designability_score.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

#include <protocols/sic_dock/designability_score.hh>
#include <core/kinematics/Stub.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>

namespace protocols{
namespace sic_dock{

using platform::Real;
using numeric::min;
using numeric::max;
typedef numeric::xyzVector<platform::Real> Vec;
typedef numeric::xyzMatrix<platform::Real> Mat;

void
get_xform_stats(
  core::kinematics::Stub const & sir,
  core::kinematics::Stub const & sjr,
  Real& dx, Real& dy, Real& dz,
  Real& ex, Real& ey, Real& ez
){
  Vec d = sir.global2local(sjr.v);
  dx = d.x();
  dy = d.y();
  dz = d.z();
  Mat R = sir.M.transposed()*sjr.M;
  // Real ang;
  // Vec axis = rotation_axis(R,ang);
  // ang = numeric::conversions::degrees(ang);
  // std::cout << axis << " " << ang << std::endl;

  Real phi,psi,theta;
  if( fabs(R.zx())-1.0 < 0.00001 ) {
    theta = -asin(R.zx());
    Real const ctheta = cos(theta);
    psi = atan2(R.zy()/ctheta,R.zz()/ctheta);
    phi = atan2(R.yx()/ctheta,R.xx()/ctheta);
  } else {
    if( R.zx() < 0.0 ) {
      theta = numeric::constants::d::pi / 2.0;
      psi = atan2(R.xy(),R.xz());
    } else {
      theta = -numeric::constants::d::pi / 2.0;
      psi = atan2(-R.xy(),-R.xz());     
    }
    phi = 0;
  }
  ex = psi;
  ey = theta;
  ez = phi;
}


XfoxmScore::XfoxmScore(
  std::string datadir
){
  hh = new char[16*16*16*24*12*24];
  he = new char[16*16*16*24*12*24];
  hl = new char[16*16*16*24*12*24];
  ee = new char[16*16*16*24*12*24];
  el = new char[16*16*16*24*12*24];
  ll = new char[16*16*16*24*12*24];
  fillarray(hh,datadir+"/hhpb.dat.gz.hist6.dat.gz.bin");
  fillarray(he,datadir+"/hepb.dat.gz.hist6.dat.gz.bin");
  fillarray(hl,datadir+"/hlpb.dat.gz.hist6.dat.gz.bin");
  fillarray(ee,datadir+"/eepb.dat.gz.hist6.dat.gz.bin");
  fillarray(el,datadir+"/elpb.dat.gz.hist6.dat.gz.bin");
  fillarray(ll,datadir+"/llpb.dat.gz.hist6.dat.gz.bin");
  // makebinary(hh,datadir+"/hhpb.dat.gz.hist6.dat.gz"); // uncomment to gen binary files
  // makebinary(he,datadir+"/hepb.dat.gz.hist6.dat.gz"); // uncomment to gen binary files
  // makebinary(hl,datadir+"/hlpb.dat.gz.hist6.dat.gz"); // uncomment to gen binary files
  // makebinary(ee,datadir+"/eepb.dat.gz.hist6.dat.gz"); // uncomment to gen binary files
  // makebinary(el,datadir+"/elpb.dat.gz.hist6.dat.gz"); // uncomment to gen binary files
  // makebinary(ll,datadir+"/llpb.dat.gz.hist6.dat.gz"); // uncomment to gen binary files
  // utility_exit_with_message("made binary file");
}
void
XfoxmScore::fillarray(
  char *a, std::string fname
){
  std::cout << "reading " << fname << std::endl;
  utility::io::izstream in(fname,std::ios::binary);
  if(!in.good()) utility_exit_with_message("bad file");
  in.read(a,16*16*16*24*12*24);
  in.close();
}
void
XfoxmScore::makebinary(
  char *a, std::string fname
){
  std::cout << "reading " << fname << std::endl;
  utility::io::izstream in(fname);
  if(!in.good()) utility_exit_with_message("bad file");
  for(int i = 0; i < 16*16*16*24*12*24; ++i){
    float f;
    in >> f;
    int tmp = (int)((log(f)+2.5)*12.0);
    a[i] =  (f==0.0f) ? ((char)-127) : ((char)max(-126,min(128,tmp)));
    // std::cout << f << " " << tmp << " " << (int)a[i] << std::endl;
    // if( i > 100) utility_exit_with_message("FOO");
  }
  in.close();
  std::cout << "writing: " << fname+".bin.gz" << std::endl;
  utility::io::ozstream out(fname+".bin",std::ios::out | std::ios::binary);
  out.write(a,16*16*16*24*12*24);
  out.close();
  // std::cout << "writing: " << fname+".txt.gz for testing" << std::endl;
  // utility::io::ozstream out2(fname+".txt.gz",std::ios::out);
  // for(int i = 0; i < 16*16*16*24*12*24; ++i) out2 << (int)a[i] << std::endl;
  // out2.close();
}

