/NuGenBioChem/Data/Importers/ProteinDataBankFile.cs

using System;

using System.Collections.Generic;

using System.IO;

using System.Windows.Media.Media3D;

using System.Globalization;





namespace NuGenBioChem.Data.Importers

{

    /// <summary>

    /// Provides protein molecule import from the .PDB file format

    /// </summary>

    public class ProteinDataBankFile : IFileImporter

    {

        #region Fields



        // Message describes the loading process

        string message = "";

        // Indicates wether loading is succesful

        bool isSuccessful;

        // Molecules from the file

        readonly MoleculeCollection molecules = new MoleculeCollection();



        // Chain's table

        readonly Dictionary<char, Chain> chains = new Dictionary<char, Chain>();

        // List of the atom

        readonly List<Atom> atoms = new List<Atom>();



        #endregion



        #region Properties



        /// <summary>

        /// Indicates whether loading were succesful

        /// </summary>

        public bool IsSuccessful

        {

            get { return isSuccessful; }

        }



        /// <summary>

        /// Gets information about loading process

        /// </summary>

        public string Messages

        {

            get { return message; }

        }



        /// <summary>

        /// Gets molecules from the file

        /// </summary>

        public MoleculeCollection Molecules

        {

            get { return molecules; }

        }



        #endregion



        #region Initialzation



        /// <summary>

        /// Loads molecule models from the specified file

        /// </summary>

        /// <param name="path">Filename</param>

        public ProteinDataBankFile(string path)

        {

            try

            {

                Parse(File.ReadLines(path));

            }

            catch (Exception exception)

            {

                message = exception.Message;

                isSuccessful = false;

            }

        }



        /// <summary>

        /// Loads molecule models from the text lines

        /// </summary>

        /// <param name="lines">Lines</param>

        public ProteinDataBankFile(string[] lines)

        {

            try

            {

                Parse(lines);

            }

            catch (Exception exception)

            {

                message = exception.Message;

                isSuccessful = false;

            }

        }



        #endregion



        #region Methods



        // Parses through all pdb-file's lines

        void Parse(IEnumerable<string> pdbLines)

        {

            foreach (string pdbLine in pdbLines)

            {

                if (pdbLine.StartsWith("REMARK"))

                    continue;

                if (pdbLine.StartsWith("ATOM"))

                {

                    ParseAtom(pdbLine);

                }

                else if (pdbLine.StartsWith("HETATM"))

                {

                    ParseHetAtom(pdbLine);

                }

                else if (pdbLine.StartsWith("HELIX"))

                {

                    ParseHelix(pdbLine);

                }

                else if (pdbLine.StartsWith("SHEET"))

                {

                    ParseSheet(pdbLine);

                }

                else if (pdbLine.StartsWith("ENDMDL") || pdbLine.StartsWith("END"))

                {

                    Molecule molecule = new Molecule();

                    molecule.Atoms.AddRange(atoms);

                    molecule.Chains.AddRange(chains.Values);



                    molecule.CalculateBonds();

                    molecules.Add(molecule);



                    atoms.Clear();

                    chains.Clear();

                }

            }



        }



        // Parses residue's atom specified by the pdb-file line

        // returns residue number where atom has been added (for residue changing control)

        void ParseAtom(string pdbLine)

        {

            Atom atom = new Atom();

            atoms.Add(atom);



            Chain chain;

            char chainId = pdbLine[21];

            // FIXME: name of the chain must be gotten from DBREF record (?)

            if (!chains.TryGetValue(chainId, out chain)) chains[chainId] = chain = new Chain() { Name = chainId.ToString() };



            int number = int.Parse(pdbLine.Substring(22, 4), CultureInfo.InvariantCulture);



            Residue residue;

            if (chain.Residues.Count == 0 || (residue = chain.Residues[chain.Residues.Count - 1]).SequenceNumber != number)

            {

                residue = new Residue();

                chain.Residues.Add(residue);

                residue.SequenceNumber = number;

                residue.Name = pdbLine.Substring(17, 3);

            }

            residue.Atoms.Add(atom);



            atom.Position = GetAtomPosition(pdbLine);

            string atomName = pdbLine.Substring(12, 4).Trim();

            if (atomName == "CA" || atomName == "C1")

            {

                // Alfa-carbon has been got

                atom.Element = Element.GetBySymbol("C");

                residue.AlfaCarbon = atom;

            }

            else

            {

                atom.Element = GetAtomElement(pdbLine);

            }

        }



        // Parses heterogenius atom specified by the pdb-file line

        void ParseHetAtom(string pdbLine)

        {

            Atom atom = new Atom();

            atoms.Add(atom);

            atom.Position = GetAtomPosition(pdbLine);

            atom.Element = GetAtomElement(pdbLine);

        }



        // Parses helix secondary structure object specified by the pdb-file line

        void ParseHelix(string pdbLine)

        {

            Chain chain;

            char chainId = pdbLine[19];

            if (!chains.TryGetValue(chainId, out chain)) chains[chainId] = chain = new Chain() { Name = chainId.ToString() };



            SecondaryStructure helix = new SecondaryStructure();

            helix.StructureType = SecondaryStructureType.Helix;

            helix.FirstResidueSequenceNumber = int.Parse(pdbLine.Substring(21, 4), CultureInfo.InvariantCulture);

            helix.LastResidueSequenceNumber = int.Parse(pdbLine.Substring(33, 4), CultureInfo.InvariantCulture);



            chain.SecondaryStructures.Add(helix);

        }



        // Parses sheet secondary structure object specified by the pdb-file line

        void ParseSheet(string pdbLine)

        {

            Chain chain;

            char chainId = pdbLine[21];

            if (!chains.TryGetValue(chainId, out chain)) chains[chainId] = chain = new Chain() { Name = chainId.ToString() };



            SecondaryStructure sheet = new SecondaryStructure();

            sheet.StructureType = SecondaryStructureType.Sheet;

            sheet.FirstResidueSequenceNumber = int.Parse(pdbLine.Substring(22, 4), CultureInfo.InvariantCulture);

            sheet.LastResidueSequenceNumber = int.Parse(pdbLine.Substring(33, 4), CultureInfo.InvariantCulture);



            chain.SecondaryStructures.Add(sheet);

        }



        // Parses position of the atom specified by the pdb-file line

        static Point3D GetAtomPosition(string pdbLine)

        {

            Point3D position = new Point3D();

            position.X = double.Parse(pdbLine.Substring(30, 8), CultureInfo.InvariantCulture);

            position.Y = double.Parse(pdbLine.Substring(38, 8), CultureInfo.InvariantCulture);

            position.Z = double.Parse(pdbLine.Substring(46, 8), CultureInfo.InvariantCulture);

            return position;

        }



        // Creates element of the atom specified by the pdb-file line

        static Element GetAtomElement(string pdbLine)

        {

            string symbol = pdbLine.Substring(76, 2).Trim();

            if (symbol.Length == 2) symbol = symbol.Substring(0, 1) + symbol.Substring(1, 1).ToLowerInvariant();

            Element result = Element.GetBySymbol(symbol);

            if (result == null)

            {

                symbol = pdbLine.Substring(12, 2).Trim().Substring(0, 1);

                result = Element.GetBySymbol(symbol);

            }

            return result;

        }



        #endregion

    }

}