Package 'RBMRB'

Title: Interface to the Biological Magnetic Resonance Data Bank ('BMRB')
Description: A comprehensive interface to the Biological Magnetic Resonance Data Bank ('BMRB') <https://bmrb.io>, mirroring all functionality of the 'PyBMRB' 'Python' package (v3.0). Provides four modules: (1) 'ChemicalShift' for fetching per-entry chemical shift data from the 'BMRB' 'REST' 'API' or local 'NMR-STAR' files; (2) 'ChemicalShiftStatistics' for database-wide statistical queries; (3) Spectra for simulating '1H-15N' 'HSQC', '1H-13C' 'HSQC', '1H-1H' 'TOCSY', and generic 2D 'NMR' spectra as interactive plots; and (4) Histogram for chemical shift distribution visualizations with optional filtering by pH, temperature, and ambiguity code. All interactive plots are rendered via 'plotly'. Uses the 'BMRB' REST API v2 <https://api.bmrb.io/v2/>.
Authors: Kumaran Baskaran [aut, cre] (ORCID: <https://orcid.org/0000-0002-0418-0286>)
Maintainer: Kumaran Baskaran <baskaran@uchc.edu>
License: GPL-3
Version: 3.0.0
Built: 2026-10-14 18:55:48 UTC
Source: https://github.com/cran/RBMRB

Help Index

Get the citation for a BMRB entry

Description

Get the citation for a BMRB entry

Usage

bmrb_citation(bmrb_id, format = "bibtex")

Arguments

bmrb_id

A single BMRB entry ID.
format

Output format: "bibtex" (default), "json-ld", or "text".

Value

A character string containing the citation.

Examples

## Not run: 
cat(bmrb_citation(15060, format = "text"))

## End(Not run)

Diagnose BMRB entry fetch problems

Description

Fetches a BMRB entry using both the zlib-compressed and plain JSON endpoints and reports what is found at each step. Run this when cs_from_bmrb returns no data.

Usage

bmrb_debug_entry(bmrb_id)

Arguments

bmrb_id

A single BMRB entry ID (integer or character).

Value

Invisibly, the parsed entry JSON list, or NULL on failure.

Examples

## Not run: 
bmrb_debug_entry(15060)

## End(Not run)

Fetch raw metadata for a BMRB entry

Description

Fetch raw metadata for a BMRB entry

Usage

bmrb_fetch_entry(bmrb_ids)

Arguments

bmrb_ids

A single BMRB entry ID or a character/integer vector.

Value

A named list of raw entry metadata (API JSON as R list).

Examples

## Not run: 
meta <- bmrb_fetch_entry(15060)
names(meta[["15060"]])

## End(Not run)

Get BMRB IDs associated with a PDB entry

Description

Get BMRB IDs associated with a PDB entry

Usage

bmrb_from_pdb(pdb_id)

Arguments

pdb_id

A PDB ID string (e.g. "2JM0").

Value

A data.frame with columns bmrb_id, match_type, and comment.

Examples

## Not run: 
bmrb_from_pdb("2JM0")

## End(Not run)

List all BMRB entry IDs

Description

Returns all public entry IDs in the specified BMRB database.

Usage

bmrb_list_entries(database = "macromolecules")

Arguments

database

One of "macromolecules" (default), "metabolomics", or "chemcomps".

Value

A character vector of BMRB entry IDs.

Examples

## Not run: 
ids <- bmrb_list_entries()
length(ids)

## End(Not run)

Get PDB IDs associated with a BMRB entry

Description

Get PDB IDs associated with a BMRB entry

Usage

bmrb_pdb_ids(bmrb_id)

Arguments

bmrb_id

A single BMRB entry ID.

Value

A data.frame with columns pdb_id, match_type, and comment.

Examples

## Not run: 
bmrb_pdb_ids(15000)

## End(Not run)

Search BMRB using the instant-search endpoint

Description

Searches BMRB by title, author name, organism, amino-acid sequence, InChI string, or other terms.

Usage

bmrb_search(term, database = "combined")

Arguments

term

A search string.
database

One of "macromolecules", "metabolomics", or "combined" (default).

Value

A data.frame with columns value, label, sub_date, authors, and link.

