From a62f425cfdc48e5b132b8f73574f1f52bdf0c0b1 Mon Sep 17 00:00:00 2001
From: Andreas Schenk <andreas_schenk@hms.harvard.edu>
Date: Thu, 7 Jun 2012 10:05:07 -0400
Subject: [PATCH] removed one more pytho removed some unnecessary pow()
---
modules/geom/src/vec3.cc | 11 +++++++----
modules/mol/alg/src/local_dist_test.cc | 2 +-
modules/mol/alg/src/trajectory_analysis.cc | 2 +-
modules/mol/base/src/coord_frame.cc | 17 +++++++++--------
4 files changed, 18 insertions(+), 14 deletions(-)
diff --git a/modules/geom/src/vec3.cc b/modules/geom/src/vec3.cc
index 8480aac85..932432a1e 100644
--- a/modules/geom/src/vec3.cc
+++ b/modules/geom/src/vec3.cc
@@ -101,7 +101,8 @@ Line3 Vec3List::FitCylinder(const Vec3& initial_direction, const Vec3& center) c
radius/=Real(n_res);
res_sum=0.0;
for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- res_sum+=pow(Distance(axis,(*i))-radius,2.);
+ Real r=Distance(axis,(*i))-radius;
+ res_sum+=r*r;
}
unsigned long k=0;
err=2.0*prec;
@@ -110,7 +111,7 @@ Line3 Vec3List::FitCylinder(const Vec3& initial_direction, const Vec3& center) c
axis_old=axis;
radius=0.0;
if (k>50) {
- delta=delta_0*pow((50./k),2.0);
+ delta=delta_0*50.0*50.0/(k*k);
}
for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
radius+=Distance(axis,(*i));
@@ -127,7 +128,8 @@ Line3 Vec3List::FitCylinder(const Vec3& initial_direction, const Vec3& center) c
}
radius/=Real(n_res);
for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- res_sum+=pow(Distance(axis,(*i))-radius,2.);
+ Real r=Distance(axis,(*i))-radius;
+ res_sum+=r*r;
}
gradient[j]=(res_sum-res_sum_old)/delta;
}
@@ -143,7 +145,8 @@ Line3 Vec3List::FitCylinder(const Vec3& initial_direction, const Vec3& center) c
radius/=Real(n_res);
res_sum=0.0;
for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- res_sum+=pow(Distance(axis,(*i))-radius,2.);
+ Real r=Distance(axis,(*i))-radius;
+ res_sum+=r*r;
}
err=fabs((res_sum-res_sum_old)/float(n_res));
k++;
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
index 4c4bd2e25..89da8c9ae 100644
--- a/modules/mol/alg/src/local_dist_test.cc
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -276,7 +276,7 @@ bool UniqueAtomIdentifier::operator==(const UniqueAtomIdentifier& rhs) const
bool ReferenceDistance::IsValid() const
{
- if (mind_ == -1.0 and maxd_ == -1.0) {
+ if (mind_ == -1.0 && maxd_ == -1.0) {
return false;
}
return true;
diff --git a/modules/mol/alg/src/trajectory_analysis.cc b/modules/mol/alg/src/trajectory_analysis.cc
index 4a2671c01..5adf3c6eb 100644
--- a/modules/mol/alg/src/trajectory_analysis.cc
+++ b/modules/mol/alg/src/trajectory_analysis.cc
@@ -396,7 +396,7 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
rmsf+=geom::Dot(v,v);
}
}
- return pow(rmsf/float(n_atoms*n_frames),0.5);
+ return sqrt(rmsf/float(n_atoms*n_frames));
}
}}} //ns
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 1c30611b3..bbaa5ccab 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -39,13 +39,12 @@ namespace ost { namespace mol {
*/
Real Eval2AngleDist(Real phi, Real phi0, Real psi, Real psi0, Real delta)
{
- Real d1,d2,d;
- d1=abs(phi-phi0);
- d2=abs(psi-psi0);
+ Real d1=abs(phi-phi0);
+ Real d2=abs(psi-psi0);
if (d1>M_PI) d1=abs(d1-2.*M_PI);
if (d2>M_PI) d1=abs(d2-2.*M_PI);
- d=(pow(d1,2.)+pow(d2,2.))/pow(delta,2.);
- return 1./(1+d);
+ Real d=(d1*d1+d2*d2)/(delta*delta);
+ return 1.0/(1.0+d);
}
}
@@ -138,7 +137,7 @@ namespace ost { namespace mol {
val=geom::Length2(av_ref-av_sele);
rmsd+=val;
}
- return pow(rmsd/indices_sele.size(),0.5);
+ return sqrt(rmsd/indices_sele.size());
}
Real CoordFrame::GetRMSD(const EntityView& reference_view,const EntityView& sele_view) const
@@ -303,8 +302,10 @@ namespace ost { namespace mol {
psi=geom::DihedralAngle(n,ca,c,n_next);
score.push_back(Eval2AngleDist(phi,phi_0,psi,psi_0,delta));
}
- score2[0]=pow(score[0]*score[1],3./2.);
- score2[n_atoms-3]=pow(score[n_atoms-3]*score[n_atoms-4],3./2.);
+ score2[0]=sqrt(score[0]*score[1]*score[0]*score[1]*score[0]*score[1]);
+ score2[n_atoms-3]=sqrt(score[n_atoms-3]*score[n_atoms-4]*
+ score[n_atoms-3]*score[n_atoms-4]*
+ score[n_atoms-3]*score[n_atoms-4]);
for (unsigned long i=1; i!=n_atoms-3; ++i) {
score2[i]=score[i-1]*score[i]*score[i+1];
}
--
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