schrodinger.application.desmond.fep_edge_report_maker module¶
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schrodinger.application.desmond.fep_edge_report_maker.
create_sketcher
()¶
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schrodinger.application.desmond.fep_edge_report_maker.
parse_res_tag
(label)¶
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schrodinger.application.desmond.fep_edge_report_maker.
get_residue_label
(rname, resid, cname)¶
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schrodinger.application.desmond.fep_edge_report_maker.
get_opacity
(opacity_val)¶
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class
schrodinger.application.desmond.fep_edge_report_maker.
FEPEdgeReportMaker
(fep_edge_data, basename=None, perturbation_type='small_molecule')¶ Bases:
object
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HELIX
= 'helix'¶
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STRAND
= 'strand'¶
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HELIX_COLOR
= '#F06040'¶
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STRAND_COLOR
= '#40C0E0'¶
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B_FACTOR
= '#9400D3'¶
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VERBOSE
= False¶
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__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 reportParameters: - basename (string) – the basename of the file of the PDF report
- perturbation_type (str) – Type of PRM job it was
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report
()¶
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get_rest_density_text
¶
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get_rest_density_plot
(rest_density_data, legend=True)¶
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get_rest_density_img
(rest_density_data, legend=True)¶
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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
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get_2d_tors_annotated_lig_pair
(tors1, tors2, tors_from, tors_to)¶ Returns structure scenes for two 2d ligands with annotations.
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remove_last_atom_highlight
(lig_item)¶ Removes previously highlighted atoms, if any, in a torsion.
Parameters: lig_item ( structure2d.structure_item
) – Ligand structure item.
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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
- lig_item (
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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
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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
- fig (
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get_torsions_plot
(tors1, tors2, tors_from, tors_to, for_print=False)¶
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gen_protein_rmsf_image
(rmsf_l0, rmsf_l1, sse_l0, sse_l1, b_factor, contact_data, show_res_type=None)¶
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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 objectParameters: - 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
- fig (
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get_2d_ligand_image
(lig_st)¶
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error
(msg)¶
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str
(str_in)¶ This is to remove the “‘s in ARK returned strings enclosed in double quotes
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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.
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__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 reportParameters: - basename (string) – the basename of the file of the PDF report
- perturbation_type (str) – Type of PRM job it was
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report
()¶
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get_2d_tors_annotated_lig_pair
(tors1, tors2, tors_from, tors_to)¶ Returns structure scenes for two 2d ligands with annotations.
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B_FACTOR
= '#9400D3'¶
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HELIX
= 'helix'¶
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HELIX_COLOR
= '#F06040'¶
-
STRAND
= 'strand'¶
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STRAND_COLOR
= '#40C0E0'¶
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VERBOSE
= False¶
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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
- lig_item (
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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
- fig (
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error
(msg)¶
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gen_protein_rmsf_image
(rmsf_l0, rmsf_l1, sse_l0, sse_l1, b_factor, contact_data, show_res_type=None)¶
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get_2d_ligand_image
(lig_st)¶
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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 objectParameters: - 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
- fig (
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get_rest_density_img
(rest_density_data, legend=True)¶
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get_rest_density_plot
(rest_density_data, legend=True)¶
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get_rest_density_text
¶
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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
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get_torsions_plot
(tors1, tors2, tors_from, tors_to, for_print=False)¶
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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
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remove_last_atom_highlight
(lig_item)¶ Removes previously highlighted atoms, if any, in a torsion.
Parameters: lig_item ( structure2d.structure_item
) – Ligand structure item.
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str
(str_in)¶ This is to remove the “‘s in ARK returned strings enclosed in double quotes
-