Reintroduce more atom members

gxrio @ a7bb5b5c

-Subproject commit 4587355dd281665f7d489360553d2f7564f398e4
+Subproject commit a7bb5b5c4b6612215a78267b89e05c39a45429b5

include/cif++/model.hpp

@@ -239,8 +239,8 @@ class atom
 	const row_handle get_row() const { return impl().row(); }
 	const row_handle get_row() const { return impl().row(); }
 	const row_handle get_row_aniso() const { return impl().row_aniso(); }
 	const row_handle get_row_aniso() const { return impl().row_aniso(); }
 
 
-	// bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
-	// std::string symmetry() const { return impl().mSymmetryOperator; }
+	bool is_symmetry_copy() const { return impl().m_symop != "1_555"; }
+	std::string symmetry() const { return impl().m_symop; }
 
 
 	// const compound &compound() const;
 	// const compound &compound() const;
 
 
@@ -269,26 +269,17 @@ class atom
 	std::string get_auth_asym_id() const { return get_property("auth_asym_id"); }
 	std::string get_auth_asym_id() const { return get_property("auth_asym_id"); }
 	std::string get_auth_seq_id() const { return get_property("auth_seq_id"); }
 	std::string get_auth_seq_id() const { return get_property("auth_seq_id"); }
 	std::string get_auth_atom_id() const { return get_property("auth_atom_id"); }
 	std::string get_auth_atom_id() const { return get_property("auth_atom_id"); }
+	std::string get_auth_alt_id() const { return get_property("auth_alt_id"); }
 	std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); }
 	std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); }
 
 
-	// const std::string &labelAtomID() const { return impl().mAtomID; }
-	// const std::string &get_label_comp_id() const { return impl().mCompID; }
-	// const std::string &get_label_asym_id() const { return impl().m_asym_id; }
-	// std::string labelEntityID() const;
-	// int get_label_seq_id() const { return impl().m_seq_id; }
-	// const std::string &labelAltID() const { return impl().mAltID; }
-
 	bool is_alternate() const { return not get_label_alt_id().empty(); }
 	bool is_alternate() const { return not get_label_alt_id().empty(); }
 
 
-	// std::string authAtomID() const;
-	// std::string authCompID() const;
-	// std::string authAsymID() const;
-	// const std::string &authSeqID() const { return impl().m_auth_seq_id; }
-	// std::string pdbxAuthInsCode() const;
-	// std::string pdbxAuthAltID() const;
-
 	// std::string labelID() const; // label_comp_id + '_' + label_asym_id + '_' + label_seq_id
 	// std::string labelID() const; // label_comp_id + '_' + label_asym_id + '_' + label_seq_id
-	// std::string pdbID() const;   // auth_comp_id + '_' + auth_asym_id + '_' + auth_seq_id + pdbx_PDB_ins_code
+	
+	std::string pdb_id() const
+	{
+		return get_label_comp_id() + '_' + get_auth_asym_id() + '_' + get_auth_seq_id() + get_pdb_ins_code();
+	}
 
 
 	bool operator==(const atom &rhs) const
 	bool operator==(const atom &rhs) const
 	{
 	{
@@ -308,12 +299,12 @@ class atom
 
 
 	// // access data in compound for this atom
 	// // access data in compound for this atom
 
 
-	// // convenience routine
-	// bool isBackBone() const
-	// {
-	// 	auto atomID = labelAtomID();
-	// 	return atomID == "N" or atomID == "O" or atomID == "C" or atomID == "CA";
-	// }
+	// convenience routine
+	bool is_back_bone() const
+	{
+		auto atomID = get_label_atom_id();
+		return atomID == "N" or atomID == "O" or atomID == "C" or atomID == "CA";
+	}
 
 
 	void swap(atom &b)
 	void swap(atom &b)
 	{
 	{

src/model.cpp

@@ -215,19 +215,6 @@ int atom::atom_impl::get_charge() const
 // 	return result;
 // 	return result;
 // }
 // }
 
 
-// std::string atom::labelID() const
-// {
-// 	return m_impl->mCompID + '_' + m_impl->m_asym_id + '_' + std::to_string(m_impl->m_seq_id) + ':' + m_impl->mAtom_id;
-// }
-
-// std::string atom::pdbID() const
-// {
-// 	return get_property<std::string>("auth_comp_id") + '_' +
-// 	       get_property<std::string>("auth_asym_id") + '_' +
-// 	       get_property<std::string>("auth_seq_id") +
-// 	       get_property<std::string>("pdbx_PDB_ins_code");
-// }
-
 // const Compound &atom::compound() const
 // const Compound &atom::compound() const
 // {
 // {
 // 	auto result = impl().compound();
 // 	auto result = impl().compound();

src/utilities.cpp

@@ -340,7 +340,7 @@ void ProgressImpl::PrintDone()
 Progress::Progress(int64_t inMax, const std::string &inAction)
 Progress::Progress(int64_t inMax, const std::string &inAction)
 	: m_impl(nullptr)
 	: m_impl(nullptr)
 {
 {
-	if (isatty(STDOUT_FILENO))
+	if (isatty(STDOUT_FILENO) and VERBOSE >= 0)
 		m_impl = new ProgressImpl(inMax, inAction);
 		m_impl = new ProgressImpl(inMax, inAction);
 }
 }