From b2658f9cecddf118da6196bea67c68bee4828ea7 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Tue, 19 Jun 2012 14:27:49 +0200
Subject: [PATCH] Removed tabs and one warning in ldt-related code
---
modules/mol/alg/src/filter_clashes.cc | 36 +++++++++----------
modules/mol/alg/src/filter_clashes.hh | 18 +++++-----
modules/mol/alg/src/lddt.cc | 24 ++++++-------
modules/mol/alg/src/local_dist_diff_test.cc | 38 ++++++++++-----------
modules/mol/alg/src/local_dist_diff_test.hh | 2 +-
5 files changed, 59 insertions(+), 59 deletions(-)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 43689bf16..27ffb8448 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -386,19 +386,19 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
} else {
LOG_VERBOSE("BOND:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << bond_str << " " << min_length << " " << max_length << " " << blength << " " << zscore << " " << "PASS")
}
- bond_count++;
+ bond_count++;
running_sum_zscore_bonds+=zscore;
- String bond_elems=bond_string_elems(ele1,ele2);
- std::map<String,Real>::const_iterator find_be = bond_length_sum.find(bond_elems);
- if (find_be==bond_length_sum.end()) {
- bond_length_sum[bond_elems]=blength;
- bond_zscore_sum[bond_elems]=zscore;
- bond_counter_sum[bond_elems]=1;
- } else {
- bond_length_sum[bond_elems]+=blength;
- bond_zscore_sum[bond_elems]+=zscore;
- bond_counter_sum[bond_elems]+=1;
- }
+ String bond_elems=bond_string_elems(ele1,ele2);
+ std::map<String,Real>::const_iterator find_be = bond_length_sum.find(bond_elems);
+ if (find_be==bond_length_sum.end()) {
+ bond_length_sum[bond_elems]=blength;
+ bond_zscore_sum[bond_elems]=zscore;
+ bond_counter_sum[bond_elems]=1;
+ } else {
+ bond_length_sum[bond_elems]+=blength;
+ bond_zscore_sum[bond_elems]+=zscore;
+ bond_counter_sum[bond_elems]+=1;
+ }
}
}
@@ -481,18 +481,18 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
LOG_SCRIPT("Average Z-Score for bond lengths: " << avg_zscore_bonds);
LOG_SCRIPT("Bonds outside of tolerance range: " << bad_bond_count << " out of " << bond_count);
LOG_SCRIPT("Bond\tAvg Length\tAvg zscore\tNum Bonds")
-
+
for (std::map<String,Real>::const_iterator bls_it=bond_length_sum.begin();bls_it!=bond_length_sum.end();++bls_it) {
String key = (*bls_it).first;
- int counter=bond_counter_sum[key];
+ int counter=bond_counter_sum[key];
Real sum_bond_length=(*bls_it).second;
- Real sum_bond_zscore=bond_zscore_sum[key];
- Real avg_length=sum_bond_length/static_cast<Real>(counter);
- Real avg_zscore=sum_bond_zscore/static_cast<Real>(counter);
+ Real sum_bond_zscore=bond_zscore_sum[key];
+ Real avg_length=sum_bond_length/static_cast<Real>(counter);
+ Real avg_zscore=sum_bond_zscore/static_cast<Real>(counter);
LOG_SCRIPT(key << "\t" << avg_length << "\t" << avg_zscore << "\t" << counter);
}
LOG_SCRIPT("Average Z-Score angle widths: " << avg_zscore_angles);
- LOG_SCRIPT("Angles outside of tolerance range: " << bad_angle_count << " out of " << angle_count);
+ LOG_SCRIPT("Angles outside of tolerance range: " << bad_angle_count << " out of " << angle_count);
return filtered;
}
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
index 731fe41c4..64ae81040 100644
--- a/modules/mol/alg/src/filter_clashes.hh
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -29,7 +29,7 @@ class ClashingDistances
{
public:
- /// \brief Default constructor (creates an empty list)
+ /// \brief Default constructor (creates an empty list)
ClashingDistances(): valid_flag_(true) {}