Examples

## Not run: 
bmrb_search("ubiquitin human")
bmrb_search("GB3", database = "macromolecules")

## End(Not run)

Get BMRB API server status

Description

Returns current server information including entry counts and database last-update timestamps from the BMRB REST API.

Usage

bmrb_status()

Value

A list with server status information.

Examples

## Not run: 
bmrb_status()

## End(Not run)

Run a connectivity self-test

Description

Performs three checks: BMRB API status, entry fetch and parse for entry 15060, and the chemical shift search endpoint. Useful for verifying that the BMRB API is reachable from your network. Progress is reported with message(), so it can be silenced with suppressMessages().

Usage

bmrb_test()

Value

A named logical vector with elements api_status, entry_fetch, and search_query (invisibly).

Examples

## Not run: 
bmrb_test()

## End(Not run)

Upload an NMR-STAR file to BMRB for temporary access

Description

Uploads a local NMR-STAR file to the BMRB server. The entry is stored for 7 days. The returned token can be used as a BMRB ID in all other package functions.

Usage

bmrb_upload_entry(file_path)

Arguments

file_path

Path to a local NMR-STAR .str file.

Value

A character string token usable as a BMRB ID (invisibly).

Examples

## Not run: 
token <- bmrb_upload_entry("my_protein.str")
n15hsqc(bmrb_ids = token)

## End(Not run)

Simulate a 1H-13C HSQC spectrum

Description

Equivalent to 'pybmrb.Spectra.c13hsqc()'. See [n15hsqc()] for parameter descriptions.

Usage

c13hsqc(
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  legend = NULL,
  draw_trace = FALSE,
  peak_list = NULL,
  output_format = "html",
  output_file = NULL,
  output_image_width = 800,
  output_image_height = 600,
  show_visualization = TRUE
)

Arguments

bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
legend

'NULL' (default), '"residue"', or '"dataset"'.
draw_trace

Draw lines connecting same-residue peaks across datasets.
peak_list

Path to a 2-column CSV file of unassigned peaks ('H_ppm', 'N_ppm') to overlay.
output_format

'"html"' (default), '"png"', '"jpg"', '"pdf"', '"svg"', or '"webp"'.
output_file

File path to save the visualization (optional).
output_image_width, output_image_height

Image dimensions in pixels.
show_visualization

Open in browser / display inline. Default 'TRUE'.

Value

Invisibly, a list with the simulated peak list.

Examples

## Not run: 
c13hsqc(bmrb_ids = 15060, legend = "residue")

## End(Not run)

Plot a conditional chemical shift histogram

Description

Shows the CS distribution of 'atom' in 'residue' before and after filtering by known chemical shifts of other atoms in the same residue. Mirrors 'pybmrb.Histogram.conditional_hist()'.

Usage

conditional_cs_hist(
  residue,
  atom,
  filtering_rules,
  ph_min = NULL,
  ph_max = NULL,
  t_min = NULL,
  t_max = NULL,
  h_tolerance = 0.1,
  c_tolerance = 2,
  n_tolerance = 2,
  standard_amino_acids = TRUE,
  histnorm = NULL,
  plot_type = "histogram",
  output_format = "html",
  output_file = NULL,
  output_image_width = 800,
  output_image_height = 600,
  show_visualization = TRUE
)

Arguments

residue

Residue name.
atom

Atom whose distribution to plot.
filtering_rules

Named list of atom = value pairs used to filter, e.g. 'list(CA = 64.5, H = 7.8)'.
ph_min, ph_max, t_min, t_max

Condition filters.
h_tolerance

Tolerance (ppm) for H filters. Default 0.1.
c_tolerance

Tolerance (ppm) for C filters. Default 2.0.
n_tolerance

Tolerance (ppm) for N filters. Default 2.0.
standard_amino_acids

Restrict to standard amino acids. Default TRUE.
histnorm

Normalisation (see [cs_hist()]).
plot_type

"histogram" (default), "box", or "violin".
output_format, output_file, output_image_width, output_image_height, show_visualization

See [cs_hist()].

Value

Invisibly, a list with 'all_values', 'filtered_values', 'labels'.

