PSampMethods.h

Go to the documentation of this file.

/*
    LoopTK: Protein Loop Kinematic Toolkit
    Copyright (C) 2007 Stanford University

    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License along
    with this program; if not, write to the Free Software Foundation, Inc.,
    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#include <iostream>
#include <time.h>
#include "PBasic.h"
#include "PChainNavigator.h"
#include "PConstants.h"
#include "PDataCollector.h"
#include "PExtension.h"
#include "PTools.h"
#include "POptimize.h"
#include "PPhiPsiDistribution.h"
#include <string>
#include <list>
#include <vector>
#include <stack>
#include <stdlib.h>
#include <math.h>
#include <map>

class SpaceRelationship {

  private:
        friend class PSampMethods;

        Real angle_c_n_ca;
        Real angle_ca_c_n;
        Real angle_o_c_n;
        Real length_c_n;
        Real length_ca_c;
        Real length_o_c;

        SpaceRelationship () {
                angle_c_n_ca = ANGLE_C_N_CA;
                angle_ca_c_n = ANGLE_CA_C_N;
                angle_o_c_n = ANGLE_O_C_N;
                length_c_n = LENGTH_C_N;
                length_ca_c = LENGTH_CA_C;
                length_o_c = LENGTH_O_C;
        }

        SpaceRelationship (PResidue *res1, PResidue *res2) {
                Vector3 ca1 = res1->getAtomPosition("CA");
                Vector3 c1 = res1->getAtomPosition("C");
                Vector3 o1 = res1->getAtomPosition("O");
                Vector3 n2 = res2->getAtomPosition("N");
                Vector3 ca2 = res2->getAtomPosition("CA");
                angle_c_n_ca = rad2deg*PMath::getAngle(c1-n2, ca2-n2);
                length_c_n = (c1-n2).norm();
                angle_ca_c_n = rad2deg*PMath::getAngle(ca1-c1,n2-c1);
                length_ca_c = (ca1-c1).norm();
                angle_o_c_n = rad2deg*PMath::getAngle(o1-c1,n2-c1);
                length_o_c = (o1-c1).norm();
        }

        void print() {
                cout << "angle_c_n_ca = " << angle_c_n_ca << endl;
                cout << "angle_ca_c_n = " << angle_ca_c_n << endl;
                cout << "angle_o_c_n = " << angle_o_c_n << endl;
                cout << "length_c_n = " << length_c_n << endl;
                cout << "length_ca_c = " << length_ca_c << endl;
                cout << "length_o_c = " << length_o_c << endl;
        }
}; // end class SapceRelationship


class PSampMethods {
  public:
        static IKSolution RandAndIKClose(PProtein *loop, bool clash_free);
        static IKSolution RandAndIKClose(PProtein *loop,const string &pdbFileName, bool clash_free);
        static IKSolutions PermuteIK(PProtein *loop, int num_wanted);
        
        static vector<PProtein*> DeformSampleBackbone(PProtein *orig_protein, int loopSid, int loopEid, int num_wanted, double deform_mag);

        static vector<PProtein*> SeedSampleBackbone (PProtein *protein, int loopSid, int loopEid, int num_wanted=1);

         /* Usage example:
         *      map<string,PPhiPsiDistribution> Map = PPhiPsiDistribution::generateRamachandran();
         *      PProtein *protein = PDBIO::readFromFile("pdbfiles/135L.pdb");
         *      int loopSid=64, loopEid=72;
         *      vector<PProtein*> newps = PSampMethods::SeedSampleBackbone(protein,loopSid,loopEid,Map);
         *      PProtein *loop = new PProtein(newps[0],loopSid,loopEid);
         *      // Write the loop to a pdb file
         *      PDBIO::writeToFile(loop,"pdbfiles/135L_seed.pdb");
         *      // Add side chain
         *      PSampMethods::addSidechain("pdbfiles/135L_seed.pdb","pdbfiles/135L_NoLoop.pdb","/home/scwrl3_lin","pdbfiles/135L_seed_withSC.pdb");
         *      // Merge the loop with side chain and the protein
         *      PProtein *new_protein = PSampMethods::MergeProtein(loop,protein,loopSid);
         *      PDBIO::writeToFile(new_protein,"pdbfiles/135_new.pdb");
         */
        static vector<PProtein*> SeedSampleBackbone (PProtein *protein, int loopSid, int loopEid, map<string,PPhiPsiDistribution> &distri_map, int num_wanted=1);

        static PProtein* MergeProtein (PProtein *loop, PProtein* original_protein, int startRid);

        static void addSidechain (string loopFile, string boundaryFile, string scwrl3_path, string outLoopFile);


    private:
        static vector<PProtein*> SeedSampleBackboneLoopOnly (PProtein* original_protein, int loopSid, int loopEid, int num_wanted=1);

        static vector<PProtein*> SeedSampleBackboneLoopOnly (PProtein* original_protein, int loopSid, int loopEid, map<string,PPhiPsiDistribution> &distri_map, int num_wanted=1);

        static vector<Real>* generateForwardOpenLoop(PProtein *loopEntire, int collisionFreeResNum);
        static vector<Real>* generateForwardOpenLoop (PProtein* loopEntire, int collisionFreeResNum, map<string,PPhiPsiDistribution> &map_distri, vector<string> &aa_names);
        static vector<Real>* generateBackwardOpenLoop (PProtein* loop);
        static vector<Real>* generateBackwardOpenLoop (PProtein* loop, map<string,PPhiPsiDistribution> &map_distri, vector<string> &aa_names);
        static Vector3 computePreCpos (PResidue *res, Real angle, Real bondLength);
        static void computeGoal (PResidue *res, SpaceRelationship *sr, Vector3 *endPriorG, Vector3 *endG, Vector3 *endNextG);
        static bool IKClose (PProtein* move_loop, Vector3 endPriorG, Vector3 endG, Vector3 endNextG);
        static void UpdateProtein(PProtein *p, vector<Real> *positiveAngles, vector<Real> *negativeAngles, bool forwardDir);
        static void UpdateProtein(PProtein *p, vector<Real> *angles, bool forwardDir);
        static double computeMaxLength (int proteinSize);


};

---