schrodinger.application.desmond.fep_edge_report_maker module¶

exception schrodinger.application.desmond.fep_edge_report_maker.InconsistentDataException¶

Bases: Exception

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.desmond.fep_edge_report_maker.create_sketcher()¶

schrodinger.application.desmond.fep_edge_report_maker.parse_res_tag(label)¶

schrodinger.application.desmond.fep_edge_report_maker.get_residue_label(rname, resid, cname)¶

schrodinger.application.desmond.fep_edge_report_maker.get_opacity(opacity_val)¶

class schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase(fep_edge_data, basename=None, perturbation_type=None)¶

Bases: object

Base class for all remport makers

VERBOSE = False¶

__init__(fep_edge_data, basename=None, perturbation_type=None)¶

This a base class for generating various types of reports.

Parameters

fep_edge_data (FEPEdgeData) – Object containing all the data for this report
basename (string) – the basename of the file of the PDF report
perturbation_type (str) – FEP_TYPE value

get_2d_ligand_image(lig_st)¶

get_rest_density_img(rest_density_data, legend=True, size_ratio=1.0)¶

get_rest_density_plot(rest_density_data, legend=True, for_print=False)¶

property get_rest_density_text¶

get_torsions_plot(tors1, tors2, tors_from, tors_to, for_print=False)¶

get_structure_item(st, rect=None)¶

Returns structure as a graphic item to draw and to annotate.

Parameters

st (structure.Structure) – Structure to draw in 2D
rect (QtCore.QRectF) – Rectangle (bounding box) for the structure

Returns

Structure item to be drawn in 2D.

Return type

structure2d.structure_item

get_2d_tors_annotated_lig_pair(tors1, tors2, tors_from, tors_to, rect=None)¶: Returns structure scenes for two 2d ligands with annotations.

class schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker(fep_edge_data, basename=None, perturbation_type='small_molecule')¶

Bases: schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase

HELIX = 'helix'¶

STRAND = 'strand'¶

HELIX_COLOR = '#F06040'¶

STRAND_COLOR = '#40C0E0'¶

B_FACTOR = '#9400D3'¶

LIGAND_TORSION_TEXT = '\n Rotatable bonds (Rb) in both ligands are enumerated and color-coded. For\n each Rb, a representative dihedral angle is monitored throughout the\n complex and solvent simulation legs, their distributions are then\n plotted. Hollow bars show solvent and filled bars show\n complex leg distributions. Input starting conformation is marked\n as a gray vertical line.\n Potential energy around each Rb overlays the plot with the dark-blue\n curve and corresponding labels on the Y-axis. Local strain energies are\n shown below the plot. The units are in kcal/mol.\n '¶

__init__(fep_edge_data, basename=None, perturbation_type='small_molecule')¶

This class generates a PDF report for an FEP/REST (+) type of job. Both Legs of the simulations are processed in the FEPEdgeData and is used by this class to compile a result. :type fep_edge_data: FEPEdgeData :param fep_edge_data: Object containing all the data for this report

Parameters

basename (string) – the basename of the file of the PDF report
perturbation_type (str) – Type of FEP job it was

report()¶

property get_rest_density_text¶

remove_last_atom_highlight(lig_item)¶

Removes previously highlighted atoms, if any, in a torsion.

Parameters: lig_item (structure2d.structure_item) – Ligand structure item.

add_atom_highlight(lig_item, torsion, color)¶

Add new highlight for atoms in the given torsion.

Parameters

lig_item (structure2d.structure_item) – Ligand structure item.
torsion (fep_edge_data.FEPTorsions) – Ligand torsion to highlight
color (QtGui.QColor) – Highlight color

on_move(event)¶

The mpl_connect motion_notify_event slot for the torsion plot figure canvas.

If the mouse is inside a torsion plot, highlight the 1st and 4th atoms in that torsion in the structure.

Because torsions can spread to multiple tabs (or pages), need to access figure and structure items for each tab.

