Lanthipeptide and recon multistate design update

database/chemical/residue_type_sets/fa_standard/patches/Nterm2_Oxobutrylation.txt

@@ -70,6 +70,7 @@ SET_ICOOR  3H4 -60.0    70.0   1.089  C4  C3  C2
 #Unpatched H gets its geometry from LOWER, which we have removed
 
 SET_POLYMER_CONNECT LOWER NONE
+ADD_PROPERTY LOWER_TERMINUS ## implies terminus
 
 # If modified, no longer canonical.
 DELETE_PROPERTY CANONICAL_AA

source/src/core/scoring/constraints/ResidueTypeConstraint.cc

@@ -74,6 +74,20 @@ ResidueTypeConstraint::ResidueTypeConstraint(
 	favor_native_bonus_( favor_native_bonus )
 {}
 
+ResidueTypeConstraint::ResidueTypeConstraint(
+	core::pose::Pose const &, //pose,
+	Size seqpos,
+	std::string const & AA_name,
+	core::Real favor_native_bonus,
+	bool base_name
+):
+	Constraint( core::scoring::res_type_constraint ),
+	seqpos_( seqpos ),
+	rsd_type_name3_( AA_name ),
+	favor_native_bonus_( favor_native_bonus ),
+	base_name_( base_name )
+{}
+
 ResidueTypeConstraint::ResidueTypeConstraint(
 	Size seqpos,
 	std::string const & aa_in,
@@ -157,6 +171,17 @@ ResidueTypeConstraint::remapped_clone( pose::Pose const&, pose::Pose const&, id:
 	return utility::pointer::make_shared< ResidueTypeConstraint >(newseqpos, AAname, rsd_type_name3_, favor_native_bonus_);
 }
 
+bool
+ResidueTypeConstraint::get_base_name_active( ) const
+{
+	return base_name_;
+}
+
+void
+ResidueTypeConstraint::set_base_name_active( bool base_name )
+{
+	base_name_ = base_name;
+}
 
 // Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into
 // emap. Although the current set of weights currently is provided, Constraint objects
@@ -168,16 +193,36 @@ ResidueTypeConstraint::score( func::XYZ_Func const & xyz_func, EnergyMap const &
 	if ( weight == 0 ) return; // what's the point?
 
 	conformation::Residue const & rsd( xyz_func.residue(seqpos_) );
-	if ( rsd.type().name3() == rsd_type_name3_ ) {
-		emap[ this->score_type() ] -= favor_native_bonus_;
+	if ( base_name_ ) {
+		if ( rsd.type().base_name() == rsd_type_name3_ ) {
+			emap[ this->score_type() ] -= favor_native_bonus_;
+		}
+	} else {
+		if ( rsd_type_name3_.length() > 3 ) {
+			TR.Warning <<
+				"Warning: base_name_ is not set (set_base_name_active(true)), but rsd_type_name3_ is greater than 3: "
+				<< rsd_type_name3_ << std::endl;
+		}
+		if ( rsd.type().name3() == rsd_type_name3_ ) {
+			emap[ this->score_type() ] -= favor_native_bonus_;
+		}
 	}
 	// no match, don't adjust score
 }
 
 core::Real
 ResidueTypeConstraint::dist( core::scoring::func::XYZ_Func const & xyz ) const {
 	conformation::Residue const & rsd( xyz.residue(seqpos_) );
-	return rsd.type().name3() == rsd_type_name3_;
+	if ( base_name_ ) {
+		return rsd.type().base_name() == rsd_type_name3_;
+	} else {
+		if ( rsd_type_name3_.length() > 3 ) {
+			TR.Warning <<
+				"Warning: base_name_ is not set (set_base_name_active(true)), but rsd_type_name3_ is greater than 3: "
+				<< rsd_type_name3_ << std::endl;
+		}
+		return rsd.type().name3() == rsd_type_name3_;
+	}
 }
 
 void
@@ -222,6 +267,7 @@ core::scoring::constraints::ResidueTypeConstraint::save( Archive & arc ) const {
 	arc( CEREAL_NVP( AAname ) ); // std::string
 	arc( CEREAL_NVP( rsd_type_name3_ ) ); // std::string
 	arc( CEREAL_NVP( favor_native_bonus_ ) ); // core::Real
+	arc( CEREAL_NVP( base_name_ ) ); // bool
 }
 
 /// @brief Automatically generated deserialization method
@@ -233,6 +279,7 @@ core::scoring::constraints::ResidueTypeConstraint::load( Archive & arc ) {
 	arc( AAname ); // std::string
 	arc( rsd_type_name3_ ); // std::string
 	arc( favor_native_bonus_ ); // core::Real
+	arc( base_name_  ); // bool
 }
 
 SAVE_AND_LOAD_SERIALIZABLE( core::scoring::constraints::ResidueTypeConstraint );

source/src/core/scoring/constraints/ResidueTypeConstraint.hh

@@ -57,6 +57,14 @@ public:
 		Real favor_native_bonus
 	);
 
+	ResidueTypeConstraint(
+		pose::Pose const & pose,
+		Size seqpos,
+		std::string const & AAname,
+		Real favor_native_bonus,
+		bool base_name
+	);
+
 	ResidueTypeConstraint(
 		Size seqpos,
 		std::string const & aa_in,
@@ -122,11 +130,18 @@ public:
 	std::string
 	get_rsd_type_name3() const;
 
+	bool
+	get_base_name_active() const;
+
+	void
+	set_base_name_active( bool base_name );
+
 private:
 	Size seqpos_;
 	std::string AAname;
 	std::string rsd_type_name3_;
 	core::Real favor_native_bonus_;
+	bool base_name_ = false;
 #ifdef    SERIALIZATION
 public:
 	template< class Archive > void save( Archive & arc ) const;