Examples

## Not run: 
  conditional_cs_hist("SER", "N",
    filtering_rules = list(CA = 55.5, HA = 4.3))

## End(Not run)

Build a generic 2D peak list for any two atoms

Description

Equivalent to 'pybmrb.Spectra.create_2d_peaklist()'.

Usage

create_2d_peaklist(
  atom_x,
  atom_y,
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  draw_trace = FALSE,
  include_preceding = FALSE,
  include_next = FALSE
)

Arguments

atom_x

Atom name for the X axis.
atom_y

Atom name for the Y axis.
bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
draw_trace

Draw lines connecting same-residue peaks across datasets.
include_preceding

Include preceding (i-1) residue Y-axis peaks.
include_next

Include following (i+1) residue Y-axis peaks.

Value

Same structure as [create_n15hsqc_peaklist()].

Build a 1H-13C HSQC peak list

Description

Equivalent to 'pybmrb.Spectra.create_c13hsqc_peaklist()'.

Usage

create_c13hsqc_peaklist(
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  draw_trace = FALSE
)

Arguments

bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
draw_trace

Draw lines connecting same-residue peaks across datasets.

Value

Same structure as [create_n15hsqc_peaklist()].

Build a 1H-15N HSQC peak list

Description

Extracts backbone amide (and optionally sidechain NH) chemical shifts from BMRB entries / NMR-STAR files and returns the 2D peak coordinates. Equivalent to 'pybmrb.Spectra.create_n15hsqc_peaklist()'.

Usage

create_n15hsqc_peaklist(
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  draw_trace = FALSE,
  include_sidechain = TRUE
)

Arguments

bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
draw_trace

Draw lines connecting same-residue peaks across datasets.
include_sidechain

Include sidechain NH2 peaks (ASN/GLN/ARG/TRP/HIS).

Value

A list with elements: 'x' (H ppm), 'y' (N ppm), 'dataset', 'residue', 'info', 'seq_id', 'cs_track' (if 'draw_trace = TRUE').

Build a 1H-1H TOCSY peak list

Description

Pairs all protons within each residue (full spin-system). Both diagonal and off-diagonal peaks are included. Equivalent to 'pybmrb.Spectra.create_tocsy_peaklist()'.

Usage

create_tocsy_peaklist(
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  draw_trace = FALSE
)

Arguments

bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
draw_trace

Draw lines connecting same-residue peaks across datasets.

Value

Same structure as [create_n15hsqc_peaklist()].

Extract chemical shifts from BMRB database entries

Description

Fetches assigned chemical shift data for one or more BMRB entries. Uses the same zlib-compressed JSON endpoint as PyBMRB / pynmrstar. Mirrors 'pybmrb.ChemicalShift.from_bmrb()'.

Usage

cs_from_bmrb(bmrb_ids, auth_tag = FALSE)

Arguments

bmrb_ids

A single BMRB entry ID or a vector of IDs.
auth_tag

Logical. Use 'Auth_seq_ID' for sequence numbering. Default FALSE.

Value

A nested named list: 'list(dataset_id = list(chain = list(seq_id = list(atom = cs_value), seq_ids = integer_vector)))'.

Examples

## Not run: 
  cs <- cs_from_bmrb(15060)
  cs_peek(cs)
  cs_from_bmrb(c(17076, 17077))

## End(Not run)

Extract chemical shifts from local NMR-STAR files

Description

Mirrors 'pybmrb.ChemicalShift.from_file()'.

Usage

cs_from_file(file_paths, auth_tag = FALSE, data_set_ids = NULL)

Arguments

file_paths

Character vector of NMR-STAR file paths.
auth_tag

Logical. Use 'Auth_seq_ID'. Default FALSE.
data_set_ids

Optional character vector of dataset labels.

Value

Same nested-list structure as [cs_from_bmrb()].

Examples

## Not run: 
  cs <- cs_from_file("my_protein.str")

## End(Not run)

Plot a chemical shift distribution histogram

Description

Fetches database-wide chemical shift data and renders an interactive distribution plot. Mirrors 'pybmrb.Histogram.hist()'.

