default is now to not calculate surface accessibility

improve progress bar

src/dssp.cpp

@@ -1562,7 +1562,7 @@ void DSSP_impl::calculateSecondaryStructure()
 
 
 	std::unique_ptr<cif::progress_bar> progress;
 	std::unique_ptr<cif::progress_bar> progress;
 	if (cif::VERBOSE == 0 or cif::VERBOSE == 1)
 	if (cif::VERBOSE == 0 or cif::VERBOSE == 1)
-		progress.reset(new cif::progress_bar(mResidues.size() - 1, "calculate distances"));
+		progress.reset(new cif::progress_bar((mResidues.size() * (mResidues.size() - 1)), "calculate distances"));
 
 
 	// Calculate the HBond energies
 	// Calculate the HBond energies
 	std::vector<std::tuple<uint32_t,uint32_t>> near;
 	std::vector<std::tuple<uint32_t,uint32_t>> near;
@@ -1582,7 +1582,7 @@ void DSSP_impl::calculateSecondaryStructure()
 		}
 		}
 
 
 		if (progress)
 		if (progress)
-			progress->consumed(1);
+			progress->consumed(mResidues.size() - i - 1);
 	}
 	}
 
 
 	if (cif::VERBOSE > 0)
 	if (cif::VERBOSE > 0)

src/mkdssp.cpp

@@ -74,6 +74,8 @@ int d_main(int argc, const char *argv[])
 		mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
 		mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
 		mcfp::make_option("no-dssp-categories", "If set, will suppress output of new DSSP output in mmCIF format"),
 		mcfp::make_option("no-dssp-categories", "If set, will suppress output of new DSSP output in mmCIF format"),
 
 
+		mcfp::make_option("calculate-accessibility", "Default is to not calculate the surface accessibility when the output format is mmCIF"),
+
 		mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
 		mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
 
 
 		mcfp::make_option("help,h", "Display help message"),
 		mcfp::make_option("help,h", "Display help message"),
@@ -156,7 +158,7 @@ int d_main(int argc, const char *argv[])
 			fmt = "cif";
 			fmt = "cif";
 	}
 	}
 
 
-	dssp dssp(f.front(), 1, pp_stretch, true);
+	dssp dssp(f.front(), 1, pp_stretch, fmt == "dssp" or config.has("calculate-accessibility"));
 
 
 	if (not output.empty())
 	if (not output.empty())
 	{
 	{