CifWrapperForSecStrAnnot1.cs

using System;
using System.IO;
using System.Collections.Generic;
using System.Linq;
using System.Runtime.CompilerServices;

using Cif;
using Cif.Tables;
using Cif.Filtering;
using Cif.Components;
using SecStrAnnotator2.Utils;

namespace SecStrAnnotator2
{
    public static class CifWrapperForSecStrAnnot1
    {
        private const string EXCEPTION_MESSAGE = "Cannot fit CIF data to PDB data model: ";
        private const char PDB_DEFAULT_ALT_LOC = ' ';
        private const char PDB_DEFAULT_INS_CODE = ' ';
        private const double DEFAULT_OCCUPANCY = 1.0;
        private const double DEFAULT_TEMP_FACTOR = 0.0;
        private const string DEFAULT_CHARGE = "  ";


        public static Cif.Components.Protein ProteinFromCifFile(string filename, string chainId = null, (int, int)[] resSeqRanges = null)
        {
            CifPackage package = CifPackage.FromFile(filename);
            if (package.BlockNames.Length < 1)
            {
                throw new FormatException(EXCEPTION_MESSAGE + "CIF file must contain at least one block");
            }
            CifCategory category = package.Blocks[0].GetCategory(ModelCollection.CATEGORY_NAME);
            // int[] rows = category.GetItem(ChainTable.ID_COLUMN).GetRowsWith(chainId.ToString()).ToArray(); // filter rows by chain ID
            // int[] seqNumbers = category.GetItem(ResidueTable.SEQ_NUMBER_COLUMN).GetIntegers(rows, 0);
            // rows = rows.Where( (r, i) => resSeqRanges.Any(range => range.Item1 <= seqNumbers[i] && seqNumbers[i] <= range.Item2) ).ToArray(); // filter rows by resi

            ModelCollection models;
            if (chainId != null || resSeqRanges != null)
            {
                Filter filter;
                if (chainId != null && resSeqRanges != null)
                    filter = Filter.StringEquals(ChainTable.ID_COLUMN, chainId) & Filter.IntegerInRange(ResidueTable.SEQ_NUMBER_COLUMN, resSeqRanges);
                else if (chainId != null)
                    filter = Filter.StringEquals(ChainTable.ID_COLUMN, chainId);
                else
                    filter = Filter.IntegerInRange(ResidueTable.SEQ_NUMBER_COLUMN, resSeqRanges);
                int[] rows = filter.GetFilteredRows(category).ToArray();
                models = ModelCollection.FromCifCategory(category, rows);
            }
            else
            {
                models = ModelCollection.FromCifCategory(category);
            }

            Model model;
            if (models.Count >= 1)
            {
                model = models.GetModel(0);
            }
            else
            {
                string rangeString = String.Join(",", resSeqRanges.Select(range => range.Item1 + ":" + range.Item2));
                // throw new FormatException(EXCEPTION_MESSAGE + $"Atom selection given by chain ID '{chainId}' and residue ranges '{rangeString}' is empty");
                Lib2.WriteWarning($"Empty model: Atom selection given by chain ID '{chainId}' and residue ranges '{rangeString}' is empty");
                model = new ModelBuilder().GetModel();
            }
            Protein protein = ProteinFromCifModel(model);
            return protein;
        }

        public static Cif.Components.Protein ProteinFromCifModel(Model model)
        {
            return new Cif.Components.Protein(model);
        }
    }
}