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/** \file
\brief TPDB class, and its tseqres helper class
*/
#include "TPDB.h"
#include <wx/textfile.h>
TPDB::TPDB ()
{
success = false ;
}
void TPDB::load ( wxString s )
{
vs.Clear () ;
wxTextFile tf ;
tf.Open ( s , *(myapp()->isoconv) ) ;
vs.Add ( tf.GetFirstLine() ) ;
while ( !tf.Eof() )
vs.Add ( tf.GetNextLine() ) ;
check4success () ;
}
void TPDB::paste ( wxString s )
{
explode ( _T("\n") , s , vs ) ;
check4success () ;
}
int TPDB::seq ( char c )
{
for ( int a = 0 ; a < seqres.size() ; a++ )
if ( seqres[a].chain == c )
return a ;
seqres.push_back ( tseqres() ) ;
seqres[seqres.size()-1].chain = c ;
seqres[seqres.size()-1].v = new TVector ;
return seqres.size()-1 ;
}
void TPDB::remap ()
{
int a , b ;
seqres.clear () ;
for ( a = 0 ; a < vs.GetCount() ; a++ )
{
wxString six = vs[a].Left ( 6 ) ;
wxString right = vs[a].Mid ( 6 ) ;
right = right.Trim () ;
right = right.Trim ( false ) ;
six = six.Trim () ;
if ( six == _T("TITLE") )
{
_name = right ;
}
else if ( six == _T("REMARK") )
{
right = right.AfterFirst ( ' ' ) ;
_desc += right + _T("\n") ;
}
else if ( six == _T("SEQRES") )
{
char chain = vs[a].GetChar ( 11 ) ;
wxArrayString v2 ;
right = vs[a].Mid ( 19 ) ;
right = right.Trim () ;
while ( !right.IsEmpty() )
{
v2.Add ( right.BeforeFirst ( ' ' ) ) ;
right = right.AfterFirst ( ' ' ) ;
}
for ( b = 0 ; b < v2.GetCount() ; b++ )
{
wxString h = v2[b] ;
h = h.Trim() ;
char c = seqres[seq(chain)].v->three2one(h.Trim(false)) ;
if ( c != ' ' ) seqres[seq(chain)].sequence += c ;
}
}
else if ( six == _T("DBREF") )
{
wxString name = vs[a].Mid(7,4).Trim(false).Trim() ;
wxString ncbi = vs[a].Mid(33,8).Trim(false).Trim() ;
wxString gb = vs[a].Mid(42,12).Trim(false).Trim() ;
char chain = vs[a].GetChar ( 12 ) ;
seqres[seq(chain)].v->addDescription ( _T("PDB : http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=") + name + _T("\n") ) ;
seqres[seq(chain)].v->addDescription ( _T("GenBank : http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=") + ncbi + _T("\n") ) ;
seqres[seq(chain)].v->addDescription ( _T("NiceProt : http://expasy.org/cgi-bin/niceprot.pl?") + gb + _T("\n") ) ;
seqres[seq(chain)].v->addDescription ( _T("SwissProt : http://expasy.org/cgi-bin/get-sprot-entry?") + ncbi + _T("\n") ) ;
}
else if ( six == _T("HELIX") )
{
wxString name = _T("alpha-") + vs[a].Mid(11,4).Trim(false).Trim() ;
wxString desc = vs[a].Mid ( 40 , 30 ) ;
int from = atoi ( vs[a].Mid(21,4).mb_str() ) ;
int to = atoi ( vs[a].Mid(33,4).mb_str() ) ;
char chain = vs[a].GetChar ( 19 ) ;
desc = _T("\n") + desc.Trim(false).Trim() ;
desc = txt("t_seq_style_alpha") + desc ;
TVectorItem vi ( name , desc , from , to , VIT_MISC ) ;
