Version Bump

(Portage version: 2.2.0_alpha26/cvs/Linux x86_64)

1 files changed, 150 insertions, 0 deletions

diff --git a/sci-libs/mmdb/files/1.23.2-allignment.patch b/sci-libs/mmdb/files/1.23.2-allignment.patch
new file mode 100644
index 000000000000..7d7c159e7daa
--- /dev/null
+++ b/sci-libs/mmdb/files/1.23.2-allignment.patch
@@ -0,0 +1,150 @@
+diff --git a/src/machine_.h b/src/machine_.h
+index 804bc6d..6ed52a6 100644
+--- a/src/machine_.h
++++ b/src/machine_.h
+@@ -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

+@@ -400,11 +404,41 @@ 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
++# define FTN_LEN(s)  s##_len
++
+ # define char_struct(s)  \

+     pstr  s;             \

+     int   s##_len;

+@@ -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
+index 61bafaa..c860e30 100644
+--- a/src/mmdb_atom.h
++++ b/src/mmdb_atom.h
+@@ -312,7 +312,7 @@ class CAtom : public CUDData  {
+ 

+     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
+index 95023b7..fcf602f 100644
+--- a/src/mmdb_chain.cpp
++++ b/src/mmdb_chain.cpp
+@@ -679,7 +679,7 @@ int  i,k,sN;
+     i  = 0;

+     sN = 1;

+     while (i<numRes)  {

+-      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_selmngr.cpp b/src/mmdb_selmngr.cpp
+index 20261c7..87b4bef 100644
+--- a/src/mmdb_selmngr.cpp
++++ b/src/mmdb_selmngr.cpp
+@@ -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
+index 3dd7925..eb6de74 100644
+--- a/src/mmdb_title.cpp
++++ b/src/mmdb_title.cpp
+@@ -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;

+@@ -1976,7 +1980,7 @@ 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)  {