Module documentation¶

Spectra¶

This module is used to visualize the one dimensional chemical shift list from BMRB entry or NMR-STAR file as a two dimensional NMR spectrum. It simulates peak positions of ¹⁵N-HSQC, ¹³C-HSQC and ¹H-¹H-TOCSY. It can also simulate a generic 2D spectrum between any two given pair of atoms. This module is useful to compare user data with any BMRB entry/list of entries as a overlaid NMR spectra.

pybmrb.Spectra.c13hsqc(bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, auth_tag: Optional[bool] = False, legend: Optional[str] = None, draw_trace: Optional[bool] = False, peak_list: Optional[str] = None, output_format: Optional[str] = 'html', output_file: Optional[str] = None, output_image_width: Optional[int] = 800, output_image_height: Optional[int] = 600, show_visualization: Optional[bool] = True) → tuple¶

Plots ¹³C-HSQC spectrum for a given BMRB entry/NMR-STAR file/PyNMRSTAR entry object; This function can be used to compare different data sets as overlaid NMR Spectra. It overlays ¹³C-HSQC for a given list of BMRB entries/NMR-STAR files/PyNMRSTAR entry objects and draw lines connecting peaks from residues at the same sequence location in different data sets

Parameters

bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
legend (str, optional) – legends are disabled by default. Residue types are indicated by color and data sets are indicated by symbol, displaying the combination of both will create a very long list of legend. Optionally either ‘residue’ or ‘dataset’ can be used to color code the scatter plot by residue type or data set and display the legend, defaults to None
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False
peak_list (str, optional) – comma-separated two column file can be given as optional unassigned peak list, which can be overlaid on the spectrum as another data set, defaults to None
output_format (str, optional) – visualizations can be exported as interactive ‘html’ file or as static images in ‘jpg’,’jpeg’,’png’,’pdf’,’webp’,’svg’, defaults to ‘html’
output_file (str, optional) – file name to export visualization
output_image_width (int, optional) – The width of the exported image in layout pixels, defaults to 800
output_image_height (int, optional) – The height of the exported image in layout pixels, defaults to 600
show_visualization (bool, optional) – Visualization automatically opens in a web browser or as embedded visualization in Jupyter Notebook. This feature can be disabled by setting this flag as False, defaults to True

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

pybmrb.Spectra.create_2d_peaklist(atom_x: str, atom_y: str, bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, auth_tag: Optional[bool] = False, draw_trace: Optional[bool] = False, include_preceding: Optional[bool] = False, include_next: Optional[bool] = False, legend: Optional[str] = None) → tuple¶

Converts one dimensional chemical shifts from BMRB entries/NMR-STAR files/PyNMRSTAR entry objects into into generic 2D peak list

Parameters

atom_x (str) – atom name for X coordinate in IUPAC format
atom_y (str) – atom name for Y coordinate in IUPAC format
bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False
include_preceding (bool, optional) – include peaks from i-1 residue on the Y axis, defaults to False
include_next (bool, optional) – include peaks from i+i residue on the Y axis, defaults to False
legend (str, optional) – legends are disabled by default. Residue types are indicated by color and data sets are indicated by symbol, displaying the combination of both will create a very long list of legend. Optionally either ‘residue’ or ‘dataset’ can be used to color code the scatter plot by residue type or data set and display the legend, defaults to None

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track,psn,seq_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

pybmrb.Spectra.create_c13hsqc_peaklist(bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, auth_tag: Optional[bool] = False, draw_trace: Optional[bool] = False) → tuple¶

Converts one dimensional chemical shifts from BMRB entries/NMR-STAR files/PyNMRSTAR entry objects into ¹³C-HSQC peak list

Parameters

bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

pybmrb.Spectra.create_n15hsqc_peaklist(bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, auth_tag: Optional[bool] = False, draw_trace: Optional[bool] = False, include_sidechain: Optional[bool] = True) → tuple¶

Converts one dimensional chemical shifts from BMRB entries/NMR-STAR files/PyNMRSTAR entry objects into ¹⁵N-HSQC peak list

Parameters

bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False
include_sidechain (bool, optional) – include peaks from side chains, defaults to True

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

pybmrb.Spectra.create_tocsy_peaklist(bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, auth_tag: Optional[bool] = False, draw_trace: Optional[bool] = False) → tuple¶

Converts one dimensional chemical shifts from BMRB entries/NMR-STAR files/PyNMRSTAR entry objects into into ¹H-¹H-TOCSY peak list