float
XfoxmScore::score(
  core::kinematics::Stub const & s1,
  core::kinematics::Stub const & s2,
  char ss1, char ss2
) const {
  using numeric::constants::d::pi_2;
  if( ss1=='L' || ss2=='L' ) return 0.0;
  if( s1.global2local(s2.v).length_squared() > 64.0 ) return 0.0; 
  char *a = hh;
  if( ss1=='E' && ss2=='E' ) a = ee;
  else if( ss2=='E' || ss1=='E' ) a = he;
  // if( ss1=='E' && ss2=='E' ) a = ee;
  // // if( ss1=='L' && ss2=='L' ) a = ll;
  // else if( ss1=='H' && ss2=='E' || ss1=='E' && ss2=='H' ) a = he;
  // // if( ss1=='H' && ss2=='L' || ss1=='L' && ss2=='H' ) a = hl;
  // // if( ss1=='E' && ss2=='L' || ss1=='L' && ss2=='E' ) a = el;    
  Real dx,dy,dz,ex,ey,ez;
  if((ss1=='E' && ss2=='H') || (ss1=='L' && ss2=='H') || (ss1=='L' && ss2=='E')){
       get_xform_stats(s2,s1,dx,dy,dz,ex,ey,ez); // reverse
  } else get_xform_stats(s1,s2,dx,dy,dz,ex,ey,ez);
  int idx = dx+8.0; // 0.0-0.999 -> 10
  int idy = dy+8.0;
  int idz = dz+8.0;
  int iex = ex/pi_2*24.0 + 12.0;
  int iey = ey/pi_2*24.0 +  6.0;
  int iez = ez/pi_2*24.0 + 12.0;
  int index = idx + 16*idy + 16*16*idz + 16*16*16*iex + 16*16*16*24*iey + 16*16*16*24*12*iez;
  if( 0 > index || index >= 16*16*16*24*12*24 ) utility_exit_with_message("FOO");
  // expensive memory lookup
  char val = a[index];
  // 
  // std::cout << (int)val << "'" << val << "'"<< std::endl;
  return val == -127 ? 0.0 : min(10.0,exp(((float)val)/12.0-2.5));
  // return val == -127 ? -15.0 : ((float)val)/12.0;
}

float
XfoxmScore::score(
  core::pose::Pose const & pose,
  platform::Size rsd1,
  platform::Size rsd2
) const {
  if(!pose.residue(rsd1).is_protein()) return 0.0;
  if(!pose.residue(rsd2).is_protein()) return 0.0;
  if(!pose.residue(rsd1).has("CB")) return 0.0;
  if(!pose.residue(rsd2).has("CB")) return 0.0;
  Vec CBi = pose.residue(rsd1).xyz("CB");
  Vec CAi = pose.residue(rsd1).xyz("CA");
  Vec  Ni = pose.residue(rsd1).xyz( "N");
  core::kinematics::Stub sir(CBi,CAi,Ni);
  Vec CBj = pose.residue(rsd2).xyz("CB");
  Vec CAj = pose.residue(rsd2).xyz("CA");
  Vec  Nj = pose.residue(rsd2).xyz( "N");
  if( CBi.distance_squared(CBj) > 64.0 ) return 0.0;
  core::kinematics::Stub sjr(CBj,CAj,Nj);
  return score(sir,sjr,pose.secstruct(rsd1),pose.secstruct(rsd2));
}

float
XfoxmScore::score(
  core::pose::Pose & pose,
  bool compute_ss   
) const {
  if(compute_ss){
    core::scoring::dssp::Dssp dssp(pose);
    dssp.insert_ss_into_pose(pose);
  }
  float tot_score = 0.0;
  for(platform::Size ir = 1; ir <= pose.n_residue(); ++ir){
    for(platform::Size jr = ir+1; jr <= pose.n_residue(); ++jr){
      float s1 = score(pose,ir,jr);
      float s2 = score(pose,jr,ir);
      // if( s1 < 0.0f ) std::cout << s1 << std::endl;
      // if( s2 < 0.0f ) std::cout << s2 << std::endl;        
      tot_score += s1;
      tot_score += s2;
    }
  }
  return tot_score;
}
float
XfoxmScore::score(
  core::pose::Pose const & pose
) const {
  float tot_score = 0.0;
  for(platform::Size ir = 1; ir <= pose.n_residue(); ++ir){
    for(platform::Size jr = ir+1; jr <= pose.n_residue(); ++jr){
      float s1 = score(pose,ir,jr);
      float s2 = score(pose,jr,ir);
      // if( s1 < 0.0f ) std::cout << s1 << std::endl;
      // if( s2 < 0.0f ) std::cout << s2 << std::endl;        
      tot_score += s1;
      tot_score += s2;
    }
  }
  return tot_score;
}


} // end namespace sic_dock
} // end namespace protocols