Reading constraints from a file

[Anonymous]

Is there a way to use a standard Rosetta constraints file in PyRosetta?

I know how to add constraints individually in the code but how can I load them from a file?

There is nothing in the documentation on this.

 

 

[Anonymous]

PyRosetta exposes basically all of the C++, so it becomes a question of “What is the C++ function that loads a constraint file”?

Looking in main/source/src/core/scoring/constraints/util.hh, I see lots of functions that might be what you want (below).  The “fullatom” ones trigger on cst_fa_file and cst_fa_weight, the centroid ones on cst_file and cst_weight.

///////////////COMMAND LINE/////////////////////////////

////////// Centroid constraints (add and replace)

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline_to_pose( core::pose::Pose & pose );

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline_to_scorefxn(

    core::scoring::ScoreFunction & scorefxn_

);

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline(

    core::pose::Pose & pose, core::scoring::ScoreFunction & scorefxn_

);

////////// FA constraints (add and replace)

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline_to_pose( core::pose::Pose & pose );

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline_to_scorefxn(

    core::scoring::ScoreFunction & scorefxn_

);

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline(

    core::pose::Pose & pose,

    core::scoring::ScoreFunction & scorefxn_

);

 

 

[Anonymous]

PyRosetta exposes basically all of the C++, so it becomes a question of “What is the C++ function that loads a constraint file”?

Looking in main/source/src/core/scoring/constraints/util.hh, I see lots of functions that might be what you want (below).  The “fullatom” ones trigger on cst_fa_file and cst_fa_weight, the centroid ones on cst_file and cst_weight.

///////////////COMMAND LINE/////////////////////////////

////////// Centroid constraints (add and replace)

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline_to_pose( core::pose::Pose & pose );

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline_to_scorefxn(

    core::scoring::ScoreFunction & scorefxn_

);

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline(

    core::pose::Pose & pose, core::scoring::ScoreFunction & scorefxn_

);

////////// FA constraints (add and replace)

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline_to_pose( core::pose::Pose & pose );

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline_to_scorefxn(

    core::scoring::ScoreFunction & scorefxn_

);

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline(

    core::pose::Pose & pose,

    core::scoring::ScoreFunction & scorefxn_

);

 

 

[Anonymous]

PyRosetta exposes basically all of the C++, so it becomes a question of “What is the C++ function that loads a constraint file”?

Looking in main/source/src/core/scoring/constraints/util.hh, I see lots of functions that might be what you want (below).  The “fullatom” ones trigger on cst_fa_file and cst_fa_weight, the centroid ones on cst_file and cst_weight.

///////////////COMMAND LINE/////////////////////////////

////////// Centroid constraints (add and replace)

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline_to_pose( core::pose::Pose & pose );

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline_to_scorefxn(

    core::scoring::ScoreFunction & scorefxn_

);

//// @brief  add constraints if specified by user.

void add_constraints_from_cmdline(

    core::pose::Pose & pose, core::scoring::ScoreFunction & scorefxn_

);

////////// FA constraints (add and replace)

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline_to_pose( core::pose::Pose & pose );

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline_to_scorefxn(

    core::scoring::ScoreFunction & scorefxn_

);

/// @brief add constraints if specified by user.

void add_fa_constraints_from_cmdline(

    core::pose::Pose & pose,

    core::scoring::ScoreFunction & scorefxn_

);

 

 

[Anonymous]

Another approach to use is to look at the regular Rosetta documentation at https://www.rosettacommons.org/docs/latest – particularly the RosettaScripts documentation. Each RosettaScripts Mover/Filter/etc. corresponds with a C++ level object, many of which can be used from Python with the appropriate getter/setter methods (verus the XML tags). 

For example, the description of the “ConstraintSetMover” is “Adds constraints to the pose using a constraints file”. A little digging around finds it at rosetta.protocols.simple_moves.ConstraintSetMover, which doesn’t have much in the way of help, but does have a constraint_file() method you can use to specify the constraint file to use, and, like all movers, an apply() method which will actually act on the Pose.

—

By the way, under the hood this mover uses the rosetta.core.scoring.constraints.ConstraintIO.get_instance().read_constraints() method to read in the constraint file, and the pose.constraint_set() method to actually set them in the pose.

 

[Anonymous]

Another approach to use is to look at the regular Rosetta documentation at https://www.rosettacommons.org/docs/latest – particularly the RosettaScripts documentation. Each RosettaScripts Mover/Filter/etc. corresponds with a C++ level object, many of which can be used from Python with the appropriate getter/setter methods (verus the XML tags). 

For example, the description of the “ConstraintSetMover” is “Adds constraints to the pose using a constraints file”. A little digging around finds it at rosetta.protocols.simple_moves.ConstraintSetMover, which doesn’t have much in the way of help, but does have a constraint_file() method you can use to specify the constraint file to use, and, like all movers, an apply() method which will actually act on the Pose.

—

By the way, under the hood this mover uses the rosetta.core.scoring.constraints.ConstraintIO.get_instance().read_constraints() method to read in the constraint file, and the pose.constraint_set() method to actually set them in the pose.

 

[Anonymous]

Another approach to use is to look at the regular Rosetta documentation at https://www.rosettacommons.org/docs/latest – particularly the RosettaScripts documentation. Each RosettaScripts Mover/Filter/etc. corresponds with a C++ level object, many of which can be used from Python with the appropriate getter/setter methods (verus the XML tags). 

For example, the description of the “ConstraintSetMover” is “Adds constraints to the pose using a constraints file”. A little digging around finds it at rosetta.protocols.simple_moves.ConstraintSetMover, which doesn’t have much in the way of help, but does have a constraint_file() method you can use to specify the constraint file to use, and, like all movers, an apply() method which will actually act on the Pose.

—

By the way, under the hood this mover uses the rosetta.core.scoring.constraints.ConstraintIO.get_instance().read_constraints() method to read in the constraint file, and the pose.constraint_set() method to actually set them in the pose.

 

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