Computational Methods for Froning, et al.

create_resfiles.cc

std::string get_line_for_resid( char chain, core::Size resnum, char aa = 'x' ){
	std::stringstream ss;
	ss << resnum << " " << chain;
	if( aa == 'x' ) ss << " NATAA";
	else ss << " PIKAA " << aa;
	ss << " USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1";
	return ss.str();
}

void make_resfile( std::string const & filename, core::Size resid, char aa, core::pose::Pose & pose, utility::graph::GraphOP packer_neighbor_graph ){
	std::ofstream outfile;
	outfile.open( filename );

	outfile << "NATRO" << std::endl << "start" << std::endl;
	outfile << get_line_for_resid( pose.pdb_info()->chain( resid ), pose.pdb_info()->number( resid ), aa ) << std::endl;

	utility::graph::Node * node = packer_neighbor_graph->get_node( resid );

	for( utility::graph::EdgeListConstIterator it = node->const_edge_list_begin();
			 it != node->const_edge_list_end(); ++it){
		core::Size const other_resid = (*it)->get_other_ind( resid );
		if( other_resid != resid ){
			outfile << get_line_for_resid( info( pose.pdb_info()->chain( other_resid ), pose.pdb_info()->number( other_resid ) ) ) << std::endl;
		}
	}

	outfile.close();
}

example_commandline.sh

rosetta_scripts.default.linuxgccrelease -parser:protocol run.xml -resfile resfile.txt -s my_protein.pdb 

example_resfile.txt

NATRO
start
114 D PIKAA E USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
115 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
116 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
117 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
118 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
119 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
120 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
121 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
138 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
139 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
140 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
141 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
142 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
143 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
144 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
145 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
146 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
147 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
159 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
160 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
161 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
162 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
163 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
164 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
165 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
166 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
167 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
168 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
169 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
170 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
171 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
172 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
173 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
174 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
175 D NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
135 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
137 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
139 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
165 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
166 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
167 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
168 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
171 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
190 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1
192 E NATAA USE_INPUT_SC EX 1 LEVEL 1 EX 2 LEVEL 1 EX 3 LEVEL 1 EX 4 LEVEL 1

point_mutant_scan.Froning_et_al.xml

<ROSETTASCRIPTS>
  <TASKOPERATIONS>
    <InitializeFromCommandline name="ifc"/>
    <ReadResfile name="rrf" filename="resfile"/>
  </TASKOPERATIONS>

  <SCOREFXNS>
    <ScoreFunction name="beta_cart_sfxn" weights="beta_nov15_cart"/>
    
    <ScoreFunction name="beta_cart_sfxn_cc" weights="beta_nov15_cart">
      <Reweight scoretype="coordinate_constraint" weight="1"/>
    </ScoreFunction>
  </SCOREFXNS>

  <MOVERS>
    <AtomCoordinateCstMover name="coor_cst"/>
    <FastRelax name="fast_relax" scorefxn="beta_cart_sfxn_cc" repeats="5" cartesian="true" task_operations="ifc,rrf"/>
    <MinMover name="min_mover" scorefxn="beta_cart_sfxn" chi="true" bb="true" cartesian="true"/>
  </MOVERS>

  <PROTOCOLS>
    <Add mover="coor_cst"/>
    <Add mover="fast_relax"/>
    <Add mover="min_mover"/>
  </PROTOCOLS>

  <OUTPUT scorefxn="beta_cart_sfxn"/>
</ROSETTASCRIPTS>

relax_crystal.xml

<ROSETTASCRIPTS>
  <TASKOPERATIONS>
    <InitializeFromCommandline name="ifc"/> <!-- pass -ex1 -ex2 --> 
  </TASKOPERATIONS>

  <SCOREFXNS>
    <ScoreFunction name="beta_sfxn_cc" weights="beta_nov15">
      <Reweight scoretype="coordinate_constraint" weight="1"/>
    </ScoreFunction>
  </SCOREFXNS>

  <MOVERS>
    <AtomCoordinateCstMover name="coor_cst"/>
    <FastRelax name="fast_relax" scorefxn="beta_sfxn_cc" repeats="5" task_operations="ifc"/>
  </MOVERS>

  <PROTOCOLS>
    <Add mover="coor_cst"/>
    <Add mover="fast_relax"/>
  </PROTOCOLS>

  <OUTPUT scorefxn="commandline"/>
</ROSETTASCRIPTS>