# Predict Transmembrane Protein Topology

## Documentation for package ‘pureseqtmr’ version 1.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

are_tmhs | Are the sequences transmembrance helices?
are_valid_protein_sequences | Determine if these are all valid protein sequences
calc_distance_to_tmh_center_from_topology | Calculate the the distance for each amino acid to the center of the TMH
calc_distance_to_tmh_center_from_topology_str | Calculate the the distance for each amino acid to the center of the TMH
calc_distance_to_tmh_center_from_topology_str_cpp_stl | Use Rcpp to calculate the distance to a TMH center
check_protein_sequence | Check one protein sequence
check_protein_sequences | Check one or more protein sequences
check_pureseqtm_installation | Checks the installation of PureseqTM. Throws a helpful error message if incomplete, else does nothing
check_topology | Check if the topology is valid.
check_topology_str | Check if the topology string is valid. Will stop if not.
convert_tmhmm_to_pureseqtm_topology | Convert a TMHMM topology to a PureseqTM topology
count_n_tmhs | Count the number of TMHs in a topology
create_pureseqtm_files | Create the five PureseqTM output files, by running PureseqTM.
create_pureseqtm_proteome_file | Create the output file of a PureseqTM proteome run
default_params_doc | This function does nothing. It is intended to inherit is parameters' documentation.
get_default_pureseqtm_folder | Get the path to the folder where this package installs PureseqTM by default
get_example_filename | Get the full path to a PureseqTM example file.
get_example_filenames | Get the full path to all PureseqTM example files
get_pureseqtm_url | Get the URL of the PureseqTM source code
get_pureseqtm_version | Get the PureseqTM version
install_pureseqtm | Install PureseqTM to a local folder
is_on_appveyor | Determines if the environment is AppVeyor
is_on_ci | Determines if the environment is a continuous integration service
is_on_github_actions | Determines if the environment is GitHub Actions
is_on_travis | Determines if the environment is Travis CI
is_protein_name_line | Is the line of text the name of a protein, as used within a FASTA filename?
is_pureseqtm_installed | Measure if PureseqTM is installed locally
is_tmh | Determine if the protein sequence contains at least one transmembrane helix.
is_topology_line | Is the line of text the topology, as used within a FASTA filename?
is_valid_protein_sequence | Determine if this a valid protein sequence
load_fasta_file_as_tibble | Parse a FASTA file to a table with a 'name' and 'sequence' column
load_fasta_file_as_tibble_cpp | Parse a FASTA file to a table with a 'name' and 'sequence' column
load_fasta_file_as_tibble_cpp_raw | Use Rcpp to load a FASTA file
load_fasta_file_as_tibble_r | Parse a FASTA file to a table with a 'name' and 'sequence' column
load_topology_file_as_tibble | Parse a topology ('.topo') file to a table with a 'name' and 'topology' column
mock_predict_topologies_from_sequences | Do a mock prediction directy on a protein sequence, as can be useful in testing Use predict_topologies_from_sequences for doing a real prediction.
mock_predict_topology | Do a mock prediction of the topology of proteins
parse_pureseqtm_proteome_text | Parse the output of a call to 'PureseqTM_proteome.sh'
plot_topology | Plot the topology
predict_topologies_from_sequences | Run PureseqTM directy on a protein sequence
predict_topology | Predict the topology of proteins from file
predict_topology_from_sequence | Run PureseqTM directy on a protein sequence
pureseqtmr | pureseqtmr: estimate the topoplogy of membrane proteins
pureseqtmr_report | Create a pureseqtmr report, to be used when reporting bugs
run_pureseqtm_proteome | Run PureseqTM on a proteome
save_tibble_as_fasta_file | Save the first two columns of a tibble as a FASTA file
tally_tmhs | Count the number of transmembrane helices in a topology
uninstall_pureseqtm | Uninstall PureseqTM