/// <summary> /// Get Peptide/RNA FASTA form of molecule doing conversion if necessary /// </summary> /// <returns></returns> public string GetFastaString() { string fasta = "", helm = ""; if (Lex.IsDefined(FastaString)) { return(FastaString); } else if (Lex.IsDefined(HelmString)) { fasta = HelmConverter.HelmToFastaString(HelmString); } else if (Lex.IsDefined(SequenceString)) { helm = HelmConverter.SequenceToHelm(SequenceString); if (Lex.IsDefined(helm)) { HelmString = helm; fasta = HelmConverter.HelmToFastaString(helm); } } FastaString = fasta; return(FastaString); }
/// <summary> /// Get HELM form of molecule doing conversion if necessary /// </summary> public string GetHelmString() { string helm = "", molfile = ""; if (Lex.IsDefined(HelmString)) { return(HelmString); } if (Lex.IsDefined(SequenceString)) { helm = HelmConverter.SequenceToHelm(SequenceString); } else if (Lex.IsDefined(FastaString)) { helm = HelmConverter.FastaToHelm(FastaString); } else { molfile = GetMolfileString(); if (Lex.IsDefined(molfile)) { MolfileString = molfile; helm = HelmConverter.MolfileToHelm(molfile); } } HelmString = helm; // save in case needed later return(HelmString); }
/// <summary> /// Get Peptide/RNA sequence form of molecule doing conversion if necessary /// </summary> /// <returns></returns> public string GetSequenceString() { string seq = "", helm = ""; if (Lex.IsDefined(SequenceString)) { return(SequenceString); } if (Lex.IsDefined(HelmString)) { seq = HelmConverter.HelmToAnalogSequence(HelmString); } else if (Lex.IsDefined(FastaString)) { helm = HelmConverter.FastaToHelm(FastaString); if (Lex.IsDefined(helm)) { HelmString = helm; seq = HelmConverter.HelmToAnalogSequence(HelmString); } } SequenceString = seq; return(SequenceString); }
/// <summary> /// Get molfile form of molecule doing a conversion from another format as necessary /// </summary> /// <returns></returns> public string GetMolfileString() { string molfile = "", helm = ""; if (Lex.IsDefined(MolfileString)) { return(MolfileString); } else if (Lex.IsDefined(ChimeString)) { molfile = ChimeStringToMolfileString(ChimeString); } else if (Lex.IsDefined(SmilesString)) { molfile = CdkMol.SmilesStringToMolfileString(SmilesString); } else if (Lex.IsDefined(InchiString)) { molfile = CdkMol.InChIStringToMolfileString(PrimaryValue.ToString()); } else if (Lex.IsDefined(HelmString)) { molfile = HelmConverter.HelmToMolfile(this, HelmString); } else if (Lex.IsDefined(SequenceString)) { helm = HelmConverter.SequenceToHelm(SequenceString); HelmString = helm; if (Lex.IsDefined(helm)) { molfile = HelmConverter.HelmToMolfile(this, HelmString); } } else if (Lex.IsDefined(FastaString)) { helm = HelmConverter.FastaToHelm(FastaString); HelmString = helm; if (Lex.IsDefined(helm)) { molfile = HelmConverter.HelmToMolfile(this, HelmString); } } else { molfile = ""; } MolfileString = molfile; // save for later possible reuse return(MolfileString); }