Constraint File Instructions

Metadata

This document was edited by Colin Smith on 12/4/2008. Yi Liu created the initial page. Thanks Oliver and Firas for providing information.

File Formats

Constraints can be specified using two different file formats, line-based and section-based. The line-based format is:

Constraint_Type1 Constraint_Def1
Constraint_Type2 Constraint_Def2
...

Constraint types and constraint definitions are defined in the next section. The section-based format is:

[ atompairs ]
...
[ angles ]
...
[ bindingsites ]
...

The section-based 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.

AtomPair: Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Func_Type Func_Def
Distance between Atom1 and Atom2

Angle: Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Atom3_Name Atom3_ResNum Func_Type Func_Def
Angle between Atom2->Atom1 vector and Atom2->Atom3 vector

Dihedral: Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Atom3_Name Atom3_ResNum Atom4_Name Atom4_ResNum Func_Type Func_Def
Dihedral angle of Atom1->Atom2->Atom3->Atom4

BigBin: ResNum Bin

Multi: Constraint_Type1 Constraint_Def1 [Constraint_Type2 Constraint_Def2 [...]]
Sum of all specified constraints

Ambiguous: Constraint_Type1 Constraint_Def1 [Constraint_Type2 Constraint_Def2 [...]]
Lowest of all specified constraints

Constraint types are all implemented as subclasses of the core::scoring::constraints::Constraint class.

Function Types

Functions are listed as "Func_Type: Func_Def".

HARMONIC: x0 sd
$f(x) = \left( \frac{x - x0}{sd} \right)^2$

CIRCULARHARMONIC: x0 sd
$f(x) = \left( \frac{NearestAngleRadians(x, x0) - x0}{sd} \right)^2$

BOUNDED: lb ub sd [rswitch (0.5)] tag
Note: Setting rswitch to anything other than 0.5 will create a discontinuity in the derivative.
$f(x) = \left \{ \begin{array}{rcl} \left( \frac{x - lb}{sd} \right)^2 & \mbox{for} & x < lb \\ 0 & \mbox{for} & lb \le x \le ub \\ \left( \frac{x - ub}{sd} \right)^2 & \mbox{for} & ub < x \le ub + rswitch \cdot sd \\ \frac{1}{sd} \left( x - \left( ub + rswitch \cdot sd \right) \right) + \left( \frac{rswitch \cdot sd}{sd} \right)^2 & \mbox{for} & x > ub + rswitch \cdot sd \end{array} \right.$

GAUSSIANFUNC: mean sd
$f(x) = -\ln \left( \frac{1}{sd \sqrt{2\pi}} * \exp \left( -\frac{(x-mean)^2}{2 sd^2} \right) \right)$

SOGFUNC: n_funcs [mean1 sdev1 weight1 [mean2 sdev2 weight2 [...]]]
$f(x) = -\ln \left( \sum_{i=1}^{n\_funcs} weight_i * \frac{1}{sdev_i \sqrt{2\pi}} * \exp \left( -\frac{(x-mean_i)^2}{2 sdev_i^2} \right) \right)$

MIXTUREFUNC: anchor gaussian_param exp_param mixture_param bg_mean bg_sd
parameters: representing the mean of h(r), representing the standard deviation of h(r)

CONSTANTFUNC: return_val
$f(x) = return\_val$

SCALARWEIGHTEDFUNC: weight Func_Type Func_Def
$f(x) = weight*Func\_Type(x, Func\_Def)$

SUMFUNC: n_funcs Func_Type1 Func_Def1 [Func_Type2 Func_Def2 [...]]
$f(x) = \sum_{i=1}^{n\_funcs} Func\_Type_i(x, Func\_Def_i)$

Function types are all implemented as subclasses of the core::scoring::constraints::Func class.

Sample Files

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

Code for Reading Constraints

There are different sets of functions for reading full-atom and non-full-atom 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:

core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn()
core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn()

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:

core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn()
core::scoring::constraints::add_constraints_from_cmdline_to_pose()

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:

core::scoring::constraints::add_fa_constraints_from_cmdline()
core::scoring::constraints::add_constraints_from_cmdline()

Other Constraint Types

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.

BackboneStub
BindingSite
Constant
Coordinate
ResidueType
Rotamer

Other Function Types

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.

PeriodicBound
ChainbreakDist
CharmmPeriodic
CircularPower
Etable
CB_Angle
CBSG_Dihedral
SG_Dist
SGSG_Dihedral
LK_Sigmoidal

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