AntiBetaRMSDCV.h

#pragma once

#include "CollectiveVariable.h"
#include "Validator/ObjectRequirement.h"
#include "Drivers/DriverException.h"
#include "Snapshot.h"
#include "schema.h"
#include "Utility/ReadBackbone.h"
#include <stdexcept>

namespace SSAGES
{

    class AntiBetaRMSDCV : public CollectiveVariable
    {
    private:

        std::vector<int> resids_;

        //std::vector<int> atomids_;
        std::vector< std::vector<std::string> > atomids_;

        std::string refpdb_;

        std::vector<Vector3> refalpha_;

        double unitconv_;

        int mode_;

    public:

        AntiBetaRMSDCV(std::vector<int> resids, std::string refpdb, double unitconv, int mode) :
        resids_(resids), refpdb_(refpdb), unitconv_(unitconv), mode_(mode)
        {
            if(resids_.size() != 2 ){
                throw std::invalid_argument("AntiBetaRMSDCV: Input must designate range of residues with 2 residue numbers.");
            }

            resids_.clear();

            if(resids[0] >= resids[1]){
                throw std::invalid_argument("AntiBetaRMSDCV: Input must list lower residue index first: please reverse residue range.");
            } else if(resids[1] - resids[0] < 5){
                throw std::invalid_argument("AntiBetaRMSDCV: Residue range must span at least 6 residues for secondary structure calculation.");
            }

            std::cout << "AntiBetaRMSDCV: Calculating antiparallel beta sheet character from residue " << resids[0] << " to " << resids[1]  << "." << std::endl;

            for(unsigned int i = resids[0]; i <= resids[1]; i++){
                resids_.push_back(i);
            }
        }


        void Initialize(const Snapshot& snapshot) override
        {
            atomids_ = ReadBackbone::GetPdbBackbone(refpdb_, resids_);

            // reference 'ideal' antiparallel beta sheet structure in nanometers
            // Reference structure taken from values used in Plumed 2.2.0
            refalpha_.push_back(unitconv_ * Vector3{ .2263, -.3795,  .1722}); // N    i
            refalpha_.push_back(unitconv_ * Vector3{ .2493, -.2426,  .2263}); // CA
            refalpha_.push_back(unitconv_ * Vector3{ .3847, -.1838,  .1761}); // CB
            refalpha_.push_back(unitconv_ * Vector3{ .1301, -.1517,  .1921}); // C
            refalpha_.push_back(unitconv_ * Vector3{ .0852, -.1504,  .0739}); // O
            refalpha_.push_back(unitconv_ * Vector3{ .0818, -.0738,  .2917}); // N    i+1
            refalpha_.push_back(unitconv_ * Vector3{-.0299,  .0243,  .2748}); // CA
            refalpha_.push_back(unitconv_ * Vector3{-.1421, -.0076,  .3757}); // CB
            refalpha_.push_back(unitconv_ * Vector3{ .0273,  .1680,  .2854}); // C
            refalpha_.push_back(unitconv_ * Vector3{ .0902,  .1993,  .3888}); // O
            refalpha_.push_back(unitconv_ * Vector3{ .0119,  .2532,  .1813}); // N    i+2
            refalpha_.push_back(unitconv_ * Vector3{ .0683,  .3916,  .1680}); // CA
            refalpha_.push_back(unitconv_ * Vector3{ .1580,  .3940,  .0395}); // CB
            refalpha_.push_back(unitconv_ * Vector3{-.0394,  .5011,  .1630}); // C
            refalpha_.push_back(unitconv_ * Vector3{-.1459,  .4814,  .0982}); // O
            refalpha_.push_back(unitconv_ * Vector3{-.2962,  .3559, -.1359}); // N    j - 2
            refalpha_.push_back(unitconv_ * Vector3{-.2439,  .2526, -.2287}); // CA
            refalpha_.push_back(unitconv_ * Vector3{-.1189,  .3006, -.3087}); // CB
            refalpha_.push_back(unitconv_ * Vector3{-.2081,  .1231, -.1520}); // C
            refalpha_.push_back(unitconv_ * Vector3{-.1524,  .1324, -.0409}); // O
            refalpha_.push_back(unitconv_ * Vector3{-.2326,  .0037, -.2095}); // N    j - 1
            refalpha_.push_back(unitconv_ * Vector3{-.1858, -.1269, -.1554}); // CA
            refalpha_.push_back(unitconv_ * Vector3{-.3053, -.2199, -.1291}); // CB
            refalpha_.push_back(unitconv_ * Vector3{-.0869, -.1949, -.2512}); // C
            refalpha_.push_back(unitconv_ * Vector3{-.1255, -.2070, -.3710}); // O
            refalpha_.push_back(unitconv_ * Vector3{ .0326, -.2363, -.2072}); // N    j
            refalpha_.push_back(unitconv_ * Vector3{ .1405, -.2992, -.2872}); // CA
            refalpha_.push_back(unitconv_ * Vector3{ .2699, -.2129, -.2917}); // CB
            refalpha_.push_back(unitconv_ * Vector3{ .1745, -.4399, -.2330}); // C
            refalpha_.push_back(unitconv_ * Vector3{ .1899, -.4545, -.1102}); // O
        }