Parameters

bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

pybmrb.Spectra.export_peak_list(peak_list: tuple, output_file_name: Optional[str] = None, output_format: str = 'csv', include_side_chain: bool = True) → dict¶

Exports the peak list return from other functions in this module in csv or sparky format

Parameters

peak_list (tuple) – Output tuple from any peak list/spectrum simulation function from the module Spectra
output_file_name (str, optional) – output file name
output_format (str, optional) – output format ‘csv’ or ‘sparky’, defaults to ‘csv’
include_side_chain (bool, optional) – whether or not include side chain resonances in the output, defaults to True

Returns

data dictionary {‘column header1’:[values],’column header1’:[values]..}

Return type

dict

pybmrb.Spectra.generic_2d(atom_x: str, atom_y: str, bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, auth_tag: Optional[bool] = False, legend: Optional[str] = None, draw_trace: Optional[bool] = False, peak_list: Optional[str] = None, include_preceding: Optional[bool] = False, include_next: Optional[bool] = False, full_walk: Optional[bool] = False, seq_walk: Optional[bool] = False, output_format: Optional[str] = 'html', output_file: Optional[str] = None, output_image_width: Optional[int] = 800, output_image_height: Optional[int] = 600, show_visualization: Optional[bool] = True) → tuple¶

Plots generic 2D spectrum for a given BMRB entry/NMR-STAR file/PyNMRSTAR entry object; This function can be used to compare different data sets as overlaid NMR Spectra. It overlays the 2D spectra for a given list of BMRB entries/NMR-STAR files/PyNMRSTAR entry objects and draw lines connecting peaks from residues at the same sequence location in different data sets

Parameters

atom_x (str) – atom name for X coordinate in IUPAC format
atom_y (str) – atom name for Y coordinate in IUPAC format
bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
legend (str, optional) – legends are disabled by default. Residue types are indicated by color and data sets are indicated by symbol, displaying the combination of both will create a very long list of legend. Optionally either ‘residue’ or ‘dataset’ can be used to color code the scatter plot by residue type or data set and display the legend, defaults to None
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False
include_preceding (bool, optional) – include peaks from i-1 residue on the Y axis, defaults to False
include_next (bool, optional) – include peaks from i+i residue on the Y axis, defaults to False
seq_walk (bool, optional) – draw line connecting i->i-1/i+1 to next i->i-1/i+1 for only continuous sequence segments, defaults to False
full_walk (bool, optional) – draw line connecting i->i-1/i+1 to next i->i-1/i+1 for the full sequence ignoring any missing residues, defaults to False
peak_list (str, optional) – comma-separated two column file can be given as optional unassigned peak list, which can be overlaid on the spectrum as another data set, defaults to None
output_format (str, optional) – visualizations can be exported as interactive ‘html’ file or as static images in ‘jpg’,’jpeg’,’png’,’pdf’,’webp’,’svg’, defaults to ‘html’
output_file (str, optional) – file name to export visualization
output_image_width (int, optional) – The width of the exported image in layout pixels, defaults to 800
output_image_height (int, optional) – The height of the exported image in layout pixels, defaults to 600
show_visualization (bool, optional) – Visualization automatically opens in a web browser or as embedded visualization in Jupyter Notebook. This feature can be disabled by setting this flag as False, defaults to True

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

pybmrb.Spectra.n15hsqc(bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, auth_tag: Optional[bool] = False, legend: Optional[str] = None, draw_trace: Optional[bool] = False, include_sidechain: Optional[bool] = True, peak_list: Optional[str] = None, output_format: Optional[str] = 'html', output_file: Optional[str] = None, output_image_width: Optional[int] = 800, output_image_height: Optional[int] = 600, show_visualization: Optional[bool] = True) → tuple¶

Plots ¹⁵N-HSQC spectrum for a given BMRB entry/NMR-STAR file/PyNMRSTAR entry object; This function can be used to compare different data sets as overlaid NMR Spectra. It overlays ¹⁵N-HSQC for a given list of BMRB entries/NMR-STAR files/PyNMRSTAR entry objects and draw lines connecting peaks from residues at the same sequence location in different data sets

