From d6e2f103953dae446183ff62dbcd8b0369ffc106 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Tue, 17 Jan 2012 16:58:24 +0100
Subject: [PATCH] Changes requested by Juergen, mainly output messages
---
modules/mol/alg/src/ldt.cc | 38 +++++++++++++++++++++++---------------
1 file changed, 23 insertions(+), 15 deletions(-)
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index 82e073106..ec2f0fd07 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -203,11 +203,12 @@ void usage()
std::cerr << " -b <value> tolerance in stddevs for bonds" << std::endl;
std::cerr << " -a <value> tolerance in stddevs for angles" << std::endl;
std::cerr << " -m <value> clashing distance for unknwon atom types" << std::endl;
+ std::cerr << " -e print version" << std::endl;
}
int main (int argc, char **argv)
{
-
+ String version = "Beta - 2012-01-17";
Real min_default_distance = 1.5;
Real min_distance_tolerance = 0.0;
Real bond_tolerance = 8.0;
@@ -224,6 +225,7 @@ int main (int argc, char **argv)
("sel,s", po::value<String>(&sel)->default_value(""), "selection for reference")
("tolerant,t", "fault tolerant mode")
("structural-checks,f", "structural checks")
+ ("version,e", "version")
("parameter-file,p", po::value<String>(), "stereo chemical parameter file")
("verbosity,v", po::value<int>(), "verbosity level")
("tolerance_bonds,b", po::value<Real>(), "tolerance in stddev for bonds")
@@ -238,6 +240,10 @@ int main (int argc, char **argv)
options(desc).positional(p).run(),
vm);
po::notify(vm);
+ if (vm.count("version")) {
+ std::cout << "Version: " << version << std::endl;
+ exit(0);
+ }
std::vector<String> files;
if (vm.count("files")) {
files=vm["files"].as<std::vector<String> >();
@@ -275,6 +281,8 @@ int main (int argc, char **argv)
exit(-1);
}
}
+
+
if (vm.count("tolerance_bonds")) {
bond_tolerance=vm["tolerance_bonds"].as<Real>();
}
@@ -292,22 +300,22 @@ int main (int argc, char **argv)
}
files.pop_back();
EntityView ref_view=ref.Select(sel);
- std::cout << "Parameter filename: " << parameter_filename << std::endl;
- std::cout << "Verbosiy level: " << verbosity_level << std::endl;
+ std::cout << "#Parameter filename: " << parameter_filename << std::endl;
+ std::cout << "#Verbosity level: " << verbosity_level << std::endl;
if (structural_checks) {
- std::cout << "Stereo-chemical and steric clash checks: On " << std::endl;
+ std::cout << "#Stereo-chemical and steric clash checks: On " << std::endl;
} else {
- std::cout << "Stereo-chemical and steric clash checks: Off " << std::endl;
+ std::cout << "#Stereo-chemical and steric clash checks: Off " << std::endl;
}
if (structural_checks) {
- std::cout << "Tolerance in stddevs for bonds: " << bond_tolerance << std::endl;
- std::cout << "Tolerance in stddevs for angles: " << angle_tolerance << std::endl;
- std::cout << "Clashing distance for unknown atom types: " << min_default_distance << std::endl;
- LOG_INFO("Log entries format:");
- LOG_INFO("BOND INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Bond" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status");
- LOG_INFO("ANGLE INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Angle" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status");
- LOG_INFO("CLASH INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "Observed" << " " << "Difference" << " " << "Status");
- LOG_INFO("LDT INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "ModelDist" << " " << "TargetDist" << " " << "Difference" << " " << "Tolerance"
+ std::cout << "#Tolerance in stddevs for bonds: " << bond_tolerance << std::endl;
+ std::cout << "#Tolerance in stddevs for angles: " << angle_tolerance << std::endl;
+ std::cout << "#Clashing distance for unknown atom types: " << min_default_distance << std::endl;
+ LOG_INFO("#Log entries format:");
+ LOG_INFO("#BOND INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Bond" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status");
+ LOG_INFO("#ANGLE INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Angle" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status");
+ LOG_INFO("#CLASH INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "Observed" << " " << "Difference" << " " << "Status");
+ LOG_INFO("#LDT INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "ModelDist" << " " << "TargetDist" << " " << "Difference" << " " << "Tolerance"
<< " " << "Status");
}
for (size_t i=0; i<files.size(); ++i) {
@@ -371,10 +379,10 @@ int main (int argc, char **argv)
ldt+=alg::LocalDistTest(v, ref_view, cutoffs[n], 8.0,labels[n]);
}
ldt/=4.0;
- std::cout << "File: " << files[i] << std::endl;
+ std::cout << "#File: " << files[i] << std::endl;
std::cout << "Global LDT score: " << ldt << std::endl;
std::cout << "Local LDT Score:" << std::endl;
- std::cout << "Chain\tResName\tResNum\tScore" << std::endl;
+ std::cout << "#Chain\tResName\tResNum\tScore" << std::endl;
for (ResidueViewIter rit=v.ResiduesBegin();rit!=v.ResiduesEnd();++rit){
ResidueView ritv = *rit;
--
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