[gentoo-commits] gentoo-x86 commit in sci-libs/mmdb/files: 1.21-allignment.patch

[Justin Lecher (jlec)]

jlec        10/06/30 20:55:04

  Added:                1.21-allignment.patch
  Log:
  Fixed broken allignment, #315387
  (Portage version: 2.2_rc67/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-libs/mmdb/files/1.21-allignment.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/mmdb/files/1.21-allignment.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/mmdb/files/1.21-allignment.patch?rev=1.1&content-type=text/plain

Index: 1.21-allignment.patch
===================================================================
diff --git a/src/file_.cpp b/src/file_.cpp
index 4071886..6bfa648 100644
--- a/src/file_.cpp
+++ b/src/file_.cpp
@@ -347,10 +347,10 @@ int  i;
           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 --git a/src/machine_.h b/src/machine_.h
old mode 100644
new mode 100755
index 2e81264..c658981
--- a/src/machine_.h
+++ b/src/machine_.h
@@ -1,4 +1,4 @@
-//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
+//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
 //  =================================================================
 //
 //   CCP4 Coordinate Library: support of coordinate-related
@@ -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 @@ typedef  double     apireal;    // FORTRAN  real*8
 
 #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 @@ typedef  double     apireal;    // FORTRAN  real*8
 
 # define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
     NAME p_mvs
-
+# endif
 #else
 
 # error  Unknown machine!!!
diff --git a/src/mmdb_atom.h b/src/mmdb_atom.h
old mode 100644
new mode 100755
index 45049c8..672e11a
--- a/src/mmdb_atom.h
+++ b/src/mmdb_atom.h
@@ -1,4 +1,4 @@
-//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
+//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
 //  =================================================================
 //
 //   CCP4 Coordinate Library: support of coordinate-related
@@ -290,7 +290,7 @@ class CAtom : public CUDData  {
     void  CalcAtomStatistics ( RSAtomStat AS );
     realtype GetDist2 ( PCAtom a );
     realtype GetDist2 ( PCAtom a, mat44 & tm );  // tm applies to A
-    realtype GetDist2 ( PCAtom a, mat33 & r, vect3 & t );// tm applies to A
+    realtype GetDist2 ( PCAtom a, mat33 & r, vect3 & t );  // tm applies to A
     realtype GetDist2 ( realtype ax, realtype ay, realtype az );
 
     // GetCosine(a1,a2) calculates cosine of angle a1-this-a2,
diff --git a/src/mmdb_chain.cpp b/src/mmdb_chain.cpp
old mode 100644
new mode 100755
index a6f66c2..1fa165b
--- a/src/mmdb_chain.cpp
+++ b/src/mmdb_chain.cpp
@@ -1,4 +1,4 @@
-//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
+//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
 //  =================================================================
 //
 //   CCP4 Coordinate Library: support of coordinate-related
@@ -672,7 +672,8 @@ int  i,k,sN;
     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 --git a/src/mmdb_rwbrook.cpp b/src/mmdb_rwbrook.cpp
old mode 100644
new mode 100755
index dc33086..ef58641
--- a/src/mmdb_rwbrook.cpp
+++ b/src/mmdb_rwbrook.cpp
@@ -1,4 +1,4 @@
-//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
+//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
 //  =================================================================
 //
 //   CCP4 Coordinate Library: support of coordinate-related
@@ -1478,7 +1478,6 @@ AltLoc   altLoc;
 SegID    sgID;
 Element  element;
 PCAtom   atom;
-pstr     p;
 char     charge[10];
 
   strcpy ( LastFunc,"MMDB_F_Atom" );
@@ -1552,10 +1551,9 @@ char     charge[10];
     } 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 @@ char     charge[10];
         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 --git a/src/mmdb_sbase0.cpp b/src/mmdb_sbase0.cpp
old mode 100644
new mode 100755
index a210d62..3bf0d52
--- a/src/mmdb_sbase0.cpp
+++ b/src/mmdb_sbase0.cpp
@@ -1,4 +1,4 @@
-//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
+//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
 //  =================================================================
 //
 //   CCP4 Coordinate Library: support of coordinate-related
@@ -1320,7 +1320,11 @@ PPCSBIndex Index1;
     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 --git a/src/mmdb_selmngr.cpp b/src/mmdb_selmngr.cpp
old mode 100644
new mode 100755
index b923529..3a9e249
--- a/src/mmdb_selmngr.cpp
+++ b/src/mmdb_selmngr.cpp
@@ -1,4 +1,4 @@
-//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
+//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
 //  =================================================================
 //
 //   CCP4 Coordinate Library: support of coordinate-related
@@ -1158,7 +1158,7 @@ void  CMMDBSelManager::Select (
              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 --git a/src/mmdb_title.cpp b/src/mmdb_title.cpp
old mode 100644
new mode 100755
index b0b2ae5..1033ae5
--- a/src/mmdb_title.cpp
+++ b/src/mmdb_title.cpp
@@ -1,4 +1,4 @@
-//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
+//  $Id: 1.21-allignment.patch,v 1.1 2010/06/30 20:55:04 jlec Exp $
 //  =================================================================
 //
 //   CCP4 Coordinate Library: support of coordinate-related
@@ -1381,6 +1381,10 @@ MakeStreamFunctions(CRemark)
 #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;
@@ -1458,7 +1462,7 @@ int      l,lkey,nAdd,j;
 
   while ((i<l) && (lkey==R350_NONE))  {
 
-    p = strcasestr ( rem->Remark,"CHAINS:" );
+    p = strcasestr( rem->Remark,"CHAINS:" );
     if (p)  p += 7;
     else  {
       p = rem->Remark;
@@ -1513,7 +1517,7 @@ pstr p1,p2;
 int  l,j,lkey;
 
   sprintf ( PN,"BIOMT%1i",biomtNo );
-  p1 = strcasestr ( rem->Remark,PN );
+  p1 = strcasestr( rem->Remark,PN );
   if (!p1)  return R350_ERRBIOMT;
 
   p1 += 6;
@@ -1972,7 +1976,7 @@ int      i,l;
     if (rem)  {
       if (rem->remarkNum==2)  {
         if (rem->Remark)  {
-          p = strcasestr ( rem->Remark,"RESOLUTION" );
+          p = strcasestr( rem->Remark,"RESOLUTION" );
           if (p)  {
             while ((*p) && (*p!=' '))  p++;
             if (*p)  {