ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_selmngr.cpp	2009-07-01 05:53:24.000000000 -0500
@@ -1158,7 +1158,7 @@
              int   selKey    // selection key
                     )  {
 int       i,j,k,n,m1,m2,c, sk,nsel;
-Boolean   noRes,modelSel,chainSel,resSel,selAND;
+Boolean   noRes,modelSel(False),chainSel,resSel,selAND;
 PCModel   model;
 PCChain   chain;
 PCResidue res;
diff -Naur src/mmdb_title.cpp ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_title.cpp
--- src/mmdb_title.cpp	2009-05-06 08:46:03.000000000 -0500
+++ ../../../ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src/mmdb/mmdb_title.cpp	2010-01-16 07:30:53.000000000 -0600
@@ -1381,6 +1381,10 @@
 #define  R350_CHAINS         2
 #define  R350_BIOMT          3
 
+#ifdef _WIN32
+#define  strcasestr(s, t) strstr(strupr(s), t)
+#endif
+
 void getRemarkKey ( RPCRemark rem, int & lkey )  {
   if (rem)  {
     if (rem->remarkNum!=350)  lkey = R350_END;