public List <List <Atom> > GetEnsemble()
{
List <List <Atom> > ensemble;
{
ensemble = new List <List <Atom> >();
ensemble.Add(new List <Atom>());
for (int i = 0; i < elements.Length; i++)
{
if (Atom.IsAtom(elements[i].line))
{
ensemble.Last().Add((Atom)elements[i]);
}
if (Endmdl.IsEndmdl(elements[i].line))
{
ensemble.Add(new List <Atom>());
}
}
if (ensemble.Last().Count == 0)
{
ensemble.Remove(ensemble.Last());
}
}
return(ensemble);
}
public static void FromFile(string filepath, out Pdb[] pdbs)
{
string[] lines = System.IO.File.ReadAllLines(filepath);
Element[] elements = new Element[lines.Length];
for (int i = 0; i < lines.Length; i++)
{
elements[i] = new Element(lines[i]);
}
elements = elements.UpdateElement();
List <List <Element> > ensembles;
{
ensembles = new List <List <Element> >();
ensembles.Add(new List <Element>());
for (int i = 0; i < elements.Length; i++)
{
//ensembles.Last().Add(elements[i]);
if (Atom.IsAtom(elements[i].line))
{
ensembles.Last().Add(elements[i]);
}
if (Endmdl.IsEndmdl(elements[i].line))
{
ensembles.Add(new List <Element>());
}
}
if (ensembles.Last().Count == 0)
{
ensembles.Remove(ensembles.Last());
}
}
pdbs = new Pdb[ensembles.Count];
for (int i = 0; i < ensembles.Count; i++)
{
pdbs[i] = new Pdb(ensembles[i].ToArray());
}
}
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));
}
