progress improvement

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@285 a1961a4f-ab94-4bcc-80e8-33b5a54de466

src/BondMap.cpp

@@ -151,8 +151,8 @@ BondMap::BondMap(const Structure& p)
 			cif::tie(asymId, seqId) = r.get("asym_id", "seq_id");
 			
 			vector<Atom> rAtoms;
-			for (auto a: db["atom_site"].find(cif::Key("label_asym_id") == asymId and cif::Key("label_seq_id") == seqId))
-				rAtoms.push_back(p.getAtomById(a["id"].as<string>()));
+			copy_if(atoms.begin(), atoms.end(), back_inserter(rAtoms),
+				[&](auto& a) { return a.labelAsymId() == asymId and a.labelSeqId() == seqId; });
 			
 			for (size_t i = 0; i + 1 < rAtoms.size(); ++i)
 			{
@@ -171,8 +171,10 @@ BondMap::BondMap(const Structure& p)
 			cif::tie(asymId) = r.get("asym_id");
 			
 			vector<Atom> rAtoms;
-			for (auto a: db["atom_site"].find(cif::Key("label_asym_id") == asymId))
-				rAtoms.push_back(p.getAtomById(a["id"].as<string>()));
+			copy_if(atoms.begin(), atoms.end(), back_inserter(rAtoms),
+				[&](auto& a) { return a.labelAsymId() == asymId; });
+//			for (auto a: db["atom_site"].find(cif::Key("label_asym_id") == asymId))
+//				rAtoms.push_back(p.getAtomById(a["id"].as<string>()));
 			
 			for (size_t i = 0; i + 1 < rAtoms.size(); ++i)
 			{

src/CifUtils.cpp

@@ -424,11 +424,13 @@ struct ProgressImpl
 
 void ProgressImpl::Run()
 {
+	bool printedAny = false;
+	
 	try
 	{
 		for (;;)
 		{
-			boost::this_thread::sleep(boost::posix_time::seconds(1));
+			boost::this_thread::sleep(boost::posix_time::seconds(5));
 			
 			boost::mutex::scoped_lock lock(mMutex);
 			
@@ -436,11 +438,13 @@ void ProgressImpl::Run()
 				break;
 			
 			PrintProgress();
+			printedAny = true;
 		}
 	}
 	catch (...) {}
 	
-	PrintDone();
+	if (printedAny)
+		PrintDone();
 }
 
 void ProgressImpl::PrintProgress()