Merge branch 'pdbexport'

src/PDB/pdb.jl

@@ -4,9 +4,10 @@
 # sudo apt-get install numpy | unless you want to compile it..
 # julia: Pkg.add("PyCall")
 module PDB
-export get_structure, get_chains, structure_to_matrix
+export get_structure, get_chains, structure_to_matrix, export_to_pdb
 
 using PyCall
+using Formatting
 @pyimport Bio.PDB as pdb
 
 # get a structure from a PDB File
@@ -55,4 +56,23 @@ function structure_to_matrix(structure::PyObject)
 	return matrix
 end
 
-end
+# Export a matrix of C_alpha atom coordinates to a PDB file
+function export_to_pdb(residueName::String,chainID::String,matrix::Array{Float64,2}, filename::String)
+	lines = String[]
+
+	atomExpr = FormatExpr("{: <6}{: >5} {: >4}{: <1}{: >3} {: <1}{: >4}{: <1}   {: >8}{: >8}{: >8}{: >6}{: >6}      {: <4}{: >2}{: <2}\n")
+
+	for i in 1:size(matrix)[1]
+		line = format(atomExpr, "ATOM", i, "CA", " ", residueName, chainID, "1", " ", matrix[i,:][1], matrix[i,:][2], matrix[i,:][3], 1.0, 0.0, "A1", "C", " ")
+
+		push!(lines, line)
+	end
+
+	f = open(filename, "w")
+	write(f,lines)
+	close(f)
+
+	return lines
+end
+
+end

test/pdb.jl

@@ -1,4 +1,5 @@
 using PyCall
+
 struc = get_structure("2HHB.pdb")
 
 # Extremely rudimentary test, basically do we get anything back from our PyCall?
@@ -13,4 +14,18 @@ chains = get_chains(struc)
 @test size(chains[1]) == (141,3)
 @test size(chains[2]) == (146,3)
 @test size(chains[3]) == (141,3)
-@test size(chains[4]) == (146,3)
+@test size(chains[4]) == (146,3)
+
+# PDB export test
+P = [31.132 16.439 58.160;
+	 6.870 17.784 4.702
+]
+
+f = open("pdb_export_test.pdb")
+pdb_expected = convert(Array{String,1},readlines(f))
+
+pdb_handler(r::Test.Success) = rm("pdb_exported_test.pdb")
+
+Test.with_handler(pdb_handler) do
+	@test pdb_expected == export_to_pdb("VAL", "A", P, "pdb_exported_test.pdb")
+end

test/pdb_export_test.pdb

@@ -0,0 +1,2 @@
+ATOM      1   CA VAL A   1      31.132  16.439   58.16   1.0   0.0      A1   C  
+ATOM      2   CA VAL A   1        6.87  17.784   4.702   1.0   0.0      A1   C