Parameters: event (matplotlib.backend_bases.MouseEvent) – The mouse event that triggered this callback

create_torsions_plot(fig, tors1, tors2, tors_from, tors_to, ipage=None, structure1_item=None, structure2_item=None, for_print=False)¶

Creates a plot for torsions using the given matplot figure.

Parameters

fig (matplotlib.figure.Figure) – Figure to draw the torsion subplots in.
tors1 (list[fep_edge_data.FEPTorsions]) – List of torsions from ligand 1.
tors2 (list[fep_edge_data.FEPTorsions]) – List of torsions from ligand 2.
tors_from (int) – Starting torsion index.
tors_to (int) – Ending torsion index
ipage (int or None) – Page index of the torsions, only needed for interactively highlighting torsion atoms.
structure1_item (structure2d.structure_item or None) – Structure item 1, only needed for interactively highlighting torsion atoms.
structure2_item (structure2d.structure_item or None) – Structure item 2, only needed for interactively highlighting torsion atoms.
for_print (bool) – Whether the figure is used for print.

Returns

A list of the energy line plot axes

Return type

list[matplotlib.axes.Axes]

gen_protein_rmsf_image(rmsf_l0, rmsf_l1, sse_l0, sse_l1, b_factor, contact_data, show_res_type=None)¶

get_protein_rmsf(for_print=True, fig=None, show_sse=False, show_b_factor=False, show_interacting_residues=(False, False, False))¶

This function returns either an img or a matplotlib object of protein RMSF plot

Parameters

for_print (bool) – return an image for PDF if True otherwise return matplotlib object
fig (matplotlib.figure.Figure) – matplotlib Figure object
show_sse (bool) – overlay secondary structure information on RMSF plot
show_b_factor (bool) – overlay b factor on the y2 axis
show_interacting_residues ((common, uniq_lig1, uniq_lig2)) – a tuple with residue indices that correspond to different contacts for ligand1, ligand2, and common

Returns

returns either an image or an matplotlib object, depends on the for_print variable

Return type

image | matplotlib ax obj

error(msg)¶

str(str_in)¶: This is to remove the “‘s in ARK returned strings enclosed in double quotes

VERBOSE = False¶

get_2d_ligand_image(lig_st)¶

get_2d_tors_annotated_lig_pair(tors1, tors2, tors_from, tors_to, rect=None)¶: Returns structure scenes for two 2d ligands with annotations.

get_rest_density_img(rest_density_data, legend=True, size_ratio=1.0)¶

get_rest_density_plot(rest_density_data, legend=True, for_print=False)¶

get_structure_item(st, rect=None)¶

Returns structure as a graphic item to draw and to annotate.

Parameters

st (structure.Structure) – Structure to draw in 2D
rect (QtCore.QRectF) – Rectangle (bounding box) for the structure

Returns

Structure item to be drawn in 2D.

Return type

structure2d.structure_item

get_torsions_plot(tors1, tors2, tors_from, tors_to, for_print=False)¶

class schrodinger.application.desmond.fep_edge_report_maker.PRMEdgeReportMaker(fep_edge_data, basename=None, perturbation_type='small_molecule')¶

Bases: schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker

This class generates a PDF report for FEP+ for protein residue mutation.

LIGAND_TORSION_TEXT = '\n Rotatable bonds (Rb) of a ligand in each end point lambda windows are\n enumerated and color-coded. For each Rb, a representative dihedral angle\n is monitored throughout the simulation for both complex and solvent\n legs. The distributions of these conformations is then plotted for each\n Rb. In addition, potential energy around each Rb overlays the histograms\n with the dark-blue curve and corresponding labels on the Y-axis.\n The energy units are reported in kcal/mol.\n '¶

__init__(fep_edge_data, basename=None, perturbation_type='small_molecule')¶

This class generates a PDF report for an FEP/REST (+) type of job. Both Legs of the simulations are processed in the FEPEdgeData and is used by this class to compile a result. :type fep_edge_data: FEPEdgeData :param fep_edge_data: Object containing all the data for this report

Parameters

basename (string) – the basename of the file of the PDF report
perturbation_type (str) – Type of PRM job it was

report()¶

B_FACTOR = '#9400D3'¶

HELIX = 'helix'¶

HELIX_COLOR = '#F06040'¶

STRAND = 'strand'¶

STRAND_COLOR = '#40C0E0'¶

VERBOSE = False¶

add_atom_highlight(lig_item, torsion, color)¶

Add new highlight for atoms in the given torsion.