/// \brief Adds or replaces an entry
@@ -40,10 +40,10 @@ public:
/// \brief Recovers a reference distance and a tolerance threshold (respectively) from the list
std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
- /// \brief Recovers the longest distance in the list, corrected by tolerance
+ /// \brief Recovers the longest distance in the list, corrected by tolerance
Real GetMaxAdjustedDistance() const;
- /// \brief Returns true if the list is empty (i.e. in an invalid, useless state)
+ /// \brief Returns true if the list is empty (i.e. in an invalid, useless state)
bool IsEmpty() const;
/// \brief Prints all distances in the list to standard output
@@ -68,19 +68,19 @@ public:
/// \brief Adds or replaces an entry
void SetParam(const String& param, const String& residue, Real value, Real st_dev);
- /// \brief Recovers mean and standard deviation (respectively) of a stereo⁻chemical item (bond or angle) from the list
+ /// \brief Recovers mean and standard deviation (respectively) of a stereo⁻chemical item (bond or angle) from the list
///
- /// Item format: Bond: X-Y, Angle:X-Y-Z
+ /// Item format: Bond: X-Y, Angle:X-Y-Z
std::pair<Real,Real> GetParam(const String& element,const String& residue) const;
/// \brief Checks if the list contains an entry for a specific stereo-chemical item (a bond or atom in a specific residue)
///
- /// Item format: Bond: X-Y, Angle:X-Y-Z
+ /// Item format: Bond: X-Y, Angle:X-Y-Z
bool ContainsParam(const String& param,const String& residue) const;
-
- /// \brief Returns true if the list is empty (i.e. in an invalid, useless state)
+
+ /// \brief Returns true if the list is empty (i.e. in an invalid, useless state)
///
- /// Item format: Bond: X-Y, Angle:X-Y-Z
+ /// Item format: Bond: X-Y, Angle:X-Y-Z
bool IsEmpty() const;
/// \brief Prints all distances in the list to standard output
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index f5f91e3ce..d77c6afa7 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -102,13 +102,13 @@ std::pair<int,int> compute_coverage (const EntityView& v,const GlobalRDMap& glob
int main (int argc, char **argv)
{
- // sets some default values for parameters
+ // sets some default values for parameters
String version = "Beta - 2012-06-13";
Real bond_tolerance = 8.0;
Real angle_tolerance = 8.0;
Real radius=15.0;
- // creates the required loading profile
+ // creates the required loading profile
IOProfile profile;
profile.bond_feasibility_check=false;
@@ -128,7 +128,7 @@ int main (int argc, char **argv)
("angle_tolerance,a", po::value<Real>(), "tolerance in stddev for angles")
("inclusion_radius,r", po::value<Real>(), "distance inclusion radius")
("files", po::value< std::vector<String> >(), "input file(s)")
- ("reference",po::value<String>(),"reference(s)")
+ ("reference",po::value<String>(),"reference(s)")
;
po::positional_options_description p;
p.add("files", -1);
@@ -207,7 +207,7 @@ int main (int argc, char **argv)
radius=vm["inclusion_radius"].as<Real>();
}
- // loads the reference file and creates the list of distances to check in lddt
+ // loads the reference file and creates the list of distances to check in lddt
String ref_file=files.back();
EntityHandle ref=load(ref_file, profile);
if (!ref) {
@@ -217,7 +217,7 @@ int main (int argc, char **argv)
EntityView ref_view=ref.Select(sel);
GlobalRDMap glob_dist_list = CreateDistanceList(ref_view,radius);
- // prints out parameters used in the lddt calculation
+ // prints out parameters used in the lddt calculation
