#include <PsiPredInterface.hh>
Public Member Functions | |
| PsiPredInterface (std::string const &cmd, std::string const &scratch_dir="") | |
| default constructor More... | |
| PsiPredInterface (PsiPredInterface const &rval) | |
| copy constructor More... | |
| PsiPredResult | run_psipred (core::pose::Pose const &pose, std::string const &blueprint_ss) |
| Runs psipred, as specified by "cmd" on the fasta file "fasta_filename", and returns the psipred filename if cached psipred output has already been saved for the AA sequence of pose, the cached output will be returned. More... | |
| utility::vector1< utility::vector1< utility::vector1< core::Real > > > | run_psipred_prob (core::pose::Pose const &pose) |
| PsiPredInterface & | operator= (const PsiPredInterface &)=delete |
| in its current form PsiPredResultMap is not assignable but compiler tries to generate assigment operator anyway More... | |
Private Member Functions | |
| std::string | convert_to_fasta (std::string const &pname, std::string const &seq) const |
| converts a pose into a fasta string More... | |
| std::string | create_fasta_file (std::string const &pname, std::string const &seq) const |
| dumps fasta sequence for the pose into a file and returns the filename or exits rosetta if not successful More... | |
| void | cleanup_after_psipred (std::string const &psipred_filename, std::string const &fasta_filename) const |
| deletes files created by psipred and convert_to_fasta More... | |
| void | set_scratch_dir (std::string const &scratch_dir) |
| Set the scratch directory. Notably adding a / if the path does not end with one. More... | |
| PsiPredResult | parse_psipred_output (std::string const &psipred_str, std::string const &blueprint_ss, std::string const &psipred_horiz_filename) const |
| Parses the psipred output and returns the predicted secondary structure and likelihoods of the blueprint secondary structure being present on the pose at each position. More... | |
| utility::vector1< utility::vector1< Real > > | parse_psipred_output_probabilities (std::string const &psipred_str) const |
| Parses the psipred output and returns the probabilities. More... | |
| std::pair< std::string, utility::vector1< core::Size > > | parse_psipred_horiz_output (std::string const &psipred_horiz_filename) const |
| Parses the psipred pass2 horiz file and returns predicted secondary structure and confidence for each position. More... | |
Private Attributes | |
| PsiPredResultMap | psipred_output_ |
| This class will cache and store Psipred output for each amino acid sequence string. They are stored in this map, which is indexed by sequence string. More... | |
| std::string | cmd_ |
| The PsiPred command. More... | |
| std::string | scratch_dir_ |
| A scratch directory to store files in. Always ends with /. More... | |
Constructor & Destructor Documentation
◆ PsiPredInterface() [1/2]
| core::io::external::PsiPredInterface::PsiPredInterface | ( | std::string const & | cmd, |
| std::string const & | scratch_dir = "" |
||
| ) |
default constructor
References set_scratch_dir().
◆ PsiPredInterface() [2/2]
| core::io::external::PsiPredInterface::PsiPredInterface | ( | PsiPredInterface const & | rval | ) |
copy constructor
References scratch_dir_, and set_scratch_dir().
Member Function Documentation
◆ cleanup_after_psipred()
|
private |
deletes files created by psipred and convert_to_fasta
References core::io::TR().
Referenced by run_psipred(), and run_psipred_prob().
◆ convert_to_fasta()
|
private |
converts a pose into a fasta string
given a pose, generates a fasta string
converts a sequence into a fasta string, given the name
Referenced by create_fasta_file().
◆ create_fasta_file()
|
private |
dumps fasta sequence for the pose into a file and returns the filename or exits rosetta if not successful
creates a fasta file returns filename if successful exits rosetta if not successful
An optional output_folder may be passed where the fasta file will be written. The string is expected to end with / and will not be returned as part of the filename
References convert_to_fasta(), protocols::abinitio::filename(), and core::io::TR().
Referenced by run_psipred(), and run_psipred_prob().
◆ operator=()
|
delete |
in its current form PsiPredResultMap is not assignable but compiler tries to generate assigment operator anyway
◆ parse_psipred_horiz_output()
|
private |
Parses the psipred pass2 horiz file and returns predicted secondary structure and confidence for each position.
References protocols::hybridization::t, and core::io::TR().
Referenced by parse_psipred_output().
◆ parse_psipred_output()
|
private |
Parses the psipred output and returns the predicted secondary structure and likelihoods of the blueprint secondary structure being present on the pose at each position.
References protocols::loops::loop_closure::ccd::helix, core::io::external::PsiPredResult::nres, parse_psipred_horiz_output(), core::io::external::PsiPredResult::pred_ss, core::io::external::PsiPredResult::psipred2_confidence, core::io::external::PsiPredResult::psipred_prob, core::scoring::sheet, and core::io::TR().
Referenced by run_psipred().
◆ parse_psipred_output_probabilities()
|
private |
Parses the psipred output and returns the probabilities.
References protocols::loops::loop_closure::ccd::helix, and core::scoring::sheet.
Referenced by run_psipred_prob().
◆ run_psipred()
| PsiPredResult core::io::external::PsiPredInterface::run_psipred | ( | core::pose::Pose const & | pose, |
| std::string const & | blueprint_ss | ||
| ) |
Runs psipred, as specified by "cmd" on the fasta file "fasta_filename", and returns the psipred filename if cached psipred output has already been saved for the AA sequence of pose, the cached output will be returned.
create fasta file, run psipred, returns psipred output if successful
References core::pose::Pose::chain_sequence(), cleanup_after_psipred(), cmd_, core::pose::Pose::conformation(), create_fasta_file(), core::io::external::PsiPredResult::nres, core::conformation::Conformation::num_chains(), parse_psipred_output(), core::io::external::PsiPredResult::pred_ss, core::io::external::PsiPredResult::psipred2_confidence, core::io::external::PsiPredResult::psipred_prob, core::io::external::runpsipred_name_mangle_check(), scratch_dir_, core::pose::Pose::sequence(), protocols::hybridization::t, core::id::to_string(), and core::io::TR().
◆ run_psipred_prob()
| utility::vector1< utility::vector1< utility::vector1< core::Real > > > core::io::external::PsiPredInterface::run_psipred_prob | ( | core::pose::Pose const & | pose | ) |
References core::pose::Pose::chain_sequence(), cleanup_after_psipred(), cmd_, core::pose::Pose::conformation(), create_fasta_file(), core::conformation::Conformation::num_chains(), parse_psipred_output_probabilities(), scratch_dir_, core::pose::Pose::sequence(), protocols::hybridization::t, core::id::to_string(), and core::io::TR().
◆ set_scratch_dir()
|
private |
Set the scratch directory. Notably adding a / if the path does not end with one.
References scratch_dir_.
Referenced by PsiPredInterface().
Member Data Documentation
◆ cmd_
|
private |
The PsiPred command.
Referenced by run_psipred(), and run_psipred_prob().
◆ psipred_output_
|
private |
This class will cache and store Psipred output for each amino acid sequence string. They are stored in this map, which is indexed by sequence string.
◆ scratch_dir_
|
private |
A scratch directory to store files in. Always ends with /.
Referenced by PsiPredInterface(), run_psipred(), run_psipred_prob(), and set_scratch_dir().
The documentation for this class was generated from the following files:
- src/core/io/external/PsiPredInterface.hh
- src/core/io/external/PsiPredInterface.cc
