src/hg/inc/lsSnpPdbChimera.h 1.3

Index: src/hg/inc/lsSnpPdbChimera.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/lsSnpPdbChimera.h,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/inc/lsSnpPdbChimera.h	5 Feb 2009 08:05:16 -0000	1.2
+++ src/hg/inc/lsSnpPdbChimera.h	13 May 2009 19:05:17 -0000	1.3
@@ -1,35 +1,46 @@
 /* lsSnpPdbChimera - Code for interfacing to LS-SNP and Chimera.  Generates
  * Chimera scripts to visualize proteins with SNPs annotated.  Takes an
  * external python script that defines methods used in the rendering.  The
  * generates a .chimerax file that contains the script as well as the code to
  * initialize Chimera for the specific PDB and SNP set.  This also includes
  * interfacing to LS-SNP/PDB, which is used to label Chimera images.
  */
 #ifndef lsSnpPdbChimera_h
 #define lsSnpPdbChimera_h
 struct sqlConnection;
 struct tempName;
 
 void lsSnpPdbChimeraSnpAnn(struct sqlConnection *conn,
                            char *pdbId, char *primarySnpId,
                            struct tempName *outName);
 /* Generate a chimerax file for the given pdb with all non-synonymous SNPs
  * that have been mapped to this protein.  If primarySnpId is not NULL, it is
  * colored differently than the other SNPs.  Fills in outName structure. */
 
 struct slName *lsSnpPdbChimeraGetSnpPdbs(struct sqlConnection *conn,
                                          char *snpId);
 /* get list of PDBs to which snpId is mapped.  */
 
 char *lsSnpPdbChimeraGetStructType(struct sqlConnection *conn, char *pdbId);
 /* Determine structure type of a PDB (NMR or X-Ray).  Constant result, don't
  * free. */
 
 boolean lsSnpPdbHasPdb(struct sqlConnection *conn, char *pdbId);
 /* determine if the specified PDB has any entries in LS-SNP */
 
 char *lsSnpPdbGetUrlPdbSnp(char *pdbId, char *snpId);
 /* get LS-SNP/PDB URL for a particular PDB and/or SNP.  One or the two
  * ids maybe null */
 
+void lsSnpPdbChimeraGenericLink(char *pdbSpec, char *script,
+                                char *trashDirName, char *trashBaseName,
+                                struct tempName *chimerax);
+/* Generate a chimerax file for the given pdbSpec, which can be a PDB id or a
+ * URL.  Copies in the lsSnpPdbChimera.py file and then adds optional script python code.
+ * Fills in chimerax structure.
+ * FIXME: This is an experiment for H1N1 flu browser, this function has
+ * nothing to do with LS/SNP.  If we decide to keep this, this should be
+ * split into a generic chimera module.
+ */
+
 #endif