std::cout << "Verbosity level: " << verbosity_level << std::endl;
if (structural_checks) {
std::cout << "Stereo-chemical and steric clash checks: On " << std::endl;
@@ -236,7 +236,7 @@ int main (int argc, char **argv)
}
LOG_INFO("LDDT INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 ModelDist TargetDist Difference Tolerance Status");
- // cycles through the models to evaluate
+ // cycles through the models to evaluate
for (size_t i=0; i<files.size(); ++i) {
EntityHandle model=load(files[i], profile);
if (!model) {
@@ -264,14 +264,14 @@ int main (int argc, char **argv)
aitv.SetElement(firstletter);
}
}
- v=v1;
+ v=v1;
std::cout << "File: " << files[i] << std::endl;
std::pair<int,int> cov = compute_coverage(v,glob_dist_list);
std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
- if (structural_checks) {
+ if (structural_checks) {
// reads in parameter files
- boost::filesystem::path loc(parameter_filename);
+ boost::filesystem::path loc(parameter_filename);
boost::filesystem::ifstream infile(loc);
if (!infile) {
std::cout << "Could not find " << parameter_filename << std::endl;
@@ -314,7 +314,7 @@ int main (int argc, char **argv)
return 0;
}
- // computes the lddt score
+ // computes the lddt score
std::vector<Real> cutoffs;
cutoffs.push_back(0.5);
cutoffs.push_back(1.0);
@@ -326,7 +326,7 @@ int main (int argc, char **argv)
std::cout << "Global LDDT score: " << lddt << std::endl;
std::cout << "(" << std::fixed << total_ov.first << " conserved distances in the model out of " << total_ov.second << " checked)" << std::endl;
- // prints the residue-by-residue statistics
+ // prints the residue-by-residue statistics
std::cout << "Local LDDT Score:" << std::endl;
std::cout << "Chain\tResName\tResNum\tScore\t(Conserved/Total)" << std::endl;
for (ResidueViewIter rit=v.ResiduesBegin();rit!=v.ResiduesEnd();++rit){
@@ -337,7 +337,7 @@ int main (int argc, char **argv)
if (ritv.HasProp(label)) {
lddt_local=ritv.GetFloatProp(label);
conserved_dist=ritv.GetIntProp(label+"_conserved");
- total_dist=ritv.GetIntProp(label+"_total");
+ total_dist=ritv.GetIntProp(label+"_total");
}
if (lddt_local!=0) {
std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << lddt_local << "\t" << "("<< conserved_dist << "/" << total_dist << ")" <<std::endl;
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 089b24026..e69978fbc 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -7,7 +7,7 @@ namespace ost { namespace mol { namespace alg {
namespace {
-// helper function
+// helper function
String swapped_name(const String& name)
{
if (name=="OE1") return "OE2";
@@ -78,12 +78,12 @@ std::pair<bool,Real> within_tolerance(Real mdl_dist, std::pair<Real,Real>& value
}
// helper function
-std::pair<Real, Real> calc_overlap1(const ResidueRDMap& res_distance_list, const ResNum& rnum,
+std::pair<long int, long int> calc_overlap1(const ResidueRDMap& res_distance_list, const ResNum& rnum,
ChainView mdl_chain,
std::vector<Real>& tol_list, bool only_fixed,
bool swap,std::vector<std::pair<long int, long int> >& overlap_list, bool log )
{
- std::pair<Real, Real> overlap(0.0, 0.0);
+ std::pair<long int, long int> overlap(0, 0);
ResidueView mdl_res=mdl_chain.FindResidue(rnum);
for (ResidueRDMap::const_iterator ai=res_distance_list.begin(); ai!=res_distance_list.end(); ++ai) {
UAtomIdentifiers uais = ai->first;
@@ -279,7 +279,7 @@ void update_existence_map (ExistenceMap& ex_map, const EntityView& ev, int ref_c
if (find_uai_ci!=ex_map.end()) {
uai_value=find_uai_ci->second;
}