vi.setParam ( _T("SEQUENCE_STYLE") , _T("1") ) ;
seqres[seq(chain)].v->items.push_back ( vi ) ;
}
else if ( six == _T("SHEET") )
{
wxString name = _T("beta-") + vs[a].Mid(11,4).Trim(false).Trim() ;
wxString desc = txt("t_seq_style_beta") ;
int from = atoi ( vs[a].Mid(22,4).mb_str() ) ;
int to = atoi ( vs[a].Mid(33,4).mb_str() ) ;
char chain = vs[a].GetChar ( 21 ) ;
TVectorItem vi ( name , desc , from , to , VIT_MISC ) ;
vi.setParam ( _T("SEQUENCE_STYLE") , _T("2") ) ;
seqres[seq(chain)].v->items.push_back ( vi ) ;
}
else if ( six == _T("TURN") )
{
wxString name = _T("turn-") + vs[a].Mid(11,4).Trim(false).Trim() ;
wxString desc = vs[a].Mid ( 40 , 30 ) ;
int from = atoi ( vs[a].Mid(20,4).mb_str() ) ;
int to = atoi ( vs[a].Mid(31,4).mb_str() ) ;
char chain = vs[a].GetChar ( 19 ) ;
TVectorItem vi ( name , desc , from , to , VIT_MISC ) ;
vi.setParam ( _T("SEQUENCE_STYLE") , _T("0") ) ;
seqres[seq(chain)].v->items.push_back ( vi ) ;
}
else if ( six == _T("SSBOND") )
{
wxString name = _T("SS") ;
wxString desc = vs[a].Mid(11,4).Trim(false).Trim() ;
int from = atoi ( vs[a].Mid(20,4).mb_str() ) ;
int to = from ;
char chain = vs[a].GetChar ( 15 ) ;
TVectorItem vi ( name , desc , from , to , VIT_MISC ) ;
vi.setParam ( _T("SEQUENCE_STYLE") , _T("5") ) ;
seqres[seq(chain)].v->items.push_back ( vi ) ;
chain = vs[a].GetChar ( 29 ) ;
desc = vs[a].Mid(25,4).Trim(false).Trim() ;
from = atoi ( vs[a].Mid(31,4).mb_str() ) ;
to = from ;
TVectorItem vi2 ( name , desc , from , to , VIT_MISC ) ;
vi2.setParam ( _T("SEQUENCE_STYLE") , _T("5") ) ;
seqres[seq(chain)].v->items.push_back ( vi2 ) ;
}
else if ( six == _T("SLTBRG") || six == _T("LINK") )
{
wxString name = _T("PDB_") + six ;
name = txt(name);
wxString desc = vs[a] ;
int id1 = atoi ( vs[a].Mid(22,4).mb_str() ) ;
int id2 = atoi ( vs[a].Mid(52,4).mb_str() ) ;
wxString name2 = vs[a].Mid(47,3) ;
char chain1 = (char) vs[a].GetChar ( 21 ) ;
char chain2 = (char) vs[a].GetChar ( 51 ) ;
name += _T(" ") + name2 + wxString::Format ( _T("%d %c") , id2 , chain2 ) ;
TVectorItem vi1 ( name , desc , id1 , id1 , VIT_MISC ) ;
vi1.setParam ( _T("SEQUENCE_STYLE") , _T("5") ) ;
seqres[seq(chain1)].v->items.push_back ( vi1 ) ;
}
}
for ( a = 0 ; a < seqres.size() ; a++ )
{
seqres[a].v->setSequence ( seqres[a].sequence ) ;
seqres[a].v->setName ( _name + _T(" (") + wxString::Format ( _T("%d") , seqres[a].chain ) + _T(")") ) ;
// seqres[a].v->setName ( _name + _T(" (") + wxString ( (char*)seqres[a].chain , *wxConvCurrent ) + _T(")") ) ;
seqres[a].v->addDescription ( _desc ) ;
}
}
void TPDB::check4success ()
{
success = false ;
if ( vs.GetCount() == 0 ) return ;
if ( vs[0].Left ( 6 ) != _T("HEADER") ) return ;
success = true ;
}
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