ParallelBetaRMSDCV.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 ParallelBetaRMSDCV : public CollectiveVariable
    {
    private:
 
        std::vector<int> resids_;
 
        //std::vector<int> atomids_;
        std::vector< std::vector<std::string> > atomids_;
 
        std::vector<int> ids_only_;
 
        std::string refpdb_;
 
        std::vector<Vector3> refalpha_;
 
        double unitconv_;
 
        int mode_;
 
        std::vector<double> refdists_;
 
    public:
 
        ParallelBetaRMSDCV(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("ParallelBetaRMSDCV: Input must designate range of residues with 2 residue numbers.");
            }
 
            resids_.clear();
 
            if(resids[0] >= resids[1]){
                throw std::invalid_argument("ParallelBetaRMSDCV: Input must list lower residue index first: please reverse residue range.");
            } else if(resids[1] - resids[0] < 5) {
                throw std::invalid_argument("ParallelBetaRMSDCV: Residue range must span at least 6 residues for secondary structure calculation.");
            }
 
            std::cout << "ParallelBetaRMSDCV: Calculating parallel beta sheet character from residue " << resids[0] << " to " << resids[1]  << "." << std::endl;
 
            for(int i = resids[0]; i <= resids[1]; i++){
                resids_.push_back(i);
            }
        }
 
 
        void Initialize(const Snapshot& snapshot) override
        {
            atomids_ = ReadBackbone::GetPdbBackbone(refpdb_, resids_);
            ids_only_.resize(atomids_[0].size());
 
            // check to find all necessary atoms
            std::transform(atomids_[0].begin(), atomids_[0].end(), ids_only_.begin(), [](std::string val) {return std::stoi(val);});
            using std::to_string;
            std::vector<int> found;
            snapshot.GetLocalIndices(ids_only_, &found);
            size_t nfound = found.size();
            MPI_Allreduce(MPI_IN_PLACE, &nfound, 1, MPI_INT, MPI_SUM, snapshot.GetCommunicator());
            if(nfound != resids_.size() * 5)
                throw BuildException({
                    "ParallelBetaRMSDCV: Expected to find " +
                    to_string(resids_.size() * 5) +
                    " atoms, but only found " +
                    to_string(nfound) + "."
                });
 
            // reference structure for parallel beta sheet, values in nanometers
            // Reference structure taken from values used in Plumed 2.2.0
            std::vector<Vector3> refalpha;
            refalpha.push_back(unitconv_ * Vector3{-.1439, -.5122, -.1144}); // N    residue i
            refalpha.push_back(unitconv_ * Vector3{-.0816, -.3803, -.1013}); // CA
            refalpha.push_back(unitconv_ * Vector3{ .0099, -.3509, -.2206}); // CB
            refalpha.push_back(unitconv_ * Vector3{-.1928, -.2770, -.0952}); // C
            refalpha.push_back(unitconv_ * Vector3{-.2991, -.2970, -.1551}); // O
            refalpha.push_back(unitconv_ * Vector3{-.1698, -.1687, -.0215}); // N    residue i+1
            refalpha.push_back(unitconv_ * Vector3{-.2681, -.0613, -.0143}); // CA
            refalpha.push_back(unitconv_ * Vector3{-.3323, -.0477,  .1267}); // CB
            refalpha.push_back(unitconv_ * Vector3{-.1984,  .0681, -.0574}); // C
            refalpha.push_back(unitconv_ * Vector3{-.0807,  .0921, -.0273}); // O
            refalpha.push_back(unitconv_ * Vector3{-.2716,  .1492, -.1329}); // N    residue i+2
            refalpha.push_back(unitconv_ * Vector3{-.2196,  .2731, -.1883}); // CA
            refalpha.push_back(unitconv_ * Vector3{-.2263,  .2692, -.3418}); // CB
            refalpha.push_back(unitconv_ * Vector3{-.2989,  .3949, -.1433}); // C
            refalpha.push_back(unitconv_ * Vector3{-.4214,  .3989, -.1583}); // O
            refalpha.push_back(unitconv_ * Vector3{ .2464, -.4352,  .2149}); // N    residue h
            refalpha.push_back(unitconv_ * Vector3{ .3078, -.3170,  .1541}); // CA
            refalpha.push_back(unitconv_ * Vector3{ .3398, -.3415,  .0060}); // CB
            refalpha.push_back(unitconv_ * Vector3{ .2080, -.2021,  .1639}); // C
            refalpha.push_back(unitconv_ * Vector3{ .0938, -.2178,  .1225}); // O
            refalpha.push_back(unitconv_ * Vector3{ .2525, -.0886,  .2183}); // N    residue h+1
            refalpha.push_back(unitconv_ * Vector3{ .1692,  .0303,  .2346}); // CA
            refalpha.push_back(unitconv_ * Vector3{ .1541,  .0665,  .3842}); // CB
            refalpha.push_back(unitconv_ * Vector3{ .2420,  .1410,  .1608}); // C
            refalpha.push_back(unitconv_ * Vector3{ .3567,  .1733,  .1937}); // O
            refalpha.push_back(unitconv_ * Vector3{ .1758,  .1976,  .0600}); // N    residue h+2
            refalpha.push_back(unitconv_ * Vector3{ .2373,  .2987, -.0238}); // CA
            refalpha.push_back(unitconv_ * Vector3{ .2367,  .2527, -.1720}); // CB
            refalpha.push_back(unitconv_ * Vector3{ .1684,  .4331, -.0148}); // C
            refalpha.push_back(unitconv_ * Vector3{ .0486,  .4430, -.0415}); // O
 
