Speed up parsing of PDB line (#50)

* Speed up parsing of PDB line

By checking the length of the line before parsing it, we can avoid the
overhead of `try/catch` for the optional fields.

* Update tests for new PDB parser

src/pdb.jl

@@ -531,136 +531,106 @@ function Base.read(filepath::AbstractString,
 end
 
 # Constructor from PDB ATOM/HETATM line
-AtomRecord(pdb_line::String, line_n::Integer=1) = AtomRecord(
-    pdb_line[1] == 'H', # This assumes the line has already been checked as an ATOM/HETATM record
-    parseserial(pdb_line, line_n),
-    parseatomname(pdb_line, line_n),
-    parsealtloc(pdb_line, line_n),
-    parseresname(pdb_line, line_n),
-    parsechainid(pdb_line, line_n),
-    parseresnumber(pdb_line, line_n),
-    parseinscode(pdb_line, line_n),
-    [
-        parsecoordx(pdb_line, line_n),
-        parsecoordy(pdb_line, line_n),
-        parsecoordz(pdb_line, line_n)
-    ],
-    parseoccupancy(pdb_line),
-    parsetempfac(pdb_line),
-    parseelement(pdb_line),
-    parsecharge(pdb_line)
-)
+function AtomRecord(pdb_line::String, line_n::Integer=1)
+    n = length(pdb_line)
+    n >= 54 || throw(PDBParseError("line too short", line_n, pdb_line))
+    AtomRecord(
+        pdb_line[1] == 'H', # This assumes the line has already been checked as an ATOM/HETATM record
+        parseserial(pdb_line, line_n),
+        parseatomname(pdb_line, line_n),
+        parsealtloc(pdb_line, line_n),
+        parseresname(pdb_line, line_n),
+        parsechainid(pdb_line, line_n),
+        parseresnumber(pdb_line, line_n),
+        parseinscode(pdb_line, line_n),
+        [
+            parsecoordx(pdb_line, line_n),
+            parsecoordy(pdb_line, line_n),
+            parsecoordz(pdb_line, line_n)
+        ],
+        n >= 60 ? parseoccupancy(pdb_line) : 1.0,
+        n >= 66 ? parsetempfac(pdb_line) : 0.0,
+        n >= 78 ? parseelement(pdb_line) : "  ",
+        n >= 80 ? parsecharge(pdb_line) : "  ",
+    )
+end
 
 function parseserial(line::String, line_n::Integer=1)
-    try
-        return parse(Int, line[7:11])
-    catch
+    ret = tryparse(Int, line[7:11])
+    if ret === nothing
         throw(PDBParseError("could not read atom serial number", line_n, line))
     end
+    return ret
 end
 
 function parseatomname(line::String, line_n::Integer=1)
-    try
-        return line[13:16]
-    catch
-        throw(PDBParseError("could not read atom name", line_n, line))
-    end
+    return line[13:16]
 end
 
 function parsealtloc(line::String, line_n::Integer=1)
-    try
-        return line[17]
-    catch
-        throw(PDBParseError("could not read alt loc identifier", line_n, line))
-    end
+    return line[17]
 end
 
 function parseresname(line::String, line_n::Integer=1)
-    try
-        return line[18:20]
-    catch
-        throw(PDBParseError("could not read residue name", line_n, line))
-    end
+    return line[18:20]
 end
 
 function parsechainid(line::String, line_n::Integer=1)
-    try
-        return string(line[22])
-    catch
-        throw(PDBParseError("could not read chain ID", line_n, line))
-    end
+    return string(line[22])
 end
 
 function parseresnumber(line::String, line_n::Integer=1)
-    try
-        return parse(Int, line[23:26])
-    catch
+    ret = tryparse(Int, line[23:26])
+    if ret === nothing
         throw(PDBParseError("could not read residue number", line_n, line))
     end
+    return ret
 end
 