Parameters

bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
legend (str, optional) – legends are disabled by default. Residue types are indicated by color and data sets are indicated by symbol, displaying the combination of both will create a very long list of legend. Optionally either ‘residue’ or ‘dataset’ can be used to color code the scatter plot by residue type or data set and display the legend, defaults to None
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False
include_sidechain (bool, optional) – include peaks from side chains, defaults to True
peak_list (str, optional) – comma-separated two column file can be given as optional unassigned peak list, which can be overlaid on the spectrum as another data set, defaults to None
output_format (str, optional) – visualizations can be exported as interactive ‘html’ file or as static images in ‘jpg’,’jpeg’,’png’,’pdf’,’webp’,’svg’, defaults to ‘html’
output_file (str, optional) – file name to export visualization
output_image_width (int, optional) – The width of the exported image in layout pixels, defaults to 800
output_image_height (int, optional) – The height of the exported image in layout pixels, defaults to 600
show_visualization (bool, optional) – Visualization automatically opens in a web browser or as embedded visualization in Jupyter Notebook. This feature can be disabled by setting this flag as False, defaults to True

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

pybmrb.Spectra.tocsy(bmrb_ids: Optional[Union[str, List[str], int, List[int]]] = None, input_file_names: Optional[Union[str, List[str]]] = None, entry_objects: Optional[Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]]] = None, auth_tag: Optional[bool] = False, legend: Optional[str] = None, draw_trace: Optional[bool] = False, peak_list: Optional[str] = None, output_format: Optional[str] = 'html', output_file: Optional[str] = None, output_image_width: Optional[int] = 800, output_image_height: Optional[int] = 600, show_visualization: Optional[bool] = True) → tuple¶

Plots ¹H-¹H-TOCSY spectrum for a given BMRB entry/NMR-STAR file/PyNMRSTAR entry object; This function can be used to compare different data sets as overlaid NMR Spectra. It overlays ¹H-¹H-TOCSY for a given list of BMRB entries/NMR-STAR files/PyNMRSTAR entry objects and draw lines connecting peaks from residues at the same sequence location in different data sets

Parameters

bmrb_ids (str/int/list, optional) – single BMRB entry ID or multiple BMRB entry IDs as list, defaults to None
input_file_names (str, optional) – single input file name or multiple input file names as list, defaults to None
entry_objects (PyNMRSTAR object/list, optional) – single PyNMRSTAR entry object or multiple PyNMRSTAR entry objects as list, defaults to None
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
legend (str, optional) – legends are disabled by default. Residue types are indicated by color and data sets are indicated by symbol, displaying the combination of both will create a very long list of legend. Optionally either ‘residue’ or ‘dataset’ can be used to color code the scatter plot by residue type or data set and display the legend, defaults to None
draw_trace (bool optional) – draw line connecting peaks from residues at the same sequence location in different data sets, defaults to False
peak_list (str, optional) – comma-separated two column file can be given as optional unassigned peak list, which can be overlaid on the spectrum as another data set, defaults to None
output_format (str, optional) – visualizations can be exported as interactive ‘html’ file or as static images in ‘jpg’,’jpeg’,’png’,’pdf’,’webp’,’svg’, defaults to ‘html’
output_file (str, optional) – file name to export visualization
output_image_width (int, optional) – The width of the exported image in layout pixels, defaults to 800
output_image_height (int, optional) – The height of the exported image in layout pixels, defaults to 600
show_visualization (bool, optional) – Visualization automatically opens in a web browser or as embedded visualization in Jupyter Notebook. This feature can be disabled by setting this flag as False, defaults to True

Returns

tuple of lists and dictionary (x,y,data_set,info,res,cs_track) if draw_trace is True cs_track={ matching atoms:[cs_values]} else cs_track={}

Return type

tuple

Histogram¶

This module generates visualizations for chemical shift distribution of a given list of atoms and residues. It can also generate chemical shift correlation plots between two atoms in the same residue and filtered chemical shift distribution based on user defined rules

pybmrb.Histogram.conditional_hist(residue: str, atom: str, filtering_rules: Optional[list], ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None, h_tolerance: Optional[float] = 0.1, c_tolerance: Optional[float] = 2.0, n_tolerance: Optional[float] = 2.0, standard_amino_acids: Optional[bool] = True, histnorm: Optional[str] = None, plot_type: Optional[str] = 'histogram', output_format: Optional[str] = 'html', output_file: Optional[str] = None, output_image_width: Optional[int] = 800, output_image_height: Optional[int] = 600, show_visualization: Optional[bool] = True) → tuple¶

