protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst Class Reference

a simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too More...

#include <AllowedSeqposForGeomCst.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst:

Public Types
typedef core::Size	Size

Public Member Functions
	AllowedSeqposForGeomCst (utility::vector1< utility::vector1< core::Size > > const &seqpos_for_geomcst)
	AllowedSeqposForGeomCst ()
	~AllowedSeqposForGeomCst () override
core::Size	num_seqpos_lists () const
utility::vector1< core::Size > const &	seqpos_for_geomcst (core::Size geomcst) const
void	initialize_from_command_line (core::pose::PoseCOP pose=nullptr)
	this function used to live in the matcher task pose can be passed in optionally to support the ALL tag in the pos file More...

Private Attributes
utility::vector1< utility::vector1< core::Size > >	seqpos_for_geomcst_

Detailed Description

a simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too

Member Typedef Documentation

Size

typedef core::Size protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::Size

Constructor & Destructor Documentation

AllowedSeqposForGeomCst() [1/2]

protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::AllowedSeqposForGeomCst

(

utility::vector1< utility::vector1< core::Size > > const &

seqpos_for_geomcst

)

AllowedSeqposForGeomCst() [2/2]

protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::AllowedSeqposForGeomCst ( )

default

~AllowedSeqposForGeomCst()

protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::~AllowedSeqposForGeomCst ( )

overridedefault

Member Function Documentation

initialize_from_command_line()

void protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line

(

core::pose::PoseCOP

pose = nullptr

)

this function used to live in the matcher task pose can be passed in optionally to support the ALL tag in the pos file

This function reads one of two files from the command line depending on which options the user has provided. These files define the set of residues on the scaffold to consider as launch-points for the geometric constraints (e.g. to consider as part of the the catalytic core in an enzyme). The file meanings and formats are below.

1. A list of residue id's to consider for all of the geometric constraints. Such a file can be generated for a scaffold and then used along side any enzyme-design .cst file. It is scaffold dependent and constraint-file independent. The file should list the residue indexes for the scaffold on one or more lines. The file format does not support comments. Residue id's start counting at 1; the input pdb resids are ignored. (It's best to renumber your scaffold resids starting from 1 to avoid confusion)

Example. <begin file> 104 106 108 109 117 118 137 139 143 144 36 6 85 87 88 89 91 92 97 <end file>

1. A list for each geometric constraint of the residues to consider. Such a file allows the user to focus on particular residues for certain geometric constraints for a particular scaffold. Such a file should be depends on both the scaffold and the match constraint file and cannot be generalized across either multiple scaffolds or multiple constraint files. The first line of the file begins with N_CST, followed by the number of geometric contraints. This must match the number of geometric constraints in the .cst file. On each subsequent line, the geometric constraint ID is given, followed by a colon and then followed by all of the residue ID's that should be considered for that geometric constraint. Each geometric constraint must appear on one line in the file, though they may be listed in any order. The file format does not support comments. flo jan 2010: it is also possible to specify that all positions in the scaffold can be used for a certain constraint. see the example for cst 4 below Example. <begin file> N_CST 3 1: 9 3: 9 2: 6 7 9 11 12 14 15 17 18 21 22 23 25 26 38 40 43 46 47 49 53 54 57 60 61 4: all <end file>

References protocols::abinitio::filename(), seqpos_for_geomcst_, core::id::to_string(), and protocols::toolbox::match_enzdes_util::TR().

Referenced by protocols::match::MatcherTask::initialize_scaffold_active_site_residue_list_from_command_line().

num_seqpos_lists()

core::Size protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::num_seqpos_lists ( ) const

inline

References seqpos_for_geomcst_.

Referenced by protocols::match::MatcherTask::initialize_scaffold_active_site_residue_list_from_command_line().

seqpos_for_geomcst()

utility::vector1< core::Size > const & protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::seqpos_for_geomcst

(

core::Size

geomcst

)

const

this function supports two behaviours

1. the same list for every geomcst. this means that if the size of seqpos_for_geomcst_ == 1 and a bigger number than 1 is passed in, it will return the first element
2. different lists for every geomcst. this means that the size of seqpos_for_geomcst_ is > 1, but if a larger number than the vector size is passed in, it's unclear what to do, so we exit

References seqpos_for_geomcst_, and core::id::to_string().

Referenced by protocols::match::MatcherTask::initialize_scaffold_active_site_residue_list_from_command_line().

Member Data Documentation

seqpos_for_geomcst_

utility::vector1< utility::vector1< core::Size > > protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::seqpos_for_geomcst_

private

Referenced by initialize_from_command_line(), num_seqpos_lists(), and seqpos_for_geomcst().

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The documentation for this class was generated from the following files:

• src/protocols/toolbox/match_enzdes_util/AllowedSeqposForGeomCst.hh
• src/protocols/toolbox/match_enzdes_util/AllowedSeqposForGeomCst.cc