- uai_value |= 1 << (ref_counter);
+ uai_value |= 1 << (ref_counter);
ex_map[uai]=uai_value;
}
}
@@ -312,8 +312,8 @@ void merge_distance_lists(GlobalRDMap& ref_dist_map, const GlobalRDMap& new_dist
// if you find the distance in the residue new, udate min and max
if (find_new_rd_ci != find_new_res_ci->second.end()) {
std::pair <Real,Real> new_minmax = find_new_rd_ci->second;
- Real min = ref_minmax.first;
- Real max = ref_minmax.second;
+ Real min = ref_minmax.first;
+ Real max = ref_minmax.second;
if (new_minmax.first < min) min = new_minmax.first;
if (new_minmax.second > max) max = new_minmax.second;
ref_dist_map_it->second[ref_rd] = std::make_pair<Real,Real>(min,max);
@@ -411,29 +411,29 @@ bool UniqueAtomIdentifier::operator<(const UniqueAtomIdentifier& rhs) const
if (chain_ < rhs.GetChainName()) {
return true;
} else if (chain_ > rhs.GetChainName()) {
- return false;
+ return false;
} else {
if (residue_ < rhs.GetResNum()) {
return true;
} else if (residue_ > rhs.GetResNum()) {
- return false;
+ return false;
} else {
if (residue_name_ < rhs.GetResidueName()) {
return true;
} else if (residue_name_ > rhs.GetResidueName()) {
- return false;
+ return false;
} else {
if (atom_ < rhs.GetAtomName()) {
return true;
} else if (atom_ > rhs.GetAtomName()) {
- return false;
+ return false;
} else {
- return false;
- }
- }
- }
+ return false;
+ }
+ }
+ }
}
-}
+}
GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist)
{
@@ -473,7 +473,7 @@ GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist)
}
GlobalRDMap CreateDistanceListFromMultipleReferences(const std::vector<EntityView>& ref_list, std::vector<Real>& cutoff_list, Real max_dist)
-{
+{
int ref_counter=0;
ExistenceMap ex_map;
GlobalRDMap glob_dist_list = CreateDistanceList(ref_list[0],max_dist);
@@ -532,7 +532,7 @@ std::pair<long int,long int> LocalDistDiffTest(const EntityView& mdl, const Glob
for (GlobalRDMap::const_iterator i=glob_dist_list.begin(), e=glob_dist_list.end(); i!=e; ++i) {
ResNum rn = i->first;
if (i->second.size()!=0) {
- std::pair<Real, Real> ov1=calc_overlap1(i->second, rn, mdl_chain, cutoff_list,
+ std::pair<long int, long int> ov1=calc_overlap1(i->second, rn, mdl_chain, cutoff_list,
false, false, overlap_list,true);
total_ov.first+=ov1.first;
total_ov.second+=ov1.second;
@@ -543,8 +543,8 @@ std::pair<long int,long int> LocalDistDiffTest(const EntityView& mdl, const Glob
int mdl_res_index =mdlr.GetIndex();
Real local_lddt=static_cast<Real>(overlap_list[mdl_res_index].first)/(static_cast<Real>(overlap_list[mdl_res_index].second) ? static_cast<Real>(overlap_list[mdl_res_index].second) : 1);
mdlr.SetFloatProp(local_lddt_property_string, local_lddt);
- mdlr.SetIntProp(local_lddt_property_string+"_conserved", overlap_list[mdl_res_index].first);
- mdlr.SetIntProp(local_lddt_property_string+"_total", overlap_list[mdl_res_index].second);
+ mdlr.SetIntProp(local_lddt_property_string+"_conserved", overlap_list[mdl_res_index].first);
+ mdlr.SetIntProp(local_lddt_property_string+"_total", overlap_list[mdl_res_index].second);
}
}
}
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 3d92b5bf9..894d54605 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -54,7 +54,7 @@ public:
bool operator==(const UniqueAtomIdentifier& rhs) const;
// required because UniqueAtomIdentifier is used as a key for a std::map
- bool operator<(const UniqueAtomIdentifier& rhs) const;
+ bool operator<(const UniqueAtomIdentifier& rhs) const;
private:
--
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