/// <summary>
/// Reads rna, peptide Fasta-Sequence(s) and generates HELMNotation
/// </summary>
/// <param name="fastaString"></param>
/// <returns></returns>
public static string FastaToHelm(string fastaString)
{
string helm = null;
string errorMsg = "Can't convert FASTA to Helm";
if (UseWebEditor)
{
throw new InvalidCastException(errorMsg); // can't do yet
}
else
{
string helm1 = HelmService.GenerateHELMFromFastaPeptide(fastaString);
if (helm1 == null)
{
throw new InvalidCastException(errorMsg);
}
string helm2 = HelmService.GenerateHELMFromFastaRNA(fastaString);
if (helm2 == null)
{
throw new InvalidCastException(errorMsg);
}
if (helm1.Length >= helm2.Length)
{
return(helm1);
}
else
{
return(helm2);
}
}
}
/// <summary>
/// Reads HELMNotation and converts it into peptide/RNA analogue (natural) sequence
/// </summary>
/// <param name="helm"></param>
/// <returns></returns>
public static string HelmToAnalogSequence(string helm)
{
string seq = null;
if (UseWebEditor)
{
Browser.SetHelm(helm);
seq = Browser.GetSequence();
}
else
{
if (IsPeptideString(helm))
{
seq = HelmService.ConvertIntoPeptideAnalogSequence(helm);
}
else if (IsRnaString(helm))
{
seq = HelmService.ConvertIntoRNAAnalogSequence(helm);
}
}
return(seq);
}
/// <summary>
/// Converts HELM Input into Fasta (RNA or Peptide)
/// <param name="helm"></param>
/// <returns></returns>
public static string HelmToFastaString(string helm)
{
string fasta = null;
if (UseWebEditor)
{
return("Can't convert Helm to FASTA");
}
else
{
fasta = HelmService.GenerateFastaFromHelm(helm);
}
return(fasta);
}
public static string FastaRnaToHelm(string fastaString)
{
string helm = null;
if (UseWebEditor)
{
throw new InvalidCastException("Can't convert FASTA to Helm"); // can't do yet
}
else
{
helm = HelmService.GenerateHELMFromFastaRNA(fastaString);
}
return(helm);
}
/// <summary>
/// SMILES generation for the whole HELM molecule
/// </summary>
/// <param name="helm"></param>
/// <returns></returns>
public static string HelmToSmiles(
MoleculeMx mol,
string helm)
{
string smiles = null;
if (UseWebEditor && DebugMx.False) // don't use this, only gets molfile at monomer level, not atoms/bonds
{
Browser.SetHelm(helm);
smiles = Browser.GetSmiles();
}
else
{
smiles = HelmService.GenerateSMILESForHELM(helm);
}
return(smiles);
}
/// <summary>
/// Reads RNA / peptide sequence and generates HELMNotation
/// </summary>
/// <param name="sequenceString"></param>
/// <returns></returns>
public static string SequenceToHelm(string seqString)
{
string helm = null;
if (UseWebEditor)
{
throw new InvalidCastException("Can't convert sequence to Helm"); // can't do yet
}
else
{
if (IsPeptideString(seqString))
{
helm = HelmService.GenerateHELMFromPeptideSequence(seqString);
}
else
{
helm = HelmService.GenerateHELMFromRnaSequence(seqString);
}
}
return(helm);
}
public static string FastaPeptideToHelm(string fastaString)
{
string helm = HelmService.GenerateHELMFromFastaPeptide(fastaString);
return(helm);
}
