public static Element UpdateElement(string line)
{
line = (line + " ").Substring(0, 80);
if (Header.IsHeader(line))
{
return(Header.FromString(line)); // Title Section
}
if (Title.IsTitle(line))
{
return(Title.FromString(line)); // Title Section
}
if (Compnd.IsCompnd(line))
{
return(Compnd.FromString(line)); // Title Section
}
if (Source.IsSource(line))
{
return(Source.FromString(line)); // Title Section
}
if (Keywds.IsKeywds(line))
{
return(Keywds.FromString(line)); // Title Section
}
if (Expdta.IsExpdta(line))
{
return(Expdta.FromString(line)); // Title Section
}
if (Nummdl.IsNummdl(line))
{
return(Nummdl.FromString(line)); // Title Section
}
if (Author.IsAuthor(line))
{
return(Author.FromString(line)); // Title Section
}
if (Revdat.IsRevdat(line))
{
return(Revdat.FromString(line)); // Title Section
}
if (Jrnl.IsJrnl(line))
{
return(Jrnl.FromString(line)); // Title Section
}
if (Remark.IsRemark(line))
{
return(Remark.FromString(line)); // Title Section
}
if (Seqres.IsSeqres(line))
{
return(Seqres.FromString(line)); // Primary Structure Section
}
if (Seqadv.IsSeqadv(line))
{
return(Seqadv.FromString(line)); // Primary Structure Section
}
if (Helix.IsHelix(line))
{
return(Helix.FromString(line)); // Secondary Structure Section
}
if (Sheet.IsSheet(line))
{
return(Sheet.FromString(line)); // Secondary Structure Section
}
if (Site.IsSite(line))
{
return(Site.FromString(line)); // Miscellaneous Features Section
}
if (Cryst1.IsCryst1(line))
{
return(Cryst1.FromString(line)); // Crystallographic and Coordinate Transformation Section
}
if (Anisou.IsAnisou(line))
{
return(Anisou.FromString(line)); // Coordinate Section
}
if (Atom.IsAtom(line))
{
return(Atom.FromString(line)); // Coordinate Section
}
if (Endmdl.IsEndmdl(line))
{
return(Endmdl.FromString(line)); // Coordinate Section
}
if (Hetatm.IsHetatm(line))
{
return(Hetatm.FromString(line)); // Coordinate Section
}
if (Model.IsModel(line))
{
return(Model.FromString(line)); // Coordinate Section
}
if (Siguij.IsSiguij(line))
{
return(Siguij.FromString(line)); // Coordinate Section
}
if (Ter.IsTer(line))
{
return(Ter.FromString(line)); // Coordinate Section
}
if (Conect.IsConect(line))
{
return(Conect.FromString(line)); // Connectivity Section
}
if (Master.IsMaster(line))
{
return(Master.FromString(line)); // Bookkeeping Section
}
if (End.IsEnd(line))
{
return(End.FromString(line)); // Bookkeeping Section
}
if (line.Substring(0, 6) == "DBREF ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SEQRES")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MODRES")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "HET ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "HETNAM")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "FORMUL")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SSBOND")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "LINK ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "ORIGX1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "ORIGX2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "ORIGX3")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SCALE1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SCALE2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SCALE3")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "CISPEP")
{
return(new Element(line)); // Connectivity Annotation Section
}
if (line.Substring(0, 6) == "HETSYN")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SEQADV")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SPRSDE")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MTRIX1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MTRIX2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MTRIX3")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MDLTYP")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SPLIT ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "CAVEAT")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "OBSLTE")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "HYDBND")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SLTBRG")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "TVECT ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "DBREF1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "DBREF2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SIGATM")
