Add print/write for PDBFile. It solves #8 and helps with #10

src/PDB/PDBParser.jl

@@ -47,3 +47,93 @@ function parse(io::Union{IO, ASCIIString}, ::Type{PDBFile}; chain::ASCIIString =
  end
  _generate_residues(residue_dict)
 end
+
+# Print PDB
+# =========
+
+# ATOM & HETATM
+# COLUMNS DATA TYPE CONTENTS
+# --------------------------------------------------------------------------------
+# 1 - 6 Record name "ATOM "
+# 7 - 11 Integer Atom serial number.
+# 13 - 16 Atom Atom name.
+# 17 Character Alternate location indicator.
+# 18 - 20 Residue name Residue name.
+# 22 Character Chain identifier.
+# 23 - 26 Integer Residue sequence number.
+# 27 AChar Code for insertion of residues.
+# 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
+# 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
+# 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
+# 55 - 60 Real(6.2) Occupancy.
+# 61 - 66 Real(6.2) Temperature factor (Default = 0.0).
+# 73 - 76 LString(4) Segment identifier, left-justified.
+# 77 - 78 LString(2) Element symbol, right-justified.
+# 79 - 80 LString(2) Charge on the atom.
+# Example:
+# 1 2 3 4 5 6 7 8
+# 12345678901234567890123456789012345678901234567890123456789012345678901234567890
+# ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92 A1 N
+# ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00 11.85 A1 C
+# ATOM 147 C VAL A 25 30.447 15.105 58.363 1.00 12.34 A1 C
+# ATOM 148 O VAL A 25 29.520 15.059 59.174 1.00 15.65 A1 O
+# ATOM 149 CB AVAL A 25 30.385 17.437 57.230 0.28 13.88 A1 C
+# ATOM 150 CB BVAL A 25 30.166 17.399 57.373 0.72 15.41 A1 C
+# ATOM 151 CG1AVAL A 25 28.870 17.401 57.336 0.28 12.64 A1 C
+# ATOM 152 CG1BVAL A 25 30.805 18.788 57.449 0.72 15.11 A1 C
+# ATOM 153 CG2AVAL A 25 30.835 18.826 57.661 0.28 13.58 A1 C
+# ATOM 154 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25 A1 C
+#
+# HETATM 1357 MG MG 168 4.669 34.118 19.123 1.00 3.16 MG2+
+# HETATM 3835 FE HEM 1 17.140 3.115 15.066 1.00 14.14 FE3+
+
+const _Format_PDB_ATOM = FormatExpr(
+# 1 2 3 4 5 6 7 8
+# 12345678901234567890123456789012345678901234567890123456789012345678901234567890
+# > <> < > <|> < |> <| > <> <> <> <> < > <><><
+ "{:<6}{:>5d} {:<4}{:>1}{:>3} {:>1}{:>4}{:>1} {:>8.3f}{:>8.3f}{:>8.3f}{:>6.2f}{:>6.2f} {:<4}{:>2}{:>2}\n"
+)
+
+function print(io::IO, res::PDBResidue, format::Type{PDBFile}, atom_index::Int, serial_number::Int)
+ number = match(r"(\d+)(\D?)", res.id.number)
+ atomname = res.atoms[atom_index].atom
+ printfmt(io, _Format_PDB_ATOM,
+ res.id.group,
+ serial_number,
+ length(atomname) <= 3 ? string(" ", atomname) : atomname, # It works with NACCESS
+ " ",
+ res.id.name,
+ res.id.chain,
+ number[1],
+ number[2],
+ res.atoms[atom_index].coordinates.x,
+ res.atoms[atom_index].coordinates.y,
+ res.atoms[atom_index].coordinates.z,
+ res.atoms[atom_index].occupancy,
+ res.atoms[atom_index].B,
+ " ",
+ res.atoms[atom_index].element,
+ " ")
+ serial_number + 1
+end
+
+function print(io::IO, res::PDBResidue, format::Type{PDBFile}, start::Int=1)
+ next = start
+ for i in 1:length(res.atoms)
+ next = print(io, res, format, i, next)
+ end
+ nothing
+end
+
+function print(io::IO, reslist::AbstractVector{PDBResidue}, format::Type{PDBFile}, start::Int=1)
+ next = start
+ for res in reslist
+ for i in 1:length(res.atoms)
+ next = print(io, res, format, i, next)
+ end
+ end
+ nothing
+end
+
+print(reslist::AbstractVector{PDBResidue}, format::Type{PDBFile}) = print(STDOUT, reslist, format)
+print(res::PDBResidue, format::Type{PDBFile}) = print(STDOUT, res, format)

test/pdb.jl

@@ -236,3 +236,19 @@ RESTful PDB Interface
 
 @test getpdbdescription("4HHB")["resolution"] == "1.74"
 @test_throws KeyError getpdbdescription("104D")["resolution"] # NMR
+
+print("""
+
+Write PDB files
+===============
+""")
+
+let code = "2VQC", io = IOBuffer()
+ pdb = read(txt(code), PDBFile)
+ print(io, pdb, PDBFile)
+ printed = split(takebuf_string(io), '\n')
+
+ @test length(printed) == 608 # Only ATOM & HETATM + 1 because the trailing \n
+ @test printed[1] == "ATOM 1 N THR A 4 2.431 19.617 6.520 1.00 24.37 N "
+ @test printed[607] == "HETATM 607 O HOH A2025 13.807 38.993 2.453 1.00 33.00 O "
+end