Class FEPEdgeReportMaker

Convert ligand_st to Canvas 2d structure

Parameters:

• ligand_st (schrodinger.structure) - Ligand structure

Returns: canvas2d.ChmMol

Canvas molecule

`res_label' for water-mediated interactions looks like this:
   (0.610, 'B:LEU_52:O', [-7.148, -19.094, -5.2140861], 3702)
   (freq, prot_label, prot_xyz, ligand_aid)

`res_label` for non-specific hydrophobic interactions looks like this:
 (0.801, 'B:LEU_52', [-5.9, -21.1, -5.4],
                            [3694, 3695, 3696, 3709, 3710, 3711])
    (freq, prot_label, [prot_xyz], fragment_aids)

`res_label` for pi-cat interactions looks like this:
 (0.16, 'B:ARG_77:CZ', [-5.9, -11.1, -5.9], [698, 699, 701, 702, 700])
    (freq, prot_label, [prot_xyz], lig_ring_aids)
in case the aromatic group is on the protein, and charged group on the
ligand:
 (1.0, 'B:TYR_99', [13.404797, 3.522047, 15.211519], 2945)
  (freq, prot_label (aromatic) , [prot_xyz], ligand_aid)

`res_label` for pi-pi interactions looks like this:
 (0.068, 'B:TYR_14', [4.0, -22.1, -8.7], [3698, 3699, 3701, 3702, 3700],
                                                                    0.0)
   (freq, prot_label, [Calpha_xyz], ligand_rings_aid, f2f_fraction)

`res_label' for metal-protein mediated interactions looks like this:
 (1.0, 'A:ASP_116:OD1', 1511, [9.3, 17.1, -3.8], 1, [7.4, 16.6, -5.2])
   (freq, prot_label, Calpha_aid, [Calpha_xyz], metal_aid,
                                            metal_label, metal_xyz)

`res_label' for metal-ligand mediated interactions looks like this:
 (1.0, 'L-FRAG_0:O1754', 1754, [9.4, 16.6, -7.0], 1, [7.4, 16.6, -5.2])
   (freq, lig_label, [ligand_xyz], metal_aid, metal_label, metal_xyz)

res_label for internal (intramolecular) hydrogen bonds looks like this:
 (0.123, 4720, 4764)
 freq, lig_donor_aid, lig_acceptor_aid

res_label for ionic bonds looks like this:
 (0.0148, 'B:ARG_13:NH2', 180, [4.014, -2.630, 8.924], 2357)
 freq, prot_label, prot_aid, [prot_ xyz], lig_aid

res_label for hydrogen bonds looks like this:
 (0.40, 'A:LYS_97:HZ1', 2005, [-9.87, 7.35, -35.22], 'L-FRAG_0:O16', 16)
 frequency, prot_label  prot_aid,  [xyz], lig_label,  lig_aid

Setup overlay for SSE elements
@param ax:          matplotlib plot
@type  ax:          matplotlib.ax
@param data_limits: list of ranges for secondary structure elements
                    along the residue index
@type  data_limits: L{(from,to)}
@param color:       which color to use
@type  color:       matplotlib color, either string or hex

Add B factor to the plot, on the Y2 axis. scale the Y2 axis to be compatible with Y1 axis.

Parameters:

• ax2 (matplotlib.ax (twinx/Y2 axis)) - matplotlib plot
• b_data (dict) - dictionary with b factor values for each residue
• color (matplotlib color, either string or hex) - which color to use
• y_range_ratio (float) - a ratio by which to scale the Y2-axis
• fsize (int) - font size to use in plots

Returns: str

a title of the plot for legends

Draw a vertical bar for reisdues that interact with the ligand

Parameters:

• ax (matplotlib.ax) - matplotlib plot
• show_res (int) - residues index to add the vbar to
• vals (float) - the hight of the vbar
• color (matplotlib color, either string or hex) - which color to use
• ymin (float) - the starting y-position of the bar

Given an matplotlib ax object, setup the plot
@param rmsf_l0:      list of rmsf valuse for protein in lambda0 sim
@type  rmsf_l0:      L{float}
@param rmsf_l1:      list of rmsf valuse for protein in lambda1 sim
@type  rmsf_l1:      L{float}
@param sse_l0:       A dictionary with 'helix' and 'strand' values which
                     contain limits of all the SSE in lambda0 protein
@type  sse_l0:       dict{'helix_limits', 'strand_limits'}
@param sse_l1:       A dictionary with 'helix' and 'strand' values which
                     contain limits of all the SSE in lambda1 protein
@type  sse_l1:       dict{'helix_limits', 'strand_limits'}
@param b_factor:     dictionary of b factor values for each residue
@type  b_factor:     dict{'residue_id'}
@param contact_data: a dictionary with residue indices that correspond
                     to different contacts for ligand1, ligand2, and
                      common
@type  contact_data: dict{'common', 'uniq_lig1', 'uniq_lig2'}
@param show_res_type: to show contact residues
@type  show_res_type: bool

Parameters:

• rmsd_l0 (float) - list of RSMD values in angstroms for lambda=0
• rmsd_l1 (float) - list of RSMD values in angstroms for lambda=1
• ts (float) - list of simulation times for each snapshot
• ts_max (float) - simulation time
• names (str) - List of names that that are in the legend
• ylabel (str) - Label that goes on the y-axis
• y_inch (float) - height of the image returned
• for_print (bool) - Bool if the figure will be used for print

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