        void Evaluate(const Snapshot& snapshot) override
        {
            // need atom positions for all atoms in atomids_
            const auto& pos = snapshot.GetPositions();
            std::vector<int> groupidx;
            std::vector<int> double_atomids(atomids_[0].size());
            std::transform(atomids_[0].begin(), atomids_[0].end(), double_atomids.begin(), [](std::string val) {return std::stod(val);});
            snapshot.GetLocalIndices(double_atomids, &groupidx);

            unsigned int resgroups = resids_.size() - 2;
            double rmsd, dist_norm, dxgrouprmsd;
            Vector3 dist_xyz, dist_ref;
            std::vector<Vector3> refxyz;
            std::vector< std::vector< Vector3 > > deriv(30, std::vector<Vector3>(30, Vector3{0,0,0}));

            std::fill(grad_.begin(), grad_.end(), Vector3{0,0,0});
            grad_.resize(snapshot.GetNumAtoms(), Vector3{0,0,0});
            val_ = 0.0;

            for(size_t i = 0; i < resgroups - 3; i++){
                for(size_t j = i + 3; j < resgroups; j++){
                    // mode: 0 for all, 1 for inter, 2 for intra
                    if((mode_ == 0) || (mode_ == 1 && atomids_[1][5 * j] != atomids_[1][5 * i]) || (mode_ == 2 && atomids_[1][5 * j] == atomids_[1][5 * i])){
                        rmsd = 0.0;
                        std::fill(refxyz.begin(), refxyz.end(), Vector3{0,0,0});
                        refxyz.resize(30, Vector3{0,0,0});
                        for(size_t k = 0; k < 15; k++){
                            refxyz[k] = pos[groupidx[5 * i + k]];
                        }
                        for(size_t k = 0; k < 15; k++){
                            refxyz[k + 15] = pos[groupidx[5 * j + k]];
                        }

                        // sum over all pairs to calculate CV
                        for(size_t k = 0; k < 29; k++){
                            for(size_t h = k + 1; h < 30; h++){
                                dist_xyz = refxyz[k] - refxyz[h];
                                dist_ref = refalpha_[k] - refalpha_[h];
                                dist_norm = dist_xyz.norm() - dist_ref.norm();
                                rmsd += dist_norm * dist_norm;
                                deriv[k][h] = dist_xyz * dist_norm / dist_xyz.norm();
                            }
                        }

                        rmsd = pow(rmsd / 435, 0.5) / 0.1;
                        val_ += (1 - pow(rmsd, 8.0)) / (1 - pow(rmsd, 12.0));

                        dxgrouprmsd = pow(rmsd, 11.0) + pow(rmsd, 7.0);
                        dxgrouprmsd /= pow(rmsd, 8.0) + pow(rmsd, 4.0) + 1;
                        dxgrouprmsd /= pow(rmsd, 8.0) + pow(rmsd, 4.0) + 1;
                        dxgrouprmsd *= -40. / 435;

                        for(size_t k = 0; k < 15; k++){
                            for(size_t h = k + 1; h < 15; h++){
                                grad_[groupidx[5 * i + k]] += dxgrouprmsd * deriv[k][h];
                                grad_[groupidx[5 * i + h]] -= dxgrouprmsd * deriv[k][h];
                            }
                            for(size_t h = 0; h < 15; h++){
                                grad_[groupidx[5 * i + k]] += dxgrouprmsd * deriv[k][h+15];
                                grad_[groupidx[5 * j + h]] -= dxgrouprmsd * deriv[k][h+15];
                            }
                        }
                        for(size_t k = 0; k < 14; k++){
                            for(size_t h = k + 1; h < 15; h++){
                                grad_[groupidx[5 * j + k]] += dxgrouprmsd * deriv[k+15][h+15];
                                grad_[groupidx[5 * j + h]] -= dxgrouprmsd * deriv[k+15][h+15];
                            }
                        }
                    }
                }
            }
        }

        static AntiBetaRMSDCV* Build(const Json::Value& json, const std::string& path)
        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::Reader reader;

            reader.parse(JsonSchema::AntiBetaRMSDCV, schema);
            validator.Parse(schema, path);

            //Validate inputs
            validator.Validate(json, path);
            if(validator.HasErrors())
                    throw BuildException(validator.GetErrors());

            std::vector<int> resids;
            for(auto& s : json["residue_ids"])
                resids.push_back(s.asInt());
            auto reference = json["reference"].asString();

            double unitconv = json.get("length_unit", 1).asDouble();

            int mode = json.get("mode", 0).asInt();

            return new AntiBetaRMSDCV(resids, reference, unitconv, mode);
        }
    };
}