Rosetta 3.4

This document was edited by Colin Smith on 12/4/2008. Yi Liu created the initial page. Thanks Oliver and Firas for providing information.
Constraints can be specified using two different file formats, linebased and sectionbased. The linebased format is:
Constraint_Type1 Constraint_Def1 Constraint_Type2 Constraint_Def2 ...
Constraint types and constraint definitions are defined in the next section. The sectionbased format is:
[ atompairs ] ... [ angles ] ... [ bindingsites ] ...
The sectionbased format is not yet documented here. It is not possible to mix both formats in the same file.
Constraints are listed as "Constraint_Type: Constraint_Def". Function types and definitions are defined in the next section. Any text after the function definition is ignored, execpt in the case of Multi and Ambiguous constraints, which accept an arbitrary number of subconstraints.
Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Func_Type Func_Def
Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Atom3_Name Atom3_ResNum Func_Type Func_Def
Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Atom3_Name Atom3_ResNum Atom4_Name Atom4_ResNum Func_Type Func_Def
ResNum Bin
Constraint_Type1 Constraint_Def1 [Constraint_Type2 Constraint_Def2 [...]]
Constraint_Type1 Constraint_Def1 [Constraint_Type2 Constraint_Def2 [...]]
Constraint types are all implemented as subclasses of the core::scoring::constraints::Constraint class.
Functions are listed as "Func_Type: Func_Def".
x0 sd
x0 sd
lb ub sd rswitch tag
rswitch
to anything other than 0.5 will create a discontinuity in the derivative. rswitch
and tag
should not be treated as optional.
mean sd
n_funcs [mean1 sdev1 weight1 [mean2 sdev2 weight2 [...]]]
anchor gaussian_param exp_param mixture_param bg_mean bg_sd
return_val
weight Func_Type Func_Def
n_funcs Func_Type1 Func_Def1 [Func_Type2 Func_Def2 [...]]
histogram_file_path experimental_value weight bin_size
Note: This function reads in any histogram and creates a cubic spline over it using the Rosetta SplineGenerator. The full path to the file must be speified. The function assumes that all bin sizes are the same, even though you must specify it for each line in the cst file. If using RosettaEPR knowledgebased potential, replace <filename> with EPR_DISTANCE, and it will read in the EPR distance histogram from the minirosetta database. See example below for using with EPR knowledgebased potential.Function types are all implemented as subclasses of the core::scoring::constraints::Func class.
AtomPair CZ 20 CA 6 GAUSSIANFUNC 5.54 2.0 AtomPair CZ 20 CA 54 GAUSSIANFUNC 5.27 2.0 AtomPair CZ 20 CA 50 GAUSSIANFUNC 5.26 2.0 AtomPair CZ 20 CA 10 GAUSSIANFUNC 4.81 2.0 AtomPair CZ 20 CA 41 GAUSSIANFUNC 9.90 2.0
AtomPair SG 5 V1 32 HARMONIC 0.0 0.2 Angle CB 5 SG 5 ZN 32 HARMONIC 1.95 0.35 AtomPair SG 8 V2 32 HARMONIC 0.0 0.2 Angle CB 8 SG 8 ZN 32 HARMONIC 1.95 0.35 AtomPair NE2 13 V3 32 HARMONIC 0.0 0.2 Angle CD2 13 NE2 13 ZN 32 HARMONIC 2.09 0.35 Dihedral CG 13 CD2 13 NE2 13 ZN 32 CIRCULARHARMONIC 3.14 0.35 AtomPair SG 18 V4 32 HARMONIC 0.0 0.2 Angle CB 18 SG 18 ZN 32 HARMONIC 1.95 0.35
AtomPair H 6 HA 134 BOUNDED 1.80 5.25 0.50 NOE ;dist 5.000 1.800 AtomPair HA 7 HA 132 HARMONIC 1.2 0.2
AtomPair CB 31 CB 43 SPLINE EPR_DISTANCE 6.0 4.0 0.5 AtomPair CB 29 CB 62 SPLINE EPR_DISTANCE 15.0 4.0 0.5
There are different sets of functions for reading fullatom and nonfullatom constraints, as indicated by the respective functions listed below. The only current difference between the functions are which command line arguments are read. The values of the arguments are processed identically.
To use constraints, both the scoring function and pose objects should be updated. The functions for adding constraints to the scoring function are:
Currently these functions only set the weights of the atom_pair_constraint, angle_constraint, and dihedral_constraint score function terms to the value of either the constraints:cst_fa_weight or constraints:cst_weight command line argument.
The functions for adding constraints to the pose object are:
These functons read a random constraint file from the list defined by either the constraints:cst_fa_file or constraints:cst_file argument.
There are also convenience functions for doing both at once:
These constraint types cannot currently be sepecified in a file. They need to have read_def methods implemented and be added to the ConstraintFactory constructor.
These function types cannot currently be sepecified in a file. They need to have read_data methods implemented and be added to the FuncFactory constructor.