Usage

cs_hist(
  residue = NULL,
  atom = NULL,
  list_of_atoms = NULL,
  filtered = TRUE,
  sd_limit = 10,
  ambiguity = "*",
  ph_min = NULL,
  ph_max = NULL,
  t_min = NULL,
  t_max = NULL,
  standard_amino_acids = TRUE,
  histnorm = NULL,
  plot_type = "histogram",
  output_format = "html",
  output_file = NULL,
  output_image_width = 800,
  output_image_height = 600,
  show_visualization = TRUE
)

Arguments

residue

Residue name (IUPAC 3-letter). Use "*" for any.
atom

Atom name (e.g. "CA", "HB*", "*").
list_of_atoms

Optional character vector of "RES-ATOM" pairs (e.g. 'c("ALA-CB","CYS-N")'). Overrides residue/atom when supplied.
filtered

Remove outliers. Default TRUE.
sd_limit

SD factor for outlier removal. Default 10.
ambiguity

Ambiguity code filter ("*" = no filter).
ph_min, ph_max

pH range filter.
t_min, t_max

Temperature range filter (Kelvin).
standard_amino_acids

Restrict to standard amino acids. Default TRUE.
histnorm

NULL (count), "percent", "probability", or "probability density".
plot_type

"histogram" (default), "box", or "violin".
output_format

"html" (default), "png", "jpg", "pdf", "svg", "webp".
output_file

File path to save the plot (optional).
output_image_width, output_image_height

Image size in pixels.
show_visualization

Display the figure. Default TRUE.

Value

Invisibly, a list with elements 'values' and 'labels'.

Examples

## Not run: 
  cs_hist("ALA", "CA")
  cs_hist(list_of_atoms = c("ALA-CB","GLY-CA","SER-CB"))
  cs_hist("ALA", "CA", histnorm = "probability density",
          plot_type = "violin")

## End(Not run)

Plot a 2D chemical shift correlation map

Description

Mirrors 'pybmrb.Histogram.hist2d()'.

Usage

cs_hist2d(
  residue,
  atom1,
  atom2,
  filtered = TRUE,
  sd_limit = 10,
  ambiguity1 = "*",
  ambiguity2 = "*",
  ph_min = NULL,
  ph_max = NULL,
  t_min = NULL,
  t_max = NULL,
  histnorm = NULL,
  plot_type = "heatmap",
  output_format = "html",
  output_file = NULL,
  output_image_width = 800,
  output_image_height = 600,
  show_visualization = TRUE
)

Arguments

residue

Residue name.
atom1

First atom (X axis).
atom2

Second atom (Y axis).
filtered, sd_limit

See [cs_hist()].
ambiguity1, ambiguity2

Per-atom ambiguity filters.
ph_min, ph_max, t_min, t_max

Condition filters.
histnorm

Normalisation (see [cs_hist()]).
plot_type

"heatmap" (default) or "contour".
output_format, output_file, output_image_width, output_image_height, show_visualization

See [cs_hist()].

Value

Invisibly, a list with elements 'atom1' and 'atom2'.

Examples

## Not run: 
  cs_hist2d("CYS", "CB", "N")
  cs_hist2d("ALA", "CA", "CB", plot_type = "contour")

## End(Not run)

Peek at a nested CS structure

Description

Reports the first few residues of each chain with message(), so the output can be silenced with suppressMessages().

Usage

cs_peek(cs_data, n_res = 5L)

Arguments

cs_data

Output of [cs_from_bmrb()] or [cs_from_file()].
n_res

Number of residues to show per chain.

Value

cs_data, invisibly.

Examples

## Not run:  cs <- cs_from_bmrb(15060); cs_peek(cs)

Compute summary statistics for a set of chemical shifts

Description

Compute summary statistics for a set of chemical shifts

Usage

cs_stats(x)

Arguments

x

Numeric vector of chemical shift values.

Value

A named numeric vector: n, mean, sd, median, min, max.

Examples

cs_stats(c(55.1, 55.3, 56.0, 54.8))

Summarise a nested chemical shift list

Description

Builds a tidy summary of datasets, chains, and atom coverage. The summary is returned rather than printed, so it prints automatically at the console and can also be assigned and reused.

Usage

cs_summary(cs_data)

Arguments

cs_data

Nested list from [cs_from_bmrb()] or [cs_from_file()].

