AlphaRMSDCV.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 AlphaRMSDCV : public CollectiveVariable
    {
    private:
 
        std::vector<int> resids_;
 
        std::vector< std::vector<std::string> > atomids_;
 
        std::vector<int> ids_only_;
 
        std::string refpdb_;
 
        double unitconv_;
 
        std::vector<double> refdists_;
 
    public:
 
        AlphaRMSDCV(std::vector<int> resids, std::string refpdb, double unitconv) :
        resids_(resids), refpdb_(refpdb), unitconv_(unitconv)
        {
            if(resids_.size() != 2 ){
                throw std::invalid_argument("AlphaRMSDCV: Input must designate range of residues with 2 residue numbers.");
            }
 
            resids_.clear();
 
            if(resids[0] >= resids[1]){
                throw std::invalid_argument("AlphaRMSDCV: Input must list lower residue index first: please reverse residue range.");
            } else if(resids[1] - resids[0] < 5) {
                throw std::invalid_argument("AlphaRMSDCV: Residue range must span at least 6 residues for alpha helix calculation.");
            }
 
            std::cout << "AlphaRMSDCV: Calculating alpha helix 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({
                    "AlphaRMSDCV: Expected to find " +
                    to_string(resids_.size() * 5) +
                    " atoms, but only found " +
                    to_string(nfound) + "."
                });
 
            // reference 'ideal' alpha helix structure, in nanometers
            // Reference structure taken from values used in Plumed 2.2.0
            std::vector<Vector3> refalpha;
            refalpha.push_back(unitconv_ * Vector3{ .0733,  .0519,  .5298 }); // N
            refalpha.push_back(unitconv_ * Vector3{ .1763,  .0810,  .4301 }); // CA
            refalpha.push_back(unitconv_ * Vector3{ .3166,  .0543,  .4881 }); // CB
            refalpha.push_back(unitconv_ * Vector3{ .1527, -.0045,  .3053 }); // C
            refalpha.push_back(unitconv_ * Vector3{ .1646,  .0436,  .1928 }); // O
            refalpha.push_back(unitconv_ * Vector3{ .1180, -.1312,  .3254 }); // N
            refalpha.push_back(unitconv_ * Vector3{ .0924, -.2203,  .2126 }); // CA
            refalpha.push_back(unitconv_ * Vector3{ .0650, -.3626,  .2626 }); // CB
            refalpha.push_back(unitconv_ * Vector3{-.0239, -.1711,  .1261 }); // C
            refalpha.push_back(unitconv_ * Vector3{-.0190, -.1815,  .0032 }); // O
            refalpha.push_back(unitconv_ * Vector3{-.1280, -.1172,  .1891 }); // N
            refalpha.push_back(unitconv_ * Vector3{-.2416, -.0661,  .1127 }); // CA
            refalpha.push_back(unitconv_ * Vector3{-.3548, -.0217,  .2056 }); // CB
            refalpha.push_back(unitconv_ * Vector3{-.1964,  .0529,  .0276 }); // C
            refalpha.push_back(unitconv_ * Vector3{-.2364,  .0659, -.0880 }); // O
            refalpha.push_back(unitconv_ * Vector3{-.1130,  .1391,  .0856 }); // N
            refalpha.push_back(unitconv_ * Vector3{-.0620,  .2565,  .0148 }); // CA
            refalpha.push_back(unitconv_ * Vector3{ .0228,  .3439,  .1077 }); // CB
            refalpha.push_back(unitconv_ * Vector3{ .0231,  .2129, -.1032 }); // C
            refalpha.push_back(unitconv_ * Vector3{ .0179,  .2733, -.2099 }); // O
            refalpha.push_back(unitconv_ * Vector3{ .1028,  .1084, -.0833 }); // N
            refalpha.push_back(unitconv_ * Vector3{ .1872,  .0593, -.1919 }); // CA
            refalpha.push_back(unitconv_ * Vector3{ .2850, -.0462, -.1397 }); // CB
            refalpha.push_back(unitconv_ * Vector3{ .1020,  .0020, -.3049 }); // C
            refalpha.push_back(unitconv_ * Vector3{ .1317,  .0227, -.4224 }); // O
            refalpha.push_back(unitconv_ * Vector3{-.0051, -.0684, -.2696 }); // N
            refalpha.push_back(unitconv_ * Vector3{-.0927, -.1261, -.3713 }); // CA
            refalpha.push_back(unitconv_ * Vector3{-.1933, -.2219, -.3074 }); // CB
            refalpha.push_back(unitconv_ * Vector3{-.1663, -.0171, -.4475 }); // C
            refalpha.push_back(unitconv_ * Vector3{-.1916, -.0296, -.5673 }); // 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();
 
            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;
            unsigned int resgroups = resids_.size() - 5;
 
            // for each set of 6 residues
            for(size_t i = 0; i < resgroups; i++){
 
                // clear temp rmsd calculation
                rmsd = 0.0;
 
                // load refxyz with the correct 30 reference atoms
                std::fill(refxyz.begin(), refxyz.end(), Vector3{0,0,0});
                refxyz.resize(30, Vector3{0,0,0});
                for(size_t j = 0; j < 30; j++){
                    localidx = snapshot.GetLocalIndex(ids_only_[5 * i + j]);
                    if(localidx != -1) refxyz[j] = pos[localidx];
                }
 
                MPI_Allreduce(MPI_IN_PLACE, refxyz.data(), 90, MPI_DOUBLE, MPI_SUM, comm);
 
                // sum over 435 pairs in refxyz and refalpha_ to calculate CV
                for(size_t j = 0; j < 29; j++){
                    for(size_t k = j + 1; k < 30; k++){
                        dist_xyz = refxyz[j] - refxyz[k];
                        dist_norm = dist_xyz.norm() - refdists_[29 * j + k];
                        rmsd += dist_norm * dist_norm;
                        deriv[j][k] = 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 j = 0; j < 29; j++){
                    for(size_t k = j + 1; k < 30; k++){
                        localidx = snapshot.GetLocalIndex(ids_only_[5 * i + j]);
                        if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[j][k];
                        localidx = snapshot.GetLocalIndex(ids_only_[5 * i + k]);
                        if(localidx != -1) grad_[localidx] += dxgrouprmsd * deriv[j][k];
                    }
                }
            }
        }
 
        static AlphaRMSDCV* 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::AlphaRMSDCV.c_str(),
                          JsonSchema::AlphaRMSDCV.c_str() + JsonSchema::AlphaRMSDCV.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();
 
            return new AlphaRMSDCV(resids, reference, unitconv);
        }
    };
}