From 2e8a52949e3d2ca31142451c73d151a57a67d222 Mon Sep 17 00:00:00 2001
From: "Maarten L. Hekkelman" <maarten@hekkelman.com>
Date: Wed, 31 May 2023 15:54:53 +0200
Subject: [PATCH] Update example and README

---
 README.md            | 47 ++++++++++++++++++++++++++++++++++++++++++++
 examples/example.cpp | 26 +++++++++++++++---------
 2 files changed, 64 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 1e95ae2..e1711e7 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,53 @@ libcifpp
 
 This library contains code to work with mmCIF and PDB files.
 
+Synopsis
+--------
+
+```c++
+// A simple program counting residues with an OXT atom
+
+#include <filesystem>
+#include <iostream>
+
+#include <cif++.hpp>
+
+namespace fs = std::filesystem;
+
+int main(int argc, char *argv[])
+{
+    if (argc != 2)
+        exit(1);
+
+    cif::file file = cif::pdb::read(argv[1]);
+
+    if (file.empty())
+    {
+        std::cerr << "Empty file" << std::endl;
+        exit(1);
+    }
+
+    auto &db = file.front();
+    auto &atom_site = db["atom_site"];
+    auto n = atom_site.find(cif::key("label_atom_id") == "OXT").size();
+
+    std::cout << "File contains " << atom_site.size() << " atoms of which "
+              << n << (n == 1 ? " is" : " are") << " OXT" << std::endl
+              << "residues with an OXT are:" << std::endl;
+
+    for (const auto &[asym, comp, seqnr] :
+            atom_site.find<std::string, std::string, int>(
+                cif::key("label_atom_id") == "OXT", "label_asym_id", "label_comp_id",
+                "label_seq_id"))
+    {
+        std::cout << asym << ' ' << comp << ' ' << seqnr << std::endl;
+    }
+
+    return 0;
+}
+
+```
+
 Requirements
 ------------
 
diff --git a/examples/example.cpp b/examples/example.cpp
index c20bc10..f08f18c 100644
--- a/examples/example.cpp
+++ b/examples/example.cpp
@@ -1,24 +1,32 @@
-#include <iostream>
 #include <filesystem>
+#include <iostream>
 
 #include <cif++.hpp>
 
 namespace fs = std::filesystem;
 
-int main()
+int main(int argc, char *argv[])
 {
-	cif::file file;
-	file.load("1cbs.cif.gz");
+	if (argc != 2)
+		exit(1);
 
-	auto& db = file.front();
+	cif::file file = cif::pdb::read(argv[1]);
+
+	if (file.empty())
+	{
+		std::cerr << "Empty file" << std::endl;
+		exit(1);
+	}
+
+	auto &db = file.front();
 	auto &atom_site = db["atom_site"];
 	auto n = atom_site.find(cif::key("label_atom_id") == "OXT").size();
 
 	std::cout << "File contains " << atom_site.size() << " atoms of which " << n << (n == 1 ? " is" : " are") << " OXT" << std::endl
-		<< "residues with an OXT are:" << std::endl;
-	
-	for (const auto& [asym, comp, seqnr]: atom_site.find<std::string,std::string,int>(
-			cif::key("label_atom_id") == "OXT", "label_asym_id", "label_comp_id", "label_seq_id"))
+			  << "residues with an OXT are:" << std::endl;
+
+	for (const auto &[asym, comp, seqnr] : atom_site.find<std::string, std::string, int>(
+			 cif::key("label_atom_id") == "OXT", "label_asym_id", "label_comp_id", "label_seq_id"))
 	{
 		std::cout << asym << ' ' << comp << ' ' << seqnr << std::endl;
 	}