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¶

__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()¶

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__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.fep_edge_report_maker', 'HELIX': 'helix', 'STRAND': 'strand', 'HELIX_COLOR': '#F06040', 'STRAND_COLOR': '#40C0E0', 'B_FACTOR': '#9400D3', 'VERBOSE': False, '__init__': <function FEPEdgeReportMaker.__init__>, '_load_modules': <function FEPEdgeReportMaker._load_modules>, 'report': <function FEPEdgeReportMaker.report>, '_cleanup_temp_files': <function FEPEdgeReportMaker._cleanup_temp_files>, '_init_report': <function FEPEdgeReportMaker._init_report>, '_replica_exchange_density': <function FEPEdgeReportMaker._replica_exchange_density>, 'get_rest_density_text': <property object>, 'get_rest_density_plot': <function FEPEdgeReportMaker.get_rest_density_plot>, 'get_rest_density_img': <function FEPEdgeReportMaker.get_rest_density_img>, '_protein_ligand_report': <function FEPEdgeReportMaker._protein_ligand_report>, '_get_lid_img': <function FEPEdgeReportMaker._get_lid_img>, '_st_to_chmmol': <staticmethod object>, '_align_chmmol': <function FEPEdgeReportMaker._align_chmmol>, '_get_aligned_chmmol': <function FEPEdgeReportMaker._get_aligned_chmmol>, '_get_lid': <function FEPEdgeReportMaker._get_lid>, '_lid_add_lig_water_exposed': <staticmethod object>, '_lid_add_water_br': <staticmethod object>, '_lid_add_hydrophobic': <staticmethod object>, '_lid_add_picat': <staticmethod object>, '_lid_add_pipi': <staticmethod object>, '_lid_add_prot_metal': <staticmethod object>, '_lid_add_lig_metal': <staticmethod object>, '_lid_add_intramolecular_hb': <staticmethod object>, '_lid_add_ionic': <staticmethod object>, '_lid_add_hbonds': <staticmethod object>, '_get_pl_text': <function FEPEdgeReportMaker._get_pl_text>, '_get_plot_pl_bar_chart': <function FEPEdgeReportMaker._get_plot_pl_bar_chart>, '_create_pl_bar_fig': <function FEPEdgeReportMaker._create_pl_bar_fig>, 'get_structure_item': <function FEPEdgeReportMaker.get_structure_item>, 'get_2d_tors_annotated_lig_pair': <function FEPEdgeReportMaker.get_2d_tors_annotated_lig_pair>, 'remove_last_atom_highlight': <function FEPEdgeReportMaker.remove_last_atom_highlight>, 'add_atom_highlight': <function FEPEdgeReportMaker.add_atom_highlight>, 'on_move': <function FEPEdgeReportMaker.on_move>, '_highlight_matching_torsion_atoms': <function FEPEdgeReportMaker._highlight_matching_torsion_atoms>, 'create_torsions_plot': <function FEPEdgeReportMaker.create_torsions_plot>, 'get_torsions_plot': <function FEPEdgeReportMaker.get_torsions_plot>, '_get_torsion_plot_img': <function FEPEdgeReportMaker._get_torsion_plot_img>, '_get_annotated_2d_lig_img': <function FEPEdgeReportMaker._get_annotated_2d_lig_img>, '_ligand_torsion_report': <function FEPEdgeReportMaker._ligand_torsion_report>, '_get_ligand_torsion_text': <function FEPEdgeReportMaker._get_ligand_torsion_text>, '_ligand_report': <function FEPEdgeReportMaker._ligand_report>, '_ligand_properties': <function FEPEdgeReportMaker._ligand_properties>, '_ligand_rmsd_wrt_protein': <function FEPEdgeReportMaker._ligand_rmsd_wrt_protein>, '_get_ligand_wrt_prot_rmsd_text': <function FEPEdgeReportMaker._get_ligand_wrt_prot_rmsd_text>, '_get_ligand_wrt_prot_rmsd_plot': <function FEPEdgeReportMaker._get_ligand_wrt_prot_rmsd_plot>, '_protein_report': <function FEPEdgeReportMaker._protein_report>, '_protein_rmsf': <function FEPEdgeReportMaker._protein_rmsf>, '_get_protein_rmsf_text': <function FEPEdgeReportMaker._get_protein_rmsf_text>, '_add_sse_span': <function FEPEdgeReportMaker._add_sse_span>, '_add_b_factor': <function FEPEdgeReportMaker._add_b_factor>, '_add_interacting_residues': <function FEPEdgeReportMaker._add_interacting_residues>, 'gen_protein_rmsf_image': <function FEPEdgeReportMaker.gen_protein_rmsf_image>, 'get_protein_rmsf': <function FEPEdgeReportMaker.get_protein_rmsf>, '_b_factor_valid': <function FEPEdgeReportMaker._b_factor_valid>, '_gen_protein_rmsf_ax': <function FEPEdgeReportMaker._gen_protein_rmsf_ax>, '_protein_rmsd': <function FEPEdgeReportMaker._protein_rmsd>, '_get_protein_rmsd_text': <function FEPEdgeReportMaker._get_protein_rmsd_text>, '_get_protein_lambda_rmsd_plot': <function FEPEdgeReportMaker._get_protein_lambda_rmsd_plot>, '_get_pair_rmsd_plot': <function FEPEdgeReportMaker._get_pair_rmsd_plot>, '_create_pair_rmsd_fig': <function FEPEdgeReportMaker._create_pair_rmsd_fig>, '_get_sequence_viewer_image': <function FEPEdgeReportMaker._get_sequence_viewer_image>, '_free_energy_convergence_profiles': <function FEPEdgeReportMaker._free_energy_convergence_profiles>, '_get_free_energy_convergence_text': <function FEPEdgeReportMaker._get_free_energy_convergence_text>, '_gen_free_energy_convergence_table': <function FEPEdgeReportMaker._gen_free_energy_convergence_table>, '_gen_free_energy_convergence_plot': <function FEPEdgeReportMaker._gen_free_energy_convergence_plot>, '_gen_free_energy_convergence_fig': <function FEPEdgeReportMaker._gen_free_energy_convergence_fig>, '_ligand_perturbation_details': <function FEPEdgeReportMaker._ligand_perturbation_details>, '_generate_2d_lig_images': <function FEPEdgeReportMaker._generate_2d_lig_images>, '_generate_aligned_2d_lig_pair': <function FEPEdgeReportMaker._generate_aligned_2d_lig_pair>, '_protein_details': <function FEPEdgeReportMaker._protein_details>, '_salt_details': <function FEPEdgeReportMaker._salt_details>, 'get_2d_ligand_image': <function FEPEdgeReportMaker.get_2d_ligand_image>, '_get_2d_ligand_image': <function FEPEdgeReportMaker._get_2d_ligand_image>, '_get_temp_image_fn': <function FEPEdgeReportMaker._get_temp_image_fn>, '_report_fep_simulation_details': <function FEPEdgeReportMaker._report_fep_simulation_details>, 'error': <function FEPEdgeReportMaker.error>, 'str': <function FEPEdgeReportMaker.str>, '__dict__': <attribute '__dict__' of 'FEPEdgeReportMaker' objects>, '__weakref__': <attribute '__weakref__' of 'FEPEdgeReportMaker' objects>, '__doc__': None})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.desmond.fep_edge_report_maker'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

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.