schrodinger.application.desmond.fep_edge_report_maker module¶
- exception schrodinger.application.desmond.fep_edge_report_maker.InconsistentDataException¶
Bases:
Exception
- 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 reportbasename (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 2Drect (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 <b>solvent</b> and filled bars show\n <b>complex</b> leg distributions. Input starting conformation is marked\n as a <font color="gray">gray</font> 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 <i>kcal/mol</i>.\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 highlightcolor (
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 objectshow_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
- 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 <i>Y</i>-axis.\n The energy units are reported in <i>kcal/mol</i>.\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()¶
- 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
- 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)¶