added another file from the modeller examples. Work in progress...

src/MODELLER/modeller-basic-example-julia/build_profile.jl

@@ -0,0 +1,44 @@
+using PyCall
+
+@pyimport modeller
+
+modeller.log[:verbose]()
+env = modeller.environ()
+
+#-- Prepare the input files
+
+#-- Read in the sequence database
+sdb = modeller.sequence_db(env)
+sdb[:read](seq_database_file="pdb_95.pir", seq_database_format="PIR",
+         chains_list="ALL", minmax_db_seq_len=(30, 4000), clean_sequences=true)
+
+#-- Write the sequence database in binary form
+sdb[:write](seq_database_file="pdb_95.bin", seq_database_format="BINARY",
+          chains_list="ALL")
+
+#-- Now, read in the binary database
+sdb[:read](seq_database_file="pdb_95.bin", seq_database_format="BINARY",
+         chains_list="ALL")
+
+#-- Read in the target sequence/alignment
+aln = modeller.alignment(env)
+aln[:append](file="TvLDH.ali", alignment_format="PIR", align_codes="ALL")
+
+#-- Convert the input sequence/alignment into
+#   profile format
+prf = aln[:to_profile]()
+
+#-- Scan sequence database to pick up homologous sequences
+prf[:build](sdb, matrix_offset=-450, rr_file="""$(pyeval("\$LIB"))/blosum62.sim.mat""",
+          gap_penalties_1d=(-500, -50), n_prof_iterations=1,
+          check_profile=False, max_aln_evalue=0.01)
+
+#-- Write out the profile in text format
+prf[:write](file="build_profile.prf", profile_format="TEXT")
+
+#-- Convert the profile back to alignment format
+aln = prf[:to_alignment]()
+
+#-- Write out the alignment file
+aln[:write](file="build_profile.ali", alignment_format="PIR")
+