Plots the distribution of the given atom in the residue along with the filtered distribution based on the chemical shift values of the other atoms in the residue

Parameters

residue (str) – residue name in IUPAC format
atom (str) – atom name in IUPAC format
filtering_rules (list) – list of atoms and chemical shift values as tuples to use as a filter; example[(‘CA’,64.5),(‘H’,7.8)]
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None
h_tolerance (float, optional) – tolerance value in ppm to filter H chemical shifts. It will allow the chemical shift value given in the filtering_rules +/- tolerance, defaults to 0.1
c_tolerance (float, optional) – tolerance value in ppm to filter C chemical shifts, It will allow the chemical shift value given in the filtering_rules +/- tolerance, defaults to 2.0
n_tolerance (float, optional) – tolerance value in ppm to filter N chemical shifts, It will allow the chemical shift value given in the filtering_rules +/- tolerance, defaults to 2.0
standard_amino_acids (bool, optional) – get data only form standard amino acids and nucleic acids when ‘*’ is used for residue, defaults to True
histnorm (str, optional) – Specifies the type of normalization used for this histogram trace. If None, the span of each bar corresponds to the number of occurrences (i.e. the number of data points lying inside the bins). If ‘percent’ / ‘probability’, the span of each bar corresponds to the percentage / fraction of occurrences with respect to the total number of sample points (here, the sum of all bin HEIGHTS equals 100% / 1). If ‘density’, the span of each bar corresponds to the number of occurrences in a bin divided by the size of the bin interval (here, the sum of all bin AREAS equals the total number of sample points). If ‘probability density’, the area of each bar corresponds to the probability that an event will fall into the corresponding bin (here, the sum of all bin AREAS equals 1) defaults to None
plot_type (str, optional) – visualization type ‘histogram’, ‘box’ or ‘violin’, defaults to ‘histogram’
output_format (str, optional) – visualizations can be exported as interactive ‘html’ file or as static images in ‘jpg’,’jpeg’,’png’,’pdf’,’webp’,’svg’, defaults to ‘html’
output_file (str, optional) – file name to export visualization
output_image_width (int, optional) – The width of the exported image in layout pixels, defaults to 800
output_image_height (int, optional) – The height of the exported image in layout pixels, defaults to 600
show_visualization (bool, optional) – Visualization automatically opens in a web browser or as embedded visualization in Jupyter Notebook. This feature can be disabled by setting this flag as False, defaults to True

Returns

chemical shift data and tags as tuple (chemical shifts, tags)

Return type

tuple

pybmrb.Histogram.hist(residue: Optional[str] = None, atom: Optional[str] = None, list_of_atoms: Optional[Union[str, List[str]]] = None, filtered: Optional[bool] = True, sd_limit: Optional[float] = 10.0, ambiguity: Optional[Union[str, int]] = '*', ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None, standard_amino_acids: Optional[bool] = True, histnorm: Optional[str] = None, plot_type: Optional[str] = 'histogram', output_format: Optional[str] = 'html', output_file: Optional[str] = None, output_image_width: Optional[int] = 800, output_image_height: Optional[int] = 600, show_visualization: Optional[bool] = True) → tuple¶

plots histogram for a given list of atoms and residues with some filters. One of either residue or atom or list of atoms is required

Parameters

residue (str) – Residue name in IUPAC format; use ‘*’ for any residue
atom (str) – Atom name in IUPAC format; Wild card supported; example HB*; use ‘*’ for any atom
list_of_atoms (list, optional) – list of atoms; example [‘ALA-CB’,’CYS-N’,’TYR-CB’], defaults to None
filtered (bool, optional) – Filters values beyond (sd_limit)*(standard deviation) on both sides of the mean, defaults to True
sd_limit (float, optional) – scaling factor used to filter data based on standard deviation, defaults to 10.0
ambiguity (str, optional) – filter based on chemical shift ambiguity code, defaults to ‘*’ means no filter
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None
standard_amino_acids (bool, optional) – get data only form standard amino acids and nucleic acids when ‘*’ is used for residue, defaults to True
histnorm (str, optional) – Specifies the type of normalization used for this histogram trace. If None, the span of each bar corresponds to the number of occurrences (i.e. the number of data points lying inside the bins). If ‘percent’ / ‘probability’, the span of each bar corresponds to the percentage / fraction of occurrences with respect to the total number of sample points (here, the sum of all bin HEIGHTS equals 100% / 1). If ‘density’, the span of each bar corresponds to the number of occurrences in a bin divided by the size of the bin interval (here, the sum of all bin AREAS equals the total number of sample points). If ‘probability density’, the area of each bar corresponds to the probability that an event will fall into the corresponding bin (here, the sum of all bin AREAS equals 1) defaults to None
plot_type (str, optional) – visualization type ‘histogram’, ‘box’ or ‘violin’, defaults to ‘histogram’
output_format (str, optional) – visualizations can be exported as interactive ‘html’ file or as static images in ‘jpg’,’jpeg’,’png’,’pdf’,’webp’,’svg’, defaults to ‘html’
output_file (str, optional) – file name to export visualization
output_image_width (int, optional) – The width of the exported image in layout pixels, defaults to 800
output_image_height (int, optional) – The height of the exported image in layout pixels, defaults to 600
show_visualization (bool, optional) – Visualization automatically opens in a web browser or as embedded visualization in Jupyter Notebook. This feature can be disabled by setting this flag as False, defaults to True