Value

A data.frame with one row per dataset and chain.

Examples

## Not run:  cs <- cs_from_bmrb(15060); cs_summary(cs)

Get a flat data.frame of chemical shifts for one or more BMRB entries

Description

Get a flat data.frame of chemical shifts for one or more BMRB entries

Usage

cs_table(bmrb_ids, auth_tag = FALSE)

Arguments

bmrb_ids

A single BMRB entry ID or a vector of IDs.
auth_tag

Logical. Use 'Auth_seq_ID' for sequence numbering. Default FALSE.

Value

A data.frame suitable for use with ggplot2 or dplyr.

Examples

## Not run:  df <- cs_table(c(15060, 17076))

Convert a nested CS list to a tidy data.frame

Description

Convert a nested CS list to a tidy data.frame

Usage

cs_to_df(cs_data)

Arguments

cs_data

Nested list from [cs_from_bmrb()] or [cs_from_file()].

Value

A data.frame with columns Dataset, Chain, Seq_ID, Atom_ID, Val.

Examples

## Not run:  cs <- cs_from_bmrb(15060); df <- cs_to_df(cs)

Export a peak list to CSV or Sparky format

Description

Converts the output of any 'create_*_peaklist()' function to a file or a data.frame. Equivalent to 'pybmrb.Spectra.export_peak_list()'.

Usage

export_peak_list(
  peak_list,
  output_file_name = NULL,
  output_format = "csv",
  include_side_chain = TRUE
)

Arguments

peak_list

List returned by any 'create_*_peaklist()' function.
output_file_name

Path to write the output file. 'NULL' returns only the data.frame without writing to disk.
output_format

'"csv"' (default) or '"sparky"'.
include_side_chain

Include sidechain peaks. Default 'TRUE'.

Value

Invisibly, a data.frame with the exported peak list.

Examples

## Not run: 
pl <- create_n15hsqc_peaklist(bmrb_ids = 15060)
export_peak_list(pl, "peaks.csv", output_format = "csv")
export_peak_list(pl, "peaks.sparky", output_format = "sparky")

## End(Not run)

Remove outliers from a numeric vector

Description

Remove outliers from a numeric vector

Usage

filter_cs_outliers(x, sd_limit = 10)

Arguments

x

Numeric vector.
sd_limit

Number of standard deviations beyond which to remove.

Value

Numeric vector with outliers removed.

Examples

filter_cs_outliers(c(52, 55, 56, 54, 300), sd_limit = 2)

Plot a generic 2D NMR correlation spectrum

Description

Generates a 2D spectrum for any two atom types. Supports sequence-walk tracing, preceding/next-residue peaks, and all the same overlay options as the other spectrum functions. Equivalent to 'pybmrb.Spectra.generic_2d()'.

Usage

generic_2d(
  atom_x,
  atom_y,
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  legend = NULL,
  draw_trace = FALSE,
  peak_list = NULL,
  include_preceding = FALSE,
  include_next = FALSE,
  seq_walk = FALSE,
  full_walk = FALSE,
  output_format = "html",
  output_file = NULL,
  output_image_width = 800,
  output_image_height = 600,
  show_visualization = TRUE
)

Arguments

atom_x

Atom name for the X axis (IUPAC, e.g. '"N"', '"CA"').
atom_y

Atom name for the Y axis.
bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
legend

'NULL' (default), '"residue"', or '"dataset"'.
draw_trace

Draw lines connecting same-residue peaks across datasets.
peak_list

Path to a 2-column CSV file of unassigned peaks ('H_ppm', 'N_ppm') to overlay.
include_preceding

Include chemical shifts from the preceding (i-1) residue on the Y axis. Default 'FALSE'.
include_next

Include chemical shifts from the following (i+1) residue on the Y axis. Default 'FALSE'.
seq_walk

Draw a trace connecting sequential i->i+/-1 pairs for continuous sequence segments. Default 'FALSE'.
full_walk

Like 'seq_walk' but ignores missing residues. Default 'FALSE'.
output_format

'"html"' (default), '"png"', '"jpg"', '"pdf"', '"svg"', or '"webp"'.
output_file

File path to save the visualization (optional).
output_image_width, output_image_height

Image dimensions in pixels.
show_visualization

Open in browser / display inline. Default 'TRUE'.