Parameters

lig_item (structure2d.structure_item) – Ligand structure item.
torsion (fep_edge_data.FEPTorsions) – Ligand torsion to highlight
color (QtGui.QColor) – Highlight color

create_torsions_plot(fig, tors1, tors2, tors_from, tors_to, ipage=None, structure1_item=None, structure2_item=None, for_print=False)¶

Creates a plot for torsions using the given matplot figure.

Parameters

fig (matplotlib.figure.Figure) – Figure to draw the torsion subplots in.
tors1 (list[fep_edge_data.FEPTorsions]) – List of torsions from ligand 1.
tors2 (list[fep_edge_data.FEPTorsions]) – List of torsions from ligand 2.
tors_from (int) – Starting torsion index.
tors_to (int) – Ending torsion index
ipage (int or None) – Page index of the torsions, only needed for interactively highlighting torsion atoms.
structure1_item (structure2d.structure_item or None) – Structure item 1, only needed for interactively highlighting torsion atoms.
structure2_item (structure2d.structure_item or None) – Structure item 2, only needed for interactively highlighting torsion atoms.
for_print (bool) – Whether the figure is used for print.

Returns

A list of the energy line plot axes

Return type

list[matplotlib.axes.Axes]

error(msg)¶

gen_protein_rmsf_image(rmsf_l0, rmsf_l1, sse_l0, sse_l1, b_factor, contact_data, show_res_type=None)¶

get_2d_ligand_image(lig_st)¶

get_2d_tors_annotated_lig_pair(tors1, tors2, tors_from, tors_to, rect=None)¶: Returns structure scenes for two 2d ligands with annotations.

get_protein_rmsf(for_print=True, fig=None, show_sse=False, show_b_factor=False, show_interacting_residues=(False, False, False))¶

This function returns either an img or a matplotlib object of protein RMSF plot

Parameters

for_print (bool) – return an image for PDF if True otherwise return matplotlib object
fig (matplotlib.figure.Figure) – matplotlib Figure object
show_sse (bool) – overlay secondary structure information on RMSF plot
show_b_factor (bool) – overlay b factor on the y2 axis
show_interacting_residues ((common, uniq_lig1, uniq_lig2)) – a tuple with residue indices that correspond to different contacts for ligand1, ligand2, and common

Returns

returns either an image or an matplotlib object, depends on the for_print variable

Return type

image | matplotlib ax obj

get_rest_density_img(rest_density_data, legend=True, size_ratio=1.0)¶

get_rest_density_plot(rest_density_data, legend=True, for_print=False)¶

property get_rest_density_text¶

get_structure_item(st, rect=None)¶

Returns structure as a graphic item to draw and to annotate.

Parameters

st (structure.Structure) – Structure to draw in 2D
rect (QtCore.QRectF) – Rectangle (bounding box) for the structure

Returns

Structure item to be drawn in 2D.

Return type

structure2d.structure_item

get_torsions_plot(tors1, tors2, tors_from, tors_to, for_print=False)¶

on_move(event)¶

The mpl_connect motion_notify_event slot for the torsion plot figure canvas.

If the mouse is inside a torsion plot, highlight the 1st and 4th atoms in that torsion in the structure.

Because torsions can spread to multiple tabs (or pages), need to access figure and structure items for each tab.

Parameters: event (matplotlib.backend_bases.MouseEvent) – The mouse event that triggered this callback

remove_last_atom_highlight(lig_item)¶

Removes previously highlighted atoms, if any, in a torsion.