Returns

chemical shift data and tags as tuple (chemical shifts, tags)

Return type

tuple

pybmrb.Histogram.hist2d(residue: str, atom1: str, atom2: str, filtered: Optional[bool] = True, sd_limit: Optional[float] = 10.0, ambiguity1: Optional[Union[str, int]] = '*', ambiguity2: Optional[Union[str, int]] = '*', ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None, histnorm: Optional[str] = None, plot_type: Optional[str] = 'heatmap', output_format: Optional[str] = 'html', output_file: Optional[str] = None, output_image_width: Optional[int] = 800, output_image_height: Optional[int] = 600, show_visualization: Optional[bool] = True) → tuple¶

Generates chemical shift correlation plot for any two atoms from a given residue.

Parameters

residue (str) – residue name in IUPAC format
atom1 (str) – atom name in IUPAC format
atom2 (str) – atom name in IUPAC format
filtered (bool, optional) – Filters values beyond (sd_limit)*(standard deviation) on both sides of the mean, defaults to True
sd_limit (float, optional) – scaling factor used to filter data based on standard deviation, defaults to 10.0
ambiguity1 (str, optional) – filter based on chemical shift ambiguity code for atom1, defaults to ‘*’ means no filter
ambiguity2 (str, optional) – filter based on chemical shift ambiguity code for atom2, defaults to ‘*’ means no filter
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None
histnorm (str, optional) – Specifies the type of normalization used for this histogram trace. If None, the span of each bar corresponds to the number of occurrences (i.e. the number of data points lying inside the bins). If ‘percent’ / ‘probability’, the span of each bar corresponds to the percentage / fraction of occurrences with respect to the total number of sample points (here, the sum of all bin HEIGHTS equals 100% / 1). If ‘density’, the span of each bar corresponds to the number of occurrences in a bin divided by the size of the bin interval (here, the sum of all bin AREAS equals the total number of sample points). If ‘probability density’, the area of each bar corresponds to the probability that an event will fall into the corresponding bin (here, the sum of all bin AREAS equals 1) defaults to None
plot_type (str, optional) – visualization type ‘contour’ or ‘heatmap’, defaults to ‘heatmap’
output_format (str, optional) – visualizations can be exported as interactive ‘html’ file or as static images in ‘jpg’,’jpeg’,’png’,’pdf’,’webp’,’svg’, defaults to ‘html’
output_file (str, optional) – file name to export visualization
output_image_width (int, optional) – The width of the exported image in layout pixels, defaults to 800
output_image_height (int, optional) – The height of the exported image in layout pixels, defaults to 600
show_visualization (bool, optional) – Visualization automatically opens in a web browser or as embedded visualization in Jupyter Notebook. This feature can be disabled by setting this flag as False, defaults to True

Returns

tuple (chemical shift list of atom1, chemical shift list of atom2)

Return type

tuple

ChemicalShift¶

This module extracts chemical shift information from BMRB entries, NMR-STAR files and PyNMRSTAR entry objects

pybmrb.ChemicalShift.from_bmrb(bmrb_ids: Union[str, List[str], int, List[int]], auth_tag: Optional[bool] = False) → dict¶

Extracts chemical shift information directly from BMRB database for a given BMRB entry or list of entries

Parameters

bmrb_ids (str/int/list) – List of BMRB entries ids or single BMRB ID
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False