Value

Invisibly, the peak list.

Examples

## Not run: 
generic_2d("N", "CA", bmrb_ids = 15000, legend = "residue")
generic_2d("N", "CA", bmrb_ids = 15000, include_next = TRUE,
           seq_walk = TRUE)

## End(Not run)

Fetch paired 2D chemical shift data for two atoms in the same residue

Description

Mirrors 'pybmrb.ChemicalShiftStatistics.get_2d_chemical_shifts()'.

Usage

get_2d_cs_data(
  residue,
  atom1,
  atom2,
  filtered = TRUE,
  sd_limit = 10,
  ambiguity1 = "*",
  ambiguity2 = "*",
  ph_min = NULL,
  ph_max = NULL,
  t_min = NULL,
  t_max = NULL
)

Arguments

residue

Residue name (IUPAC 3-letter).
atom1

First atom (X axis).
atom2

Second atom (Y axis).
filtered, sd_limit

See [get_cs_data()].
ambiguity1, ambiguity2

Per-atom ambiguity filters.
ph_min, ph_max, t_min, t_max

Condition filters.

Value

Named list with 'atom1' and 'atom2' numeric vectors.

Examples

## Not run:  paired <- get_2d_cs_data("ALA", "CA", "CB")

Fetch chemical shift data from the BMRB database

Description

Downloads chemical shifts for the given residue and atom combination from the BMRB database. Mirrors 'pybmrb.ChemicalShiftStatistics.get_data()'.

Usage

get_cs_data(
  residue = "*",
  atom = "*",
  filtered = TRUE,
  sd_limit = 10,
  ambiguity = "*",
  ph_min = NULL,
  ph_max = NULL,
  t_min = NULL,
  t_max = NULL,
  standard_amino_acids = TRUE,
  database = "macromolecules"
)

Arguments

residue

Residue in IUPAC 3-letter format (e.g. "ALA"). "*" = any.
atom

Atom name (e.g. "CA", "HB*"). "*" = any.
filtered

Remove outliers beyond sd_limit * SD. Default TRUE.
sd_limit

SD factor for outlier removal. Default 10.
ambiguity

Ambiguity code filter ("*" = no filter; 1 = unambiguous).
ph_min, ph_max

pH range filter (optional).
t_min, t_max

Temperature range in Kelvin (optional).
standard_amino_acids

Restrict to standard amino acids. Default TRUE.
database

"macromolecules" (default) or "metabolomics".

Value

A data.frame with columns Val, Comp_ID, Atom_ID, Ambiguity_code, Entry_ID, Comp_index_ID, pH, Temperature_K and others.

Examples

## Not run: 
  df <- get_cs_data("ALA", "CA")
  df <- get_cs_data("*", "HB*")

## End(Not run)

Fetch raw BMRB chemical shift data (no outlier filtering)

Description

Mirrors 'pybmrb.ChemicalShiftStatistics.get_data_from_bmrb()'.

Usage

get_cs_from_bmrb_db(
  residue = "*",
  atom = "*",
  list_of_atoms = NULL,
  ambiguity = "*",
  ph_min = NULL,
  ph_max = NULL,
  t_min = NULL,
  t_max = NULL,
  standard_amino_acids = TRUE,
  database = "macromolecules"
)

Arguments

residue

Residue in IUPAC 3-letter format (e.g. "ALA"). "*" = any.
atom

Atom name (e.g. "CA", "HB*"). "*" = any.
list_of_atoms

Optional "RES-ATOM" vector, e.g. 'c("ALA-CB","GLY-CA")'.
ambiguity

Ambiguity code filter ("*" = no filter; 1 = unambiguous).
ph_min, ph_max

pH range filter (optional).
t_min, t_max

Temperature range in Kelvin (optional).
standard_amino_acids

Restrict to standard amino acids. Default TRUE.
database

"macromolecules" (default) or "metabolomics".

Value

A data.frame of raw chemical shift records.