Parameters: lig_item (structure2d.structure_item) – Ligand structure item.

str(str_in)¶: This is to remove the “‘s in ARK returned strings enclosed in double quotes

class schrodinger.application.desmond.fep_edge_report_maker.ABFEPReportMaker(fep_edge_data, basename=None, perturbation_type='small_molecule')¶

Bases: schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker

report()¶

create_torsions_plot(fig, tors1, tors2, tors_from, tors_to, ipage=None, structure1_item=None, structure2_item=None, for_print=False)¶

Creates a plot for torsions using the given matplot figure.

Parameters

fig (matplotlib.figure.Figure) – Figure to draw the torsion subplots in.
tors1 (list[fep_edge_data.FEPTorsions]) – List of torsions from ligand 1.
tors2 (list[fep_edge_data.FEPTorsions]) – List of torsions from ligand 2.
tors_from (int) – Starting torsion index.
tors_to (int) – Ending torsion index
ipage (int or None) – Page index of the torsions, only needed for interactively highlighting torsion atoms.
structure1_item (structure2d.structure_item or None) – Structure item 1, only needed for interactively highlighting torsion atoms.
structure2_item (structure2d.structure_item or None) – Structure item 2, only needed for interactively highlighting torsion atoms.
for_print (bool) – Whether the figure is used for print.

Returns

A list of the energy line plot axes

Return type

list[matplotlib.axes.Axes]

on_move(event)¶

The mpl_connect motion_notify_event slot for the torsion plot figure canvas.

If the mouse is inside a torsion plot, highlight the 1st and 4th atoms in that torsion in the structure.

Because torsions can spread to multiple tabs (or pages), need to access figure and structure items for each tab.

Parameters: event (matplotlib.backend_bases.MouseEvent) – The mouse event that triggered this callback

B_FACTOR = '#9400D3'¶

HELIX = 'helix'¶

HELIX_COLOR = '#F06040'¶

LIGAND_TORSION_TEXT = '\n Rotatable bonds (Rb) in both ligands are enumerated and color-coded. For\n each Rb, a representative dihedral angle is monitored throughout the\n complex and solvent simulation legs, their distributions are then\n plotted. Hollow bars show solvent and filled bars show\n complex leg distributions. Input starting conformation is marked\n as a gray vertical line.\n Potential energy around each Rb overlays the plot with the dark-blue\n curve and corresponding labels on the Y-axis. Local strain energies are\n shown below the plot. The units are in kcal/mol.\n '¶

STRAND = 'strand'¶

STRAND_COLOR = '#40C0E0'¶

VERBOSE = False¶

__init__(fep_edge_data, basename=None, perturbation_type='small_molecule')¶

This class generates a PDF report for an FEP/REST (+) type of job. Both Legs of the simulations are processed in the FEPEdgeData and is used by this class to compile a result. :type fep_edge_data: FEPEdgeData :param fep_edge_data: Object containing all the data for this report

Parameters

basename (string) – the basename of the file of the PDF report
perturbation_type (str) – Type of FEP job it was

add_atom_highlight(lig_item, torsion, color)¶

Add new highlight for atoms in the given torsion.

Parameters

lig_item (structure2d.structure_item) – Ligand structure item.
torsion (fep_edge_data.FEPTorsions) – Ligand torsion to highlight
color (QtGui.QColor) – Highlight color

error(msg)¶

gen_protein_rmsf_image(rmsf_l0, rmsf_l1, sse_l0, sse_l1, b_factor, contact_data, show_res_type=None)¶

get_2d_ligand_image(lig_st)¶

get_2d_tors_annotated_lig_pair(tors1, tors2, tors_from, tors_to, rect=None)¶: Returns structure scenes for two 2d ligands with annotations.

get_protein_rmsf(for_print=True, fig=None, show_sse=False, show_b_factor=False, show_interacting_residues=(False, False, False))¶