Returns

Chemical shift dictionary {data_set_id:{chain_id:{seq_id:{atom_id:cs_value}},’seq_ids’:[1,2,3,4..]}}

Return type

dict

pybmrb.ChemicalShift.from_entry_object(entry_objects: Union[pynmrstar.entry.Entry, List[pynmrstar.entry.Entry]], auth_tag: Optional[bool] = False, data_set_id: Optional[Union[str, List[str]]] = None) → dict¶

Extracts chemical shift information from one or more PyNMRSTAR entry object

Parameters

entry_objects (pynmrstar.Entry/list) – list of pynmrstar entry object or single entry object
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
data_set_id (str, optional) – User defined data set id defaults to None

Returns

Chemical shift dictionary {data_set_id:{chain_id:{seq_id:{atom_id:cs_value}},’seq_ids’:[1,2,3,4..]}}

Return type

dict

pybmrb.ChemicalShift.from_file(input_file_names: Union[str, List[str]], auth_tag: bool = False, data_set_id: Optional[Union[str, List[str]]] = None) → dict¶

Extracts chemical shift information one or more NMR-STAR files

Parameters

input_file_names (str/list) – list of NMR-STAR file names with full path or single file name with full path
auth_tag (bool, optional) – Use sequence numbers from _Atom_chem_shift.Auth_seq_ID instead of _Atom_chem_shift.Comp_index_ID in the NMR-STAR file/BMRB entry, defaults to False
data_set_id (str, optional) – User defined data set id defaults to None

Returns

Chemical shift dictionary {data_set_id:{chain_id:{seq_id:{atom_id:cs_value}},’seq_ids’:[1,2,3,4..]}}

Return type

dict

ChemicalShiftStatistics¶

This module fetches chunks of chemical shift data from BMRB database for given list of atoms or residues. It exports the chemical shift data for Histogram module. This module is not intended to call directly, but can be used for data mining.

pybmrb.ChemicalShiftStatistics.get_2d_chemical_shifts(residue: str, atom1: str, atom2: str, filtered: Optional[bool] = True, sd_limit: Optional[float] = 10, ambiguity1: Optional[Union[str, int]] = '*', ambiguity2: Optional[Union[str, int]] = '*', ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None) → tuple¶

Fetches chemical shift data for a given residue and combines the desired two atoms chemical shift value from the same residue as two dimensional list

Parameters

residue (str) – residue name in IUPAC format
atom1 (str) – atom name in IUPAC format
atom2 (str) – atom name in IUPAC format
filtered (bool, optional) – Filters values beyond (sd_limit)*(standard deviation) on both sides of the mean, defaults to True
sd_limit (float, optional) – scaling factor used to filter data based on standard deviation, defaults to 10.0
ambiguity1 (str, optional) – filter based on chemical shift ambiguity code for atom1, defaults to ‘*’ means no filter
ambiguity2 (str, optional) – filter based on chemical shift ambiguity code for atom2, defaults to ‘*’ means no filter
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None

Returns

tuple of lists (atom1_cs,atom2_cs as list)

Return type

tuple

pybmrb.ChemicalShiftStatistics.get_data(residue: str, atom: str, filtered: Optional[bool] = True, sd_limit: Optional[float] = 10.0, ambiguity: Optional[Union[str, int]] = '*', ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None, standard_amino_acids: Optional[bool] = True) → tuple¶

Fetches the data from BMRB-API for given residue and atom and filters based of the values provided in the parameters

Parameters

residue (str) – Residue name in IUPAC format; use ‘*’ for any residue
atom (str) – Atom name in IUPAC format; Wild card supported; example HB*; use ‘*’ for any atom
filtered (bool, optional) – Filters values beyond (sd_limit)*(standard deviation) on both sides of the mean, defaults to True
sd_limit (float, optional) – scaling factor used to filter data based on standard deviation, defaults to 10.0
ambiguity (str, optional) – filter based on chemical shift ambiguity code, defaults to * means no filter
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None
standard_amino_acids (bool, optional) – get data only form standard amino acids and nucleic acids when * is used for residue, defaults to True

Returns

column names and chemical shift data as tuple (columns,data)

Return type

tuple

pybmrb.ChemicalShiftStatistics.get_data_from_bmrb(residue: Optional[str] = None, atom: Optional[str] = None, list_of_atoms: Optional[Union[str, List[str]]] = None, filtered: Optional[bool] = True, sd_limit: Optional[float] = 10.0, ambiguity: Optional[Union[str, int]] = '*', ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None, standard_amino_acids: Optional[bool] = True) → tuple¶

