Imported Upstream version 2.0.5

1 files changed, 72 insertions, 34 deletions

diff --git a/mmdb2/mmdb_model.cpp b/mmdb2/mmdb_model.cpp
index ca1d537..23e63ae 100644
--- a/mmdb2/mmdb_model.cpp
+++ b/mmdb2/mmdb_model.cpp
@@ -22,7 +22,7 @@
 //
 //  =================================================================
 //
-//    12.09.13   <--  Date of Last Modification.
+//    11.09.15   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
@@ -46,7 +46,7 @@
 //                  mmdb::CisPep          ( CisPep data                )
 //                  mmdb::Model        ( PDB model                     )
 //
-//  Copyright (C) E. Krissinel 2000-2013
+//  Copyright (C) E. Krissinel 2000-2015
 //
 //  =================================================================
 //
@@ -2116,14 +2116,15 @@ namespace mmdb  {
     strcpy ( chainID2," "    );  // chain ID of 2nd linked atom
     seqNum2 = 0;                 // sequence number of 2nd linked atom
     strcpy ( insCode2," "    );  // insertion code of 2nd linked atom
-    s1 = 1;  // sym id of 1st atom
-    i1 = 5;
-    j1 = 5;
-    k1 = 5;
-    s2 = 1;  // sym id of 2nd atom
-    i2 = 5;
-    j2 = 5;
-    k2 = 5;
+    s1   = 1;  // sym id of 1st atom
+    i1   = 5;
+    j1   = 5;
+    k1   = 5;
+    s2   = 1;  // sym id of 2nd atom
+    i2   = 5;
+    j2   = 5;
+    k2   = 5;
+    dist = -1.0;  // no distance
   }
 
 
@@ -2157,6 +2158,9 @@ namespace mmdb  {
     PutInteger ( &(S[70]),j2,1 );
     PutInteger ( &(S[71]),k2,1 );
 
+    if (dist>0.0)
+      PutRealF ( &(S[73]),dist,5,3 );
+
   }
 
 
@@ -2184,6 +2188,8 @@ namespace mmdb  {
     Loop->AddLoopTag ( CIFTAG_CONN_PTNR1_SYMMETRY );
     Loop->AddLoopTag ( CIFTAG_CONN_PTNR2_SYMMETRY );
 
+    Loop->AddLoopTag ( CIFTAG_CONN_DIST );
+
   }
 
 
@@ -2219,6 +2225,8 @@ namespace mmdb  {
     sprintf ( S,"%i%i%i%i",s2,i2,j2,k2 );
     Loop->AddString  ( S );
 
+    Loop->AddReal    ( dist     );
+
   }
 
   ERROR_CODE Link::ConvertPDBASCII ( cpstr S )  {
@@ -2245,6 +2253,8 @@ namespace mmdb  {
     GetInteger   ( j2,&(S[70]),1 );
     GetInteger   ( k2,&(S[71]),1 );
 
+    if (!GetReal(dist,&(S[73]),5))  dist = -1.0;
+
     return Error_NoError;
 
   }
@@ -2336,6 +2346,10 @@ namespace mmdb  {
       s2 = atoi(S);
     }
 
+    rc = CIFGetReal ( dist,Loop,CIFTAG_CONN_DIST,n );
+    if (rc==Error_NoData)   return Error_EmptyCIF;
+    if (rc!=Error_NoError)  return rc;
+
     n++;
 
     return Error_NoError;
@@ -2368,10 +2382,12 @@ namespace mmdb  {
     j2 = PLink(Link)->j2;
     k2 = PLink(Link)->k2;
 
+    dist = PLink(Link)->dist;
+
   }
 
   void  Link::write ( io::RFile f )  {
-  byte Version=1;
+  byte Version=2;
 
     f.WriteByte ( &Version    );
 
@@ -2399,6 +2415,8 @@ namespace mmdb  {
     f.WriteInt ( &j2 );
     f.WriteInt ( &k2 );
 
+    f.WriteReal ( &dist );
+
   }
 
   void  Link::read ( io::RFile f )  {
@@ -2430,6 +2448,9 @@ namespace mmdb  {
     f.ReadInt ( &j2 );
     f.ReadInt ( &k2 );
 
+    if (Version>1)
+      f.ReadReal ( &dist );
+
   }
 
   MakeStreamFunctions(Link)
@@ -2553,7 +2574,7 @@ namespace mmdb  {
   void  LinkR::MakeCIF ( mmcif::PData CIF, int N )  {
   UNUSED_ARGUMENT(N);
   mmcif::PLoop Loop;
-  int         RC;
+  int          RC;
 
     RC = CIF->AddLoop ( CIFCAT_STRUCT_LINKR,Loop );
     if (RC!=mmcif::CIFRC_Ok) // the category was (re)created, provide tags
@@ -5048,6 +5069,7 @@ namespace mmdb  {
     ncontacts = 0;
     manager->SeekContacts ( Ca,nres, Ca,nres, 2.0,10.0, 2,
                             contact,ncontacts,0 );
+    manager->RemoveBricks();
     if (ncontacts<=0)  {
       delete[] Res;
       delete[] Ca;
@@ -5268,12 +5290,16 @@ namespace mmdb  {
 
   void  Model::write ( io::RFile f )  {
   int  i,k;
-  byte Version=3;
-
-    f.WriteByte ( &Version );
-
-    ProModel::write ( f );
-
+  byte Version=4;
+  bool compactBinary = false;
+  
+    PManager M = GetCoordHierarchy();
+    if (M)
+      compactBinary = M->isCompactBinary();
+
+    f.WriteByte ( &Version       );
+    f.WriteBool ( &compactBinary );
+    
     f.WriteInt ( &serNum  );
     f.WriteInt ( &nChains );
 
@@ -5284,25 +5310,31 @@ namespace mmdb  {
       if (chain[i]) chain[i]->write ( f );
     }
 
-    hetCompounds.write ( f );
-    helices     .write ( f );
-    sheets      .write ( f );
-    turns       .write ( f );
-    links       .write ( f );
-    linkRs      .write ( f );
+    if (!compactBinary)  {
+
+      ProModel::write ( f );
+  
+      hetCompounds.write ( f );
+      helices     .write ( f );
+      sheets      .write ( f );
+      turns       .write ( f );
+      links       .write ( f );
+      linkRs      .write ( f );
+      
+    }
 
   }
 
   void  Model::read ( io::RFile f )  {
   int  i,k;
   byte Version;
+  bool compactBinary;
 
     FreeMemory();
 
-    f.ReadByte ( &Version );
-
-    ProModel::read ( f );
-
+    f.ReadByte ( &Version       );
+    f.ReadBool ( &compactBinary );
+    
     f.ReadInt ( &serNum  );
     f.ReadInt ( &nChains );
     nChainsAlloc = nChains;
@@ -5318,12 +5350,18 @@ namespace mmdb  {
       }
     }
 
-    hetCompounds.read ( f );
-    helices     .read ( f );
-    sheets      .read ( f );
-    turns       .read ( f );
-    if (Version>1)  links .read ( f );
-    if (Version>2)  linkRs.read ( f );
+    if (!compactBinary)  {
+      
+      ProModel::read ( f );
+  
+      hetCompounds.read ( f );
+      helices     .read ( f );
+      sheets      .read ( f );
+      turns       .read ( f );
+      links       .read ( f );
+      linkRs      .read ( f );
+      
+    }
 
   }