This function returns either an img or a matplotlib object of protein RMSF plot

Parameters

for_print (bool) – return an image for PDF if True otherwise return matplotlib object
fig (matplotlib.figure.Figure) – matplotlib Figure object
show_sse (bool) – overlay secondary structure information on RMSF plot
show_b_factor (bool) – overlay b factor on the y2 axis
show_interacting_residues ((common, uniq_lig1, uniq_lig2)) – a tuple with residue indices that correspond to different contacts for ligand1, ligand2, and common

Returns

returns either an image or an matplotlib object, depends on the for_print variable

Return type

image | matplotlib ax obj

get_rest_density_img(rest_density_data, legend=True, size_ratio=1.0)¶

get_rest_density_plot(rest_density_data, legend=True, for_print=False)¶

property get_rest_density_text¶

get_structure_item(st, rect=None)¶

Returns structure as a graphic item to draw and to annotate.

Parameters

st (structure.Structure) – Structure to draw in 2D
rect (QtCore.QRectF) – Rectangle (bounding box) for the structure

Returns

Structure item to be drawn in 2D.

Return type

structure2d.structure_item

get_torsions_plot(tors1, tors2, tors_from, tors_to, for_print=False)¶

remove_last_atom_highlight(lig_item)¶

Removes previously highlighted atoms, if any, in a torsion.

Parameters: lig_item (structure2d.structure_item) – Ligand structure item.

str(str_in)¶: This is to remove the “‘s in ARK returned strings enclosed in double quotes

class schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker(fep_edge_data, basename=None, perturbation_type='solubility')¶

Bases: schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase

This class generates plots, images and PDF reports for Solubility FEP jobs.

VERBOSE = False¶

TORSIONS_PER_PAGE = 10¶

__init__(fep_edge_data, basename=None, perturbation_type='solubility')¶

This class generates a PDF report for an FEP/REST (+) type of job. Both Legs of the simulations are processed in the FEPEdgeData and is used by this class to compile a result. :type fep_edge_data: FEPEdgeData :param fep_edge_data: Object containing all the data for this report

Parameters

basename (string) – the basename of the file of the PDF report
perturbation_type (str) – FEP Type

report()¶

get_torsions_plot(all_tors, tors_from, tors_to, for_print=False)¶

create_torsions_plot(fig, all_tors, tors_from, tors_to, for_print=False)¶

Creates a plot for torsions using the given matplot figure.

Parameters

fig (matplotlib.figure.Figure) – Figure to draw the torsion subplots in.
tors (list[list[[fep_edge_data.FEPTorsions]]) – a List of List of torsions from each sublimation leg.
tors_from (int) – Starting torsion index.
tors_to (int) – Ending torsion index
for_print (bool) – Whether the figure is used for print.

Returns

A list of the energy line plot axes

Return type

list[matplotlib.axes.Axes]

create_mol_env_fig(fig, for_print=False)¶

get_mol_series_plot(data, ylabel, for_print=True)¶

Parameters

data (List(Tuple)`) – a list of tuples for scatter plot [(x-vals, y-vals, lables)…]
ylabel (str) – Label that goes on the y-axis
for_print (bool) – Bool if the figure will be used for print

create_mol_series_fig(data, fig, ylabel, for_print=False)¶

get_2d_ligand_image(lig_st)¶

get_2d_tors_annotated_lig_pair(tors1, tors2, tors_from, tors_to, rect=None)¶: Returns structure scenes for two 2d ligands with annotations.

get_rest_density_img(rest_density_data, legend=True, size_ratio=1.0)¶

get_rest_density_plot(rest_density_data, legend=True, for_print=False)¶

property get_rest_density_text¶

get_structure_item(st, rect=None)¶

Returns structure as a graphic item to draw and to annotate.

Parameters

st (structure.Structure) – Structure to draw in 2D
rect (QtCore.QRectF) – Rectangle (bounding box) for the structure

Returns

Structure item to be drawn in 2D.

Return type

structure2d.structure_item