This document was edited by Colin Smith on 12/4/2008. Yi Liu created the initial page. Thanks Oliver and Firas for providing information.
Constraints can be specified using two different file formats, linebased and sectionbased. The linebased format is:
Constraint_Type1 Constraint_Def1 Constraint_Type2 Constraint_Def2 ...
Constraint types and constraint definitions are defined in the next section. The sectionbased format is:
[ atompairs ] ... [ angles ] ... [ bindingsites ] ...
The sectionbased format is not yet documented here. It is not possible to mix both formats in the same file.
Constraints are listed as "Constraint_Type: Constraint_Def". Function types and definitions are defined in the next section. Any text after the function definition is ignored, execpt in the case of Multi and Ambiguous constraints, which accept an arbitrary number of subconstraints.
Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Func_Type Func_Def
Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Atom3_Name Atom3_ResNum Func_Type Func_Def
Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Atom3_Name Atom3_ResNum Atom4_Name Atom4_ResNum Func_Type Func_Def
ResNum Bin
Constraint_Type1 Constraint_Def1 [Constraint_Type2 Constraint_Def2 [...]]
Constraint_Type1 Constraint_Def1 [Constraint_Type2 Constraint_Def2 [...]]
Constraint types are all implemented as subclasses of the core::scoring::constraints::Constraint class.
Functions are listed as "Func_Type: Func_Def".
x0 sd
x0 sd
lb ub sd [rswitch (0.5)] tag
rswitch
to anything other than 0.5 will create a discontinuity in the derivative.
mean sd
n_funcs [mean1 sdev1 weight1 [mean2 sdev2 weight2 [...]]]
anchor gaussian_param exp_param mixture_param bg_mean bg_sd
return_val
weight Func_Type Func_Def
n_funcs Func_Type1 Func_Def1 [Func_Type2 Func_Def2 [...]]
histogram_file_path experimental_value weight bin_size
Note: This function reads in any histogram and creates a cubic spline over it using the Rosetta SplineGenerator. The full path to the file must be speified. The function assumes that all bin sizes are the same, even though you must specify it for each line in the cst file. If using RosettaEPR knowledgebased potential, replace <filename> with EPR_DISTANCE, and it will read in the EPR distance histogram from the minirosetta database. See example below for using with EPR knowledgebased potential.Function types are all implemented as subclasses of the core::scoring::constraints::Func class.
AtomPair CZ 20 CA 6 GAUSSIANFUNC 5.54 2.0 AtomPair CZ 20 CA 54 GAUSSIANFUNC 5.27 2.0 AtomPair CZ 20 CA 50 GAUSSIANFUNC 5.26 2.0 AtomPair CZ 20 CA 10 GAUSSIANFUNC 4.81 2.0 AtomPair CZ 20 CA 41 GAUSSIANFUNC 9.90 2.0
AtomPair SG 5 V1 32 HARMONIC 0.0 0.2 Angle CB 5 SG 5 ZN 32 HARMONIC 1.95 0.35 AtomPair SG 8 V2 32 HARMONIC 0.0 0.2 Angle CB 8 SG 8 ZN 32 HARMONIC 1.95 0.35 AtomPair NE2 13 V3 32 HARMONIC 0.0 0.2 Angle CD2 13 NE2 13 ZN 32 HARMONIC 2.09 0.35 Dihedral CG 13 CD2 13 NE2 13 ZN 32 CIRCULARHARMONIC 3.14 0.35 AtomPair SG 18 V4 32 HARMONIC 0.0 0.2 Angle CB 18 SG 18 ZN 32 HARMONIC 1.95 0.35
AtomPair H 6 HA 134 BOUNDED 1.80 5.25 0.50 NOE ;dist 5.000 1.800 AtomPair HA 7 HA 132 HARMONIC 1.2 0.2
AtomPair CB 31 CB 43 SPLINE EPR_DISTANCE 6.0 4.0 0.5 AtomPair CB 29 CB 62 SPLINE EPR_DISTANCE 15.0 4.0 0.5
There are different sets of functions for reading fullatom and nonfullatom constraints, as indicated by the respective functions listed below. The only current difference between the functions are which command line arguments are read. The values of the arguments are processed identically.
To use constraints, both the scoring function and pose objects should be updated. The functions for adding constraints to the scoring function are:
Currently these functions only set the weights of the atom_pair_constraint, angle_constraint, and dihedral_constraint score function terms to the value of either the constraints:cst_fa_weight or constraints:cst_weight command line argument.
The functions for adding constraints to the pose object are:
These functons read a random constraint file from the list defined by either the constraints:cst_fa_file or constraints:cst_file argument.
There are also convenience functions for doing both at once:
These constraint types cannot currently be sepecified in a file. They need to have read_def methods implemented and be added to the ConstraintFactory constructor.
These function types cannot currently be sepecified in a file. They need to have read_data methods implemented and be added to the FuncFactory constructor.