Package schrodinger :: Package application :: Package desmond :: Module fep_edge_report_maker :: Class PRMEdgeReportMaker

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Class PRMEdgeReportMaker

        object --+    
                 |    
FEPEdgeReportMaker --+
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                    PRMEdgeReportMaker

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

Instance Methods

__init__(self, fep_edge_data, basename=None, perturbation_type='small_molecule')
This class generates a PDF report for an FEP/REST (+) type of job.

report(self)

_ligand_details(self)

_fragment_perturbation_details(self)

_protein_ligand_report(self)

_get_pl_text(self)

_get_free_energy_convergence_text(self)

_get_ligand_torsion_text(self)

get_2d_tors_annotated_lig_pair(self, tors1, tors2, tors_from, tors_to)
Returns structure scenes for two 2d ligands with annotations.

_generate_2d_lig_images(self)
Generate 2d images of the ligands.

_generate_aligned_2d_lig_pair(self)
Generate *aligned* 2d images of the ligands.

_ligand_properties(self)

_protein_details(self)

_ligand_report(self)
Generate ligand report

Inherited from FEPEdgeReportMaker: add_atom_highlight, create_torsions_plot, error, gen_protein_rmsf_image, get_2d_ligand_image, get_protein_rmsf, get_rest_density_img, get_rest_density_plot, get_structure_item, get_torsions_plot, on_move, remove_last_atom_highlight, str

Inherited from FEPEdgeReportMaker (private): _add_b_factor, _add_interacting_residues, _add_sse_span, _align_chmmol, _b_factor_valid, _cleanup_temp_files, _create_pair_rmsd_fig, _create_pl_bar_fig, _free_energy_convergence_profiles, _gen_free_energy_convergence_fig, _gen_free_energy_convergence_plot, _gen_free_energy_convergence_table, _gen_protein_rmsf_ax, _get_2d_ligand_image, _get_aligned_chmmol, _get_annotated_2d_lig_img, _get_lid, _get_lid_img, _get_ligand_wrt_prot_rmsd_plot, _get_ligand_wrt_prot_rmsd_text, _get_pair_rmsd_plot, _get_plot_pl_bar_chart, _get_protein_lambda_rmsd_plot, _get_protein_rmsd_text, _get_protein_rmsf_text, _get_sequence_viewer_image, _get_temp_image_fn, _get_torsion_plot_img, _highlight_matching_torsion_atoms, _init_report, _ligand_perturbation_details, _ligand_rmsd_wrt_protein, _ligand_torsion_report, _load_modules, _protein_report, _protein_rmsd, _protein_rmsf, _reaction_details, _replica_exchange_density, _report_fep_simulation_details

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods

Inherited from FEPEdgeReportMaker (private): _lid_add_hbonds, _lid_add_hydrophobic, _lid_add_intramolecular_hb, _lid_add_ionic, _lid_add_lig_metal, _lid_add_lig_water_exposed, _lid_add_picat, _lid_add_pipi, _lid_add_prot_metal, _lid_add_water_br, _st_to_chmmol

Class Variables

Inherited from FEPEdgeReportMaker: B_FACTOR, HELIX, HELIX_COLOR, STRAND, STRAND_COLOR, VERBOSE

Properties

Inherited from FEPEdgeReportMaker: get_rest_density_text

Inherited from object: __class__

Method Details

init(self, fep_edge_data, basename=None, perturbation_type=`'small_molecule'`)
(Constructor)

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.

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) - Type of PRM job it was

Overrides: object.__init__

report(self)

Overrides: FEPEdgeReportMaker.report

_protein_ligand_report(self)

Overrides: FEPEdgeReportMaker._protein_ligand_report

_get_pl_text(self)

Overrides: FEPEdgeReportMaker._get_pl_text

_get_free_energy_convergence_text(self)

Overrides: FEPEdgeReportMaker._get_free_energy_convergence_text

_get_ligand_torsion_text(self)

Overrides: FEPEdgeReportMaker._get_ligand_torsion_text

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

Returns structure scenes for two 2d ligands with annotations.

Overrides: FEPEdgeReportMaker.get_2d_tors_annotated_lig_pair

_generate_2d_lig_images(self)

Generate 2d images of the ligands. Try to align them first, or just regular 2d images, if nothing works, return a string.

Overrides: FEPEdgeReportMaker._generate_2d_lig_images

_generate_aligned_2d_lig_pair(self)

Generate *aligned* 2d images of the ligands.

Overrides: FEPEdgeReportMaker._generate_aligned_2d_lig_pair

_ligand_properties(self)

Overrides: FEPEdgeReportMaker._ligand_properties

_protein_details(self)

Overrides: FEPEdgeReportMaker._protein_details

_ligand_report(self)

Generate ligand report

Overrides: FEPEdgeReportMaker._ligand_report