Examples

## Not run: 
  df  <- get_cs_from_bmrb_db("ALA", "CB")
  df2 <- get_cs_from_bmrb_db(list_of_atoms = c("ALA-CB","GLY-CA"))

## End(Not run)

Simulate a 1H-15N HSQC spectrum

Description

Plots an interactive 1H-15N HSQC spectrum for one or more BMRB entries and/or NMR-STAR files. Overlay multiple datasets as scatter plots; optionally draw trace lines connecting peaks from the same residue position across datasets. Equivalent to 'pybmrb.Spectra.n15hsqc()'.

Usage

n15hsqc(
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  legend = NULL,
  draw_trace = FALSE,
  include_sidechain = TRUE,
  peak_list = NULL,
  output_format = "html",
  output_file = NULL,
  output_image_width = 800,
  output_image_height = 600,
  show_visualization = TRUE
)

Arguments

bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
legend

'NULL' (default), '"residue"', or '"dataset"'.
draw_trace

Draw lines connecting same-residue peaks across datasets.
include_sidechain

Include sidechain NH2 peaks (ASN/GLN/ARG/TRP/HIS).
peak_list

Path to a 2-column CSV file of unassigned peaks ('H_ppm', 'N_ppm') to overlay.
output_format

'"html"' (default), '"png"', '"jpg"', '"pdf"', '"svg"', or '"webp"'.
output_file

File path to save the visualization (optional).
output_image_width, output_image_height

Image dimensions in pixels.
show_visualization

Open in browser / display inline. Default 'TRUE'.

Value

Invisibly, a list with elements 'x' (H ppm), 'y' (N ppm), 'dataset', 'residue', 'info', and (when 'draw_trace = TRUE') 'cs_track'.

Examples

## Not run: 
# Single entry
n15hsqc(bmrb_ids = 15060, legend = "residue")

# Compare two entries with trace lines
n15hsqc(bmrb_ids = c(17076, 17077), legend = "dataset", draw_trace = TRUE)

# Overlay user's own NMR-STAR file with BMRB entry
n15hsqc(bmrb_ids = 15060, input_file_names = "MyData.str",
        legend = "dataset")

## End(Not run)

Get the installed RBMRB version

Description

Returns the version of the installed RBMRB package as a string.

Usage

RBMRB_version()

Value

A character string with the package version.

Examples

RBMRB_version()

List the 20 standard amino acid codes

Description

List the 20 standard amino acid codes

Usage

standard_amino_acids()

Value

Character vector of 3-letter amino acid codes.

Examples

standard_amino_acids()

List standard nucleic acid residue codes

Description

List standard nucleic acid residue codes

Usage

standard_nucleic_acids()

Value

Character vector of RNA and DNA residue codes.

Examples

standard_nucleic_acids()

Simulate a 1H-1H TOCSY spectrum

Description

Equivalent to 'pybmrb.Spectra.tocsy()'. See [n15hsqc()] for shared parameter descriptions.

Usage

tocsy(
  bmrb_ids = NULL,
  input_file_names = NULL,
  auth_tag = FALSE,
  legend = NULL,
  draw_trace = FALSE,
  peak_list = NULL,
  output_format = "html",
  output_file = NULL,
  output_image_width = 800,
  output_image_height = 600,
  show_visualization = TRUE
)

Arguments

bmrb_ids

BMRB entry ID(s) – integer, character, or vector.
input_file_names

Path(s) to local NMR-STAR '.str' files.
auth_tag

Use 'Auth_seq_ID' for sequence numbering.
legend

'NULL' (default), '"residue"', or '"dataset"'.
draw_trace

Draw lines connecting same-residue peaks across datasets.
peak_list

Path to a 2-column CSV file of unassigned peaks ('H_ppm', 'N_ppm') to overlay.
output_format

'"html"' (default), '"png"', '"jpg"', '"pdf"', '"svg"', or '"webp"'.
output_file

File path to save the visualization (optional).
output_image_width, output_image_height

Image dimensions in pixels.
show_visualization

Open in browser / display inline. Default 'TRUE'.

Value

Invisibly, a list with the simulated peak list.

Examples

## Not run: 
tocsy(bmrb_ids = 15060, legend = "residue")
tocsy(bmrb_ids = c(17074, 17076, 17077), legend = "dataset",
      draw_trace = TRUE)

## End(Not run)