 function parseinscode(line::String, line_n::Integer=1)
-    try
-        return line[27]
-    catch
-        throw(PDBParseError("could not read insertion code", line_n, line))
-    end
+    return line[27]
 end
 
 function parsecoordx(line::String, line_n::Integer=1)
-    try
-        return parse(Float64, line[31:38])
-    catch
+    ret = tryparse(Float64, line[31:38])
+    if ret === nothing
         throw(PDBParseError("could not read x coordinate", line_n, line))
     end
+    return ret
 end
 
 function parsecoordy(line::String, line_n::Integer=1)
-    try
-        return parse(Float64, line[39:46])
-    catch
+    ret = tryparse(Float64, line[39:46])
+    if ret === nothing
         throw(PDBParseError("could not read y coordinate", line_n, line))
     end
+    return ret
 end
 
 function parsecoordz(line::String, line_n::Integer=1)
-    try
-        return parse(Float64, line[47:54])
-    catch
+    ret = tryparse(Float64, line[47:54])
+    if ret === nothing
         throw(PDBParseError("could not read z coordinate", line_n, line))
     end
+    return ret
 end
 
 function parseoccupancy(line::String)
-    try
-        return parse(Float64, line[55:60])
-    catch
-        return 1.0
-    end
+    ret = tryparse(Float64, line[55:60])
+    return ret === nothing ? 1.0 : ret
 end
 
 function parsetempfac(line::String)
-    try
-        return parse(Float64, line[61:66])
-    catch
-        return 0.0
-    end
+    ret = tryparse(Float64, line[61:66])
+    return ret === nothing ? 0.0 : ret
 end
 
 function parseelement(line::String)
-    try
-        return line[77:78]
-    catch
-        return "  "
-    end
+    return line[77:78]
 end
 
 function parsecharge(line::String)
-    try
-        return line[79:80]
-    catch
-        return "  "
-    end
+    return line[79:80]
 end
 
 # Form a string of a certain length from a value by adding spaces to the left

test/runtests.jl

@@ -860,20 +860,18 @@ end
     @test parsecharge(line) == "1+"
 
     line_short = "ATOM    591  C"
+    @test_throws PDBParseError("line too short", 37, line_short) AtomRecord(line_short, 37)
     @test_throws PDBParseError    parseserial("ATOM         C   GLY A  80      29.876  54.131  35.806  1.00 40.97           C1+")
-    @test_throws PDBParseError  parseatomname(line_short)
-    @test_throws PDBParseError    parsealtloc(line_short)
-    @test_throws PDBParseError   parseresname(line_short)
-    @test_throws PDBParseError   parsechainid(line_short)
     @test_throws PDBParseError parseresnumber("ATOM    591  C   GLY A          29.876  54.131  35.806  1.00 40.97           C1+")
-    @test_throws PDBParseError   parseinscode(line_short)
     @test_throws PDBParseError    parsecoordx("ATOM    591  C   GLY A  80      xxxxxx  54.131  35.806  1.00 40.97           C1+")
     @test_throws PDBParseError    parsecoordy("ATOM    591  C   GLY A  80      29.876  xxxxxx  35.806  1.00 40.97           C1+")
     @test_throws PDBParseError    parsecoordz("ATOM    591  C   GLY A  80      29.876  54.131  xxxxxx  1.00 40.97           C1+")
-    @test parseoccupancy(line_short) == 1.0
-    @test parsetempfac(line_short) == 0.0
-    @test parseelement(line_short) == "  "
-    @test parsecharge(line_short) == "  "
+    line_medium = "ATOM    591  C   GLY A  80      29.876  54.131  35.806"
+    rec = AtomRecord(line_medium, 55)
+    @test rec.occupancy == 1.0
+    @test rec.temp_factor == 0.0
+    @test rec.element == "  "
+    @test rec.charge == "  "
 
     # Test AtomRecord constructor
     line_a = "ATOM    669  CA  ILE A  90      31.743  33.110  31.221  1.00 25.76           C  "