public Pdb GetTransformed(Trans3 trans)
{
Element[] nelements = new Element[elements.Length];
for (int i = 0; i < elements.Length; i++)
{
if (typeof(Atom).IsInstanceOfType(elements[i]))
{
Atom atom = (Atom)elements[i];
Vector pt = atom.coord;
pt = trans.DoTransform(pt);
atom = Atom.FromString(atom.GetUpdatedLine(pt));
nelements[i] = atom;
}
else if (typeof(Hetatm).IsInstanceOfType(elements[i]))
{
Hetatm hetatm = (Hetatm)elements[i];
Vector pt = hetatm.coord;
pt = trans.DoTransform(pt);
hetatm = Hetatm.FromString(hetatm.GetUpdatedLine(pt));
nelements[i] = hetatm;
}
else
{
nelements[i] = elements[i].UpdateElement();
}
}
return(new Pdb(nelements));
}
public static Atom FromHetatm(Hetatm hetatm)
{
string header = hetatm.line.Substring(0, 6);
string data = hetatm.line.Substring(6);
HDebug.Assert(header.ToUpper() == Hetatm.RecordName.ToUpper());
HDebug.Assert(header + data == hetatm.line);
string atom_line = Atom.RecordName + data;
Atom atom = Atom.FromString(atom_line);
return(atom);
}
public static List <Tuple <Hetatm, int> > UpdateHetatms(Element[] elements)
{
int[] collection = Collect(elements, Hetatm.RecordName);
List <Tuple <Hetatm, int> > hetatms = new List <Tuple <Hetatm, int> >();
foreach (int idx in collection)
{
string line = elements[idx].line;
Hetatm hetatm = Hetatm.FromString(line);
elements[idx] = hetatm;
hetatms.Add(new Tuple <Hetatm, int>(hetatm, idx));
}
return(hetatms);
}
public static Hetatm FromData(int serial, string name, string resName, char chainID, int resSeq, double x, double y, double z, char?altLoc = null, char?iCode = null, double?occupancy = null, double?tempFactor = null, string element = null, string charge = null, string segment = null)
{
Hetatm hetatm = Hetatm.FromString(LineFromData(RecordName, serial, name, resName, chainID, resSeq, x, y, z
, altLoc: altLoc
, iCode: iCode
, occupancy: occupancy
, tempFactor: tempFactor
, element: element
, charge: charge
, segment: segment
));
return(hetatm);
}
public Pdb CloneUpdateCoord(Dictionary <IAtom, Vector> iatom2coord)
{
Element[] newelements = new Element[elements.Length];
for (int i = 0; i < elements.Length; i++)
{
Element elem = elements[i];
if (elem is IAtom)
{
if (iatom2coord.ContainsKey(elem as IAtom))
{
Vector coord = iatom2coord[elem as IAtom];
Element nelem = null;
if (elem is Atom)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Atom atom = elem as Atom;
nelem = Atom.FromString(atom.GetUpdatedLine(coord));
}
if (elem is Hetatm)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Hetatm hetatm = elem as Hetatm;
nelem = Hetatm.FromString(hetatm.GetUpdatedLine(coord));
}
if (nelem == null)
{
throw new NotImplementedException();
}
elem = nelem;
}
}
newelements[i] = elem.UpdateElement();
}
return(new Pdb(newelements));
}
public Pdb CloneReplaceChainID(string IDfrom, string IDto)
{
if (IDfrom == null)
{
throw new ArgumentException("IDfrom is null");
}
if (IDto == null)
{
throw new ArgumentException("IDto is null");
}
if (IDfrom.Length != IDto.Length)
{
throw new ArgumentException("IDFrom.leng != IDto.leng");
}
Dictionary <char, char> from2to = GetPairChainID(IDfrom, IDto);
if (from2to.ContainsKey('_'))
{
throw new ArgumentException("wildkey('_') is not allowed in IDfrom");
}
Element[] newelements = new Element[elements.Length];
for (int i = 0; i < elements.Length; i++)
{
Element elem = elements[i];
char? ch = null;
if (elem is Atom)
{
HDebug.Assert(ch == null); ch = (elem as Atom).chainID;
}
if (elem is Hetatm)
{
HDebug.Assert(ch == null); ch = (elem as Hetatm).chainID;
}
if (elem is Anisou)
{
HDebug.Assert(ch == null); ch = (elem as Anisou).chainID;
}
if (ch != null)
{
if (from2to.ContainsKey(ch.Value))
{
if (from2to[ch.Value] == '_')
{
// if wildcard ('_') is in IDto, delete that atom
continue;
}
Element nelem = null;
if (elem is Atom)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Atom atom = elem as Atom;
nelem = Atom.FromData(
serial: atom.serial,
name: atom.name,
resName: atom.resName,
chainID: from2to[atom.chainID],
resSeq: atom.resSeq,
x: atom.x,
y: atom.y,
z: atom.z,
altLoc: atom.altLoc,
iCode: atom.iCode,
occupancy: atom.occupancy,
tempFactor: atom.tempFactor,
element: atom.element,
charge: atom.charge
);
}
if (elem is Hetatm)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Hetatm hetatm = elem as Hetatm;
nelem = Hetatm.FromData(
serial: hetatm.serial,
name: hetatm.name,
resName: hetatm.resName,
chainID: from2to[hetatm.chainID],
resSeq: hetatm.resSeq,
x: hetatm.x,
y: hetatm.y,
z: hetatm.z,
altLoc: hetatm.altLoc,
iCode: hetatm.iCode,
occupancy: hetatm.occupancy,
tempFactor: hetatm.tempFactor,
element: hetatm.element,
charge: hetatm.charge
);
}
if (elem is Anisou)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Anisou anisou = elem as Anisou;
nelem = Anisou.FromData(anisou.line
, chainID: from2to[anisou.chainID]
);
}
if (nelem == null)
{
throw new NotImplementedException();
}
elem = nelem;
}
}
newelements[i] = elem.UpdateElement();
}
newelements = newelements.HRemoveAll(null);
return(new Pdb(newelements));
}
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));
}
