struct slName *spPdbAccs(struct sqlConnection *conn, char *acc)
/* Get list of PDB associations associated with this. */
{
return spExtDbAcc1List(conn, acc, "PDB");
}
static void domainsPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out protein domains. */
{
char *db = sqlGetDatabase(conn);
struct slName *el, *list;
list = spExtDbAcc1List(spConn, swissProtAcc, "Interpro");
if (list != NULL)
{
char query[256], **row, **row2;
struct sqlResult *sr, *sr2;
hPrintf("<B>InterPro Domains: </B> ");
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/protein/%s\" TARGET=_blank>",
swissProtAcc);
hPrintf("Graphical view of domain structure</A><BR>");
sqlSafef(query, sizeof(query),
"select extAcc1,extAcc2 from extDbRef,extDb"
" where extDbRef.acc = '%s'"
" and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb"
, swissProtAcc);
sr = sqlGetResult(spConn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
//hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
//hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
char interPro[256];
char *pdb = hPdbFromGdb(db);
safef(interPro, 128, "%s.interProXref", pdb);
if (hTableExists(db, interPro))
{
sqlSafef(query, sizeof(query),
"select description from %s where accession = '%s' and interProId = '%s'",
interPro, swissProtAcc, row[0]);
sr2 = sqlGetResult(conn, query);
if ((row2 = sqlNextRow(sr2)) != NULL)
{
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
hPrintf("%s</A> - %s <BR>\n", row[0], row2[0]);
}
sqlFreeResult(&sr2);
}
else
{
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
}
}
hPrintf("<BR>\n");
slFreeList(&list);
}
if (kgVersion == KG_III)
{
/* Do Pfam domains here. */
list = getPfamDomainList(conn, geneId);
if (list != NULL)
{
hPrintf("<B>Pfam Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query),
"select description from pfamDesc where pfamAC='%s'", el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
/* Do SCOP domains here */
list = getDomainList(conn, geneId, "Scop");
if (list != NULL)
{
hPrintf("<B>SCOP Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query),
"select description from scopDesc where acc='%s'", el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://scop.berkeley.edu/sunid=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
}
else
{
list = spExtDbAcc1List(spConn, swissProtAcc, "Pfam");
if (list != NULL)
{
char *pfamDescSql = genomeSetting("pfamDescSql");
hPrintf("<B>Pfam Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query), pfamDescSql, el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
}
list = spExtDbAcc1List(spConn, swissProtAcc, "PDB");
if (list != NULL)
{
struct sqlConnection *conn2 = sqlConnect(db);
char query[256], **row;
struct sqlResult *sr;
int column = 0, maxColumn=3, rowCount=0;
hPrintf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>");
sqlSafef(query, sizeof(query),
"select extAcc1,extAcc2 from extDbRef,extDb"
" where extDbRef.acc = '%s'"
" and extDb.val = 'PDB' and extDb.id = extDbRef.extDb"
, swissProtAcc);
sr = sqlGetResult(spConn, query);
hPrintf("<TABLE><TR>\n");
while ((row = sqlNextRow(sr)) != NULL)
{
if (++column > maxColumn)
{
hPrintf("</TR><TR>");
column = 1;
if (rowCount == 0)
{
hPrintf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn);
hPrintf("</TR><TR>");
}
++rowCount;
}
hPrintf("<TD>");
hPrintf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]);
if (rowCount < 1)
hPrintf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_asym_r_250.jpg\"><BR>", row[0]);
hPrintf("%s</A> - %s ", row[0], row[1]);
// include links LS-SNP and to launch viewer in PDB chimera
struct tempName chimerax;
lsSnpPdbChimeraSnpAnn(conn, row[0], NULL, &chimerax);
hPrintf(" <A HREF=\"%s\">Chimera</A>", chimerax.forHtml);
if (lsSnpPdbHasPdb(conn2, row[0]))
hPrintf(" <A HREF=\"%s\" TARGET=_blank>LS-SNP</A>", lsSnpPdbGetUrlPdbSnp(row[0], NULL));
hPrintf("</TD>\n");
}
hPrintf("</TR></TABLE>\n");
hPrintf("<A href=\"../goldenPath/help/chimera.html\" TARGET=_blank>Chimera help</A>\n");
hPrintf("<BR><BR>\n");
slFreeList(&list);
sqlDisconnect(&conn2);
}
/* Do modBase link. */
{
hPrintf("<B>ModBase Predicted Comparative 3D Structure on ");
modBaseAnchor(swissProtAcc);
hPrintf("%s", swissProtAcc);
hPrintf("</A></B><BR>\n");
hPrintf("<TABLE><TR>");
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", swissProtAcc);
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", swissProtAcc);
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", swissProtAcc);
hPrintf("</TR><TR>\n");
hPrintf("<TD ALIGN=CENTER>Front</TD>");
hPrintf("<TD ALIGN=CENTER>Top</TD>");
hPrintf("<TD ALIGN=CENTER>Side</TD>");
hPrintf("</TR></TABLE>\n");
hPrintf("<I>The pictures above may be empty if there is no "
"ModBase structure for the protein. The ModBase structure "
"frequently covers just a fragment of the protein. You may "
"be asked to log onto ModBase the first time you click on the "
"pictures. It is simplest after logging in to just click on "
"the picture again to get to the specific info on that model.</I>");
}
}
struct slName *spEmblAccs(struct sqlConnection *conn, char *acc)
/* Get list of EMBL/Genbank mRNAaccessions associated with this. */
{
return spExtDbAcc1List(conn, acc, "EMBL");
}