Fetches the data from BMRB-API for given residue/list of residues (and/or) atom/list of atoms and: filters based of the values provided in the parameters

Parameters

residue (str) – Residue name in IUPAC format; use ‘*’ for any residue
atom (str) – Atom name in IUPAC format; Wild card supported; example HB*; use ‘*’ for any atom
list_of_atoms (list, optional) – list of atoms; example [‘ALA-CB’,’CYS-N’,’TYR-CB’], defaults to None
filtered (bool, optional) – Filters values beyond (sd_limit)*(standard deviation) on both sides of the mean, defaults to True
sd_limit (float, optional) – scaling factor used to filter data based on standard deviation, defaults to 10.0
ambiguity (str, optional) – filter based on chemical shift ambiguity code, defaults to ‘*’ means no filter
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None
standard_amino_acids (bool, optional) – get data only form standard amino acids and nucleic acids when ‘*’ is used for residue, defaults to True

Returns

column names and chemical shift data as tuple (columns,data)

Return type

tuple

pybmrb.ChemicalShiftStatistics.get_filtered_data_from_bmrb(residue: str, atom: str, filtering_rules: Optional[list], ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None, h_tolerance: Optional[float] = 0.1, c_tolerance: Optional[float] = 2.0, n_tolerance: Optional[float] = 2.0, standard_amino_acids: Optional[bool] = True) → list¶

Fetches the chemical shift data for a given residue and filters them using chemical shift values of other atoms in the same residue as a filter

Parameters

residue (str) – residue name in IUPAC format
atom (str) – atom name in IUPAC format
filtering_rules (list) – list of atoms and chemical shift values as tuples to use as a filter; example[(‘CA’,64.5),(‘H’,7.8)]
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None
h_tolerance (float, optional) – tolerance value in ppm to filter H chemical shifts. It will allow the chemical shift value given in the filtering_rules +/- tolerance, defaults to 0.1
c_tolerance (float, optional) – tolerance value in ppm to filter C chemical shifts, It will allow the chemical shift value given in the filtering_rules +/- tolerance, defaults to 2.0
n_tolerance (float, optional) – tolerance value in ppm to filter N chemical shifts, It will allow the chemical shift value given in the filtering_rules +/- tolerance, defaults to 2.0
standard_amino_acids (bool, optional) – get data only form standard amino acids and nucleic acids when ‘*’ is used for residue, defaults to True

Returns

chemical shift values as list

Return type

list

pybmrb.ChemicalShiftStatistics.get_statistics(residue: str, atom: str, list_of_atoms: Optional[Union[str, List[str]]] = None, filtered: Optional[bool] = True, sd_limit: Optional[float] = 10.0, ambiguity: Optional[Union[str, int]] = '*', ph_min: Optional[float] = None, ph_max: Optional[float] = None, t_min: Optional[float] = None, t_max: Optional[float] = None, standard_amino_acids: Optional[bool] = True, verbose: bool = False) → dict¶

Provides chemical shift statistics like Mean, Median, Standard deviation for a given residue/atom/list of atoms

Parameters

residue (str) – Residue name in IUPAC format; use ‘*’ for any residue
atom (str) – Atom name in IUPAC format; Wild card supported; example HB*; use ‘*’ for any atom
list_of_atoms (list, optional) – list of atoms; example [‘ALA-CB’,’CYS-N’,’TYR-CB’], defaults to None
filtered (bool, optional) – Filters values beyond (sd_limit)*(standard deviation) on both sides of the mean, defaults to True
sd_limit (float, optional) – scaling factor used to filter data based on standard deviation, defaults to 10.0
ambiguity (str, optional) – filter based on chemical shift ambiguity code, defaults to ‘*’ means no filter
ph_min (float, optional) – minimum value for the filter based on PH value, defaults to None
ph_max (float, optional) – maximum value for the filter based on PH value, defaults to None
t_min (float, optional) – minimum value for the filter based on temperature value, defaults to None
t_max (float, optional) – maximum value for the filter based on temperature value, defaults to None
standard_amino_acids (bool, optional) – get data only form standard amino acids and nucleic acids when ‘*’ is used for residue, defaults to True
verbose (bool, optional) – display the statistics on screen; defaults to False

Returns

chemical shift statistics as a dictionary

Return type

dict