Exemple #1
0
        public static Dictionary <AminoAcidReference, AminoAcidAngles> MeasureAngles(Peptide peptide)
        {
            var             measurements = new Dictionary <AminoAcidReference, AminoAcidAngles>();
            AminoAcidAngles lastAngles   = null;

            UnitPoint3D lastNitrogenPosition    = null;
            UnitPoint3D lastCarbonAlphaPosition = null;
            UnitPoint3D lastCarbonPosition      = null;

            foreach (var aminoAcid in peptide.AminoAcids)
            {
                PdbAminoAcidAtomNamer.AssignNames(aminoAcid);
                var nitrogen         = aminoAcid.GetAtomFromName("N");
                var carbonAlpha      = aminoAcid.GetAtomFromName("CA");
                var carbon           = aminoAcid.GetAtomFromName("C");
                var nitrogenPosition = nitrogen != null && nitrogen.IsPositionFixed
                    ? nitrogen.Position
                    : null;
                var carbonAlphaPosition = carbonAlpha != null && carbonAlpha.IsPositionFixed
                    ? carbonAlpha.Position
                    : null;
                var carbonPosition = carbon != null && carbon.IsPositionFixed
                    ? carbon.Position
                    : null;

                if (lastAngles != null &&
                    lastNitrogenPosition != null &&
                    lastCarbonAlphaPosition != null &&
                    lastCarbonPosition != null &&
                    nitrogenPosition != null)
                {
                    var psi = DihedralAngleCalculator.Calculate(
                        lastNitrogenPosition,
                        lastCarbonAlphaPosition,
                        lastCarbonPosition,
                        nitrogenPosition);
                    lastAngles.Psi = psi;
                }

                UnitValue omega = null;
                if (lastCarbonAlphaPosition != null &&
                    lastCarbonPosition != null &&
                    nitrogenPosition != null &&
                    carbonAlphaPosition != null)
                {
                    omega = DihedralAngleCalculator.Calculate(
                        lastCarbonAlphaPosition,
                        lastCarbonPosition,
                        nitrogenPosition,
                        carbonAlphaPosition);
                }
                UnitValue phi = null;
                if (lastCarbonPosition != null &&
                    nitrogenPosition != null &&
                    carbonAlphaPosition != null &&
                    carbonPosition != null)
                {
                    phi = DihedralAngleCalculator.Calculate(
                        lastCarbonPosition,
                        nitrogenPosition,
                        carbonAlphaPosition,
                        carbonPosition);
                }

                var angles = new AminoAcidAngles
                {
                    Omega = omega,
                    Phi   = phi
                };
                measurements.Add(aminoAcid, angles);

                lastNitrogenPosition    = nitrogenPosition;
                lastCarbonAlphaPosition = carbonAlphaPosition;
                lastCarbonPosition      = carbonPosition;
                lastAngles = angles;
            }
            return(measurements);
        }
Exemple #2
0
        public static Dictionary <ApproximatedAminoAcid, AminoAcidAngles> MeasureAngles(ApproximatePeptide peptide)
        {
            var             measurements = new Dictionary <ApproximatedAminoAcid, AminoAcidAngles>();
            AminoAcidAngles lastAngles   = null;

            UnitPoint3D lastNitrogenPosition    = null;
            UnitPoint3D lastCarbonAlphaPosition = null;
            UnitPoint3D lastCarbonPosition      = null;

            foreach (var aminoAcid in peptide.AminoAcids)
            {
                var nitrogenPosition    = aminoAcid.NitrogenPosition;
                var carbonAlphaPosition = aminoAcid.CarbonAlphaPosition;
                var carbonPosition      = aminoAcid.CarbonPosition;

                if (lastAngles != null &&
                    lastNitrogenPosition != null &&
                    lastCarbonAlphaPosition != null &&
                    lastCarbonPosition != null &&
                    nitrogenPosition != null)
                {
                    var psi = DihedralAngleCalculator.Calculate(
                        lastNitrogenPosition,
                        lastCarbonAlphaPosition,
                        lastCarbonPosition,
                        nitrogenPosition);
                    lastAngles.Psi = psi;
                }

                UnitValue omega = null;
                if (lastCarbonAlphaPosition != null &&
                    lastCarbonPosition != null &&
                    nitrogenPosition != null &&
                    carbonAlphaPosition != null)
                {
                    omega = DihedralAngleCalculator.Calculate(
                        lastCarbonAlphaPosition,
                        lastCarbonPosition,
                        nitrogenPosition,
                        carbonAlphaPosition);
                }
                UnitValue phi = null;
                if (lastCarbonPosition != null &&
                    nitrogenPosition != null &&
                    carbonAlphaPosition != null &&
                    carbonPosition != null)
                {
                    phi = DihedralAngleCalculator.Calculate(
                        lastCarbonPosition,
                        nitrogenPosition,
                        carbonAlphaPosition,
                        carbonPosition);
                }

                var angles = new AminoAcidAngles
                {
                    Omega = omega,
                    Phi   = phi
                };
                measurements.Add(aminoAcid, angles);

                lastNitrogenPosition    = nitrogenPosition;
                lastCarbonAlphaPosition = carbonAlphaPosition;
                lastCarbonPosition      = carbonPosition;
                lastAngles = angles;
            }
            return(measurements);
        }