schrodinger.application.desmond.fep_edge_report_maker module

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.FEPEdgeReportMaker(fep_edge_data, basename=None, perturbation_type='small_molecule')

Bases: object

HELIX = 'helix'
STRAND = 'strand'
HELIX_COLOR = '#F06040'
STRAND_COLOR = '#40C0E0'
B_FACTOR = '#9400D3'
VERBOSE = False
report()
get_rest_density_text
get_rest_density_plot(rest_density_data, legend=True)
get_rest_density_img(rest_density_data, legend=True)
get_structure_item(st)

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

Parameters:st – Structure to draw in 2D

@typr st: structure.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)

Returns structure scenes for two 2d ligands with annotations.

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)

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 of torsions from ligand 1.
  • tors2 (list) – 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.
Type:

list
get_torsions_plot(tors1, tors2, tors_from, tors_to, for_print=False)
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 :param for_print: return an image for PDF if True otherwise return

matplotlib object
Parameters:
  • 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_2d_ligand_image(lig_st)
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.

report()
get_2d_tors_annotated_lig_pair(tors1, tors2, tors_from, tors_to)

Returns structure scenes for two 2d ligands with annotations.