{
return(new Element(line));
}
HDebug.Assert(false);
return(new Element(line));
}
private Master _master; //bookkeeping
public Pdb(string filepath)
{
string[] lines = File.ReadAllLines(filepath);
string recName;
foreach (string line in lines)
{
recName = GetFromString(0, 5, line);
switch (recName)
{
case "HEADER":
_header = new Header(
GetFromString(10, 49, line),
GetFromString(50, 58, line),
GetFromString(62, 65, line));
break;
case "TITLE ":
_title.Add(new Title(
TestCont(GetFromString(8, 9, line)),
GetFromString(10, 79, line)));
break;
case "CAVEAT":
_caveat.Add(new Caveat(
TestCont(GetFromString(8, 9, line)),
GetFromString(11, 14, line),
GetFromString(19, 78, line)));
break;
case "COMPND":
_compnd.Add(new Compnd(
TestCont(GetFromString(7, 9, line)),
GetFromString(10, 79, line)));
break;
case "SOURCE":
_source.Add(new Source(
TestCont(GetFromString(7, 9, line)),
GetFromString(10, 78, line)));
break;
case "KEYWDS":
_keywds.Add(new Keywds(
TestCont(GetFromString(8, 9, line)),
GetFromString(10, 78, line)));
break;
case "EXPDTA":
_expdata.Add(new Expdata(
TestCont(GetFromString(8, 9, line)),
GetFromString(10, 78, line)));
break;
case "NUMMDL":
_nummdl = new Nummdl(Convert.ToUInt32(GetFromString(10, 13, line)));
break;
case "MDLTYP":
_mdltyp.Add(new Mdltyp(
TestCont(GetFromString(8, 9, line)),
GetFromString(10, 79, line)));
break;
case "AUTHOR":
_author.Add(new Author(
TestCont(GetFromString(8, 9, line)),
GetFromString(10, 78, line)));
break;
case "REVDAT":
_revdat.Add(new Revdat(
Convert.ToUInt32(GetFromString(7, 9, line)),
TestCont(GetFromString(10, 11, line)),
GetFromString(13, 21, line),
GetFromString(23, 26, line),
Convert.ToInt32(GetFromString(31, 31, line)),
GetFromString(39, 44, line),
GetFromString(46, 51, line),
GetFromString(53, 58, line),
GetFromString(60, 65, line)));
break;
case "JNRL ":
_jrnl.Add(new Jrnl(GetFromString(12, 78, line)));
break;
case "ATOM ":
_atoms.Add(new Atom(
Convert.ToUInt32(GetFromString(6, 10, line)),
GetFromString(12, 15, line),
Convert.ToChar(GetFromString(16, 16, line)),
GetFromString(17, 19, line),
Convert.ToChar(GetFromString(21, 21, line)),
Convert.ToUInt32(GetFromString(22, 25, line)),
Convert.ToChar(GetFromString(26, 26, line)),
new Vector3(Convert.ToDouble(GetFromString(30, 37, line)),
Convert.ToDouble(GetFromString(38, 45, line)),
Convert.ToDouble(GetFromString(46, 53, line))),
Convert.ToDouble(GetFromString(54, 59, line)),
Convert.ToDouble(GetFromString(60, 65, line)),
GetFromString(76, 77, line),
TestCharge(GetFromString(78, 79, line)),
false,
new Color(255, 255, 255, 255)
));
break;
case "HETATM":
_hetatoms.Add(new Atom(
Convert.ToUInt32(GetFromString(6, 10, line)),
GetFromString(12, 15, line),
Convert.ToChar(GetFromString(16, 16, line)),
GetFromString(17, 19, line),
Convert.ToChar(GetFromString(21, 21, line)),
Convert.ToUInt32(GetFromString(22, 25, line)),
Convert.ToChar(GetFromString(26, 26, line)),
new Vector3(Convert.ToDouble(GetFromString(30, 37, line)),
Convert.ToDouble(GetFromString(38, 45, line)),
Convert.ToDouble(GetFromString(46, 53, line))),
Convert.ToDouble(GetFromString(54, 59, line)),
Convert.ToDouble(GetFromString(60, 65, line)),
GetFromString(76, 77, line),
TestCharge(GetFromString(78, 79, line)),
true,
new Color(255, 255, 255, 255)
));
break;
case "END ":
Console.WriteLine("Finished reading!");
break;
default:
//Console.WriteLine("Unknown type.");
break;
}
}
}
