55f6362c793e0d7cc4d2ff0ec614a5e316354b82
markd
  Thu Dec 19 21:53:29 2024 -0800
don't install lsSnpPdbChimera.py any more

diff --git src/hg/hgGene/domains.c src/hg/hgGene/domains.c
index df9977c..22736b3 100644
--- src/hg/hgGene/domains.c
+++ src/hg/hgGene/domains.c
@@ -1,226 +1,226 @@
 /* domains - do protein domains section. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "trashDir.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "spDb.h"
 #include "hgGene.h"
 #include "hdb.h"
-#include "lsSnpPdbChimera.h"
+#include "lsSnpPdbChimera.h"  // only used for MuPIT, lsSNP/PDB is deceased
 
 
 static boolean domainsExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if there's some pfam domains in swissProt on this one. 
  * on this one. */
 {
 return swissProtAcc != NULL;
 }
 
 void modBaseAnchor(char *swissProtAcc)
 /* Print out anchor to modBase. */
 {
 hPrintf("<A HREF=\"http://salilab.org/modbase/search?databaseID=%s\" TARGET=_blank>", swissProtAcc);
 //hPrintf("<A HREF=\"http://salilab.org/modbase-cgi/model_search.cgi?searchkw=name&kword=%s\" TARGET=_blank>", swissProtAcc);
 }
 
 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=\"https://www.ebi.ac.uk/interpro/entry/pfam/%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=\"https://www.ebi.ac.uk/interpro/entry/pfam/%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;
     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");
     hPrintf("<A href=\"http://mupit.icm.jhu.edu/MuPIT_Interactive/Help.html\" TARGET=_blank>MuPIT help</A>\n");
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	hPrintf("<TD>");
 	hPrintf("<A HREF=\"http://www.rcsb.org/structure/%s\" TARGET=_blank>", row[0]);
         hPrintf("%s</A> - %s ", row[0], row[1]);
         // include links to MuPIT (formerly LS-SNP)
         if (lsSnpPdbHasPdb(conn2, row[0]))
             hPrintf(" <A HREF=\"%s\" TARGET=_blank>MuPIT</A>", lsSnpPdbGetUrlPdbSnp(row[0], NULL));
 	hPrintf("</TD>\n");
 	}
     hPrintf("</TR></TABLE>\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&degree=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&degree=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 section *domainsSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create domains section. */
 {
 struct section *section = sectionNew(sectionRa, "domains");
 section->exists = domainsExists;
 section->print = domainsPrint;
 return section;
 }