            // calculate all necessary pairwise distances for reference structure
            std::fill(refdists_.begin(), refdists_.end(), 0.0);
            refdists_.resize(900, 0.0);
            for(size_t k = 0; k < 29; k++){
                for(size_t h = k + 1; h < 30; h++){
                    refdists_[29 * k + h] = (refalpha[k] - refalpha[h]).norm();
                }
            }
        }
 
 
        void Evaluate(const Snapshot& snapshot) override
        {
            // need atom positions for all atoms
            const auto& pos = snapshot.GetPositions();
            auto& comm = snapshot.GetCommunicator();
 
            unsigned int resgroups = resids_.size() - 2;
            double rmsd, dist_norm, dxgrouprmsd;
            int localidx;
            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++){
                            localidx = snapshot.GetLocalIndex(ids_only_[5 * i + k]);
                            if(localidx != -1) refxyz[k] = pos[localidx];
                        }
                        for(size_t k = 0; k < 15; k++){
                            localidx = snapshot.GetLocalIndex(ids_only_[5 * j + k]);
                            if(localidx != -1) refxyz[k + 15] = pos[localidx];
                        }
 
                        MPI_Allreduce(MPI_IN_PLACE, refxyz.data(), 90, MPI_DOUBLE, MPI_SUM, comm);
 
                        // 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_norm = dist_xyz.norm() - refdists_[29 * k + h];
                                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++){
                                localidx = snapshot.GetLocalIndex(ids_only_[5 * i + k]);
                                if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[k][h];
                                localidx = snapshot.GetLocalIndex(ids_only_[5 * i + h]);
                                if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[k][h];
                            }
                            for(size_t h = 0; h < 15; h++){
                                localidx = snapshot.GetLocalIndex(ids_only_[5 * i + k]);
                                if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[k][h + 15];
                                localidx = snapshot.GetLocalIndex(ids_only_[5 * j + h]);
                                if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[k][h + 15];
                            }
                        }
                        for(size_t k = 0; k < 14; k++){
                            for(size_t h = k + 1; h < 15; h++){
                                localidx = snapshot.GetLocalIndex(ids_only_[5 * j + k]);
                                if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[k + 15][h + 15];
                                localidx = snapshot.GetLocalIndex(ids_only_[5 * j + h]);
                                if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[k + 15][h + 15];
                            }
                        }
                    }
                }
            }
        }
 
        static ParallelBetaRMSDCV* Build(const Json::Value& json, const std::string& path)
        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::CharReaderBuilder rbuilder;
            Json::CharReader* reader = rbuilder.newCharReader();
 
            reader->parse(JsonSchema::ParallelBetaRMSDCV.c_str(),
                          JsonSchema::ParallelBetaRMSDCV.c_str() + JsonSchema::ParallelBetaRMSDCV.size(),
                          &schema, nullptr);
            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 ParallelBetaRMSDCV(resids, reference, unitconv, mode);
        }
    };
}