From 1f002f88493cca47e52e2c0e8c54f49743a57911 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <vmariani@localhost.localdomain>
Date: Thu, 21 Jun 2012 01:50:53 +0200
Subject: [PATCH] Improved lddt output and documentation
---
modules/mol/alg/doc/molalg.rst | 4 ++++
modules/mol/alg/src/lddt.cc | 9 +++++----
2 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 29f3750b7..cf8360fc8 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -175,6 +175,10 @@
Returns the name of the atom, as a String
+ .. method:: Print()
+
+ Prints the information to standard output
+
.. class:: ResidueRDMap
Dictionary-like object containing the a list of distances that originate from the a single residue residue, to
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index a24873fbe..a0108f06a 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -352,12 +352,13 @@ int main (int argc, char **argv)
String label="localldt";
std::pair<int,int> total_ov=alg::LocalDistDiffTest(v, glob_dist_list, cutoffs, sequence_separation, label);
Real lddt = static_cast<Real>(total_ov.first)/(static_cast<Real>(total_ov.second) ? static_cast<Real>(total_ov.second) : 1);
- 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;
+ std::cout << "Global LDDT score: " << std::setprecision(4) << lddt << std::endl;
+ std::cout << "(" << std::fixed << total_ov.first << " conserved distances out of " << total_ov.second
+ << " checked, over " << cutoffs.size() << " thresholds)" << std::endl;
// prints the residue-by-residue statistics
std::cout << "Local LDDT Score:" << std::endl;
- std::cout << "Chain\tResName\tResNum\tScore\t(Conserved/Total)" << std::endl;
+ std::cout << "Chain\tResName\tResNum\tScore\t(Conserved/Total, over " << cutoffs.size() << " thresholds)" << std::endl;
for (ResidueViewIter rit=v.ResiduesBegin();rit!=v.ResiduesEnd();++rit){
ResidueView ritv = *rit;
Real lddt_local = 0;
@@ -369,7 +370,7 @@ int main (int argc, char **argv)
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;
+ std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << std::setprecision(4) << lddt_local << "\t" << "("<< conserved_dist << "/" << total_dist << ")" <<std::endl;
}
}
std::cout << std::endl;
--
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