Copyright Schrodinger, LLC. All rights reserved.
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convert_ct_to_2d(ligand_st,
output_file_name_prefix,
parameters={}) |
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| generate_twod_and_paths_data(ligand_st,
output_file_name_prefix,
parameters) |
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render_2d_image(ligand_st,
output_file_name_prefix,
twod_and_paths,
parameters={},
return_rmsd_times_data=True,
progress_callback=None,
sketcher=None) |
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| find_spot_for_residue(res_placements,
res_uid,
min_distance_for_line,
new_all_uids_to_check,
all_res_lines_to_check,
pic_center,
residue_radius,
final_image_dim,
all_ligand_bonds,
all_ligand_atom_placements,
ligand_rings,
parameters,
all_hbonds,
all_hbonds_wat_prot,
all_overlapped_res_found_spot,
all_atoms_overlapped_within_watermap_ids,
number_vectors=10,
move_factor=0.75) |
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| spread_residues_if_overlapped(res_placements,
res_uid1,
res_uid2,
residue_radius,
final_image_dim,
all_ligand_bonds,
all_ligand_atom_placements,
ligand_rings,
parameters) |
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move_residue_away_from_hbond(res_placements,
res_uid,
from_res_uid,
ligpt,
rr,
final_image_dim,
all_ligand_bonds,
all_ligand_atom_placements,
ligand_rings,
parameters,
all_hbonds,
all_pipi_stacking,
all_picats,
max_loop=8,
all_uids_avoided=set([])) |
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| initialize_res_placements_to_screen(res_placements,
ct_scale,
pic_center,
pic_info,
sketcher_best_2D=False) |
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| check_hbond_distance_and_move_away(res_placements,
from_res_uid,
ligpt,
min_distance_for_line,
atom_label_bbx) |
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| compute_all_hbond_res_overlaps(parameters,
all_hbond_res_overlaps,
res_placements,
residue_radius,
all_hbonds,
all_hbonds_wat_prot,
all_pipi_stacking,
all_picats,
no) |
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| compute_residue_overlaps(all_uids_to_check,
res_placements,
residue_diameter) |
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| compute_residue_overlap(res_uid1,
res_placements,
residue_diameter) |
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move_residues(final_image_dim,
res_placements,
pic_info,
pic_center,
ct_scale,
residue_radius,
all_hbonds,
all_hbonds_wat_prot,
all_ligand_atom_placements,
all_ligand_bonds,
all_pipi_stacking,
all_picats,
ligand_rings,
move=False,
parameters={},
all_atoms_not_overlapped_but_over_atom=None,
all_atoms_overlapped_within_watermap_ids=None,
sketcher_best_2D=False) |
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| fill_parameters(parameters) |
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| determine_image_size_and_ligand_position(dim_arg,
final_image_dim,
res_placements_2d_bbx,
residue_radius) |
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generate_lid_picture_draw(lidobj,
painter,
pic_info,
parameters,
final_image_dim,
ct3d_atoms,
best_ct,
pic_2d_center,
all_hbonds,
all_hbonds_wat_prot,
all_pipi_stacking,
all_picats,
ct_scale,
residue_radius,
res_placements,
complex_st,
lig_H_to_non,
lig_atom_elements,
ligand_rings,
atom_to_solv_exposure,
all_residues,
all_cofactors_uids,
all_waters,
all_metals,
all_ligand_bonds,
all_atoms_within_watermap=[],
all_atoms_included_within_watermap=None,
all_atoms_selected_within_watermap=None,
all_atoms_overlapped_within_watermap=None,
hydration_sites_to_color=None,
move=True,
rotation=None,
sketcher=None,
sketcher_all_res=None,
sketcher_all_metals=None,
sketcher_all_waters=None,
workspace_vm=[]) |
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generate_2D_image_from_protein_ligand(lidobj,
prot_st,
ligand_st,
prefix='out',
parameters={},
generate_3d_img=False,
render_data=None,
complex_info=None,
image_size=[800.0, 600.0],
outdir='',
progress_callback=None,
all_atoms_included_within_watermap=None,
all_atoms_selected_within_watermap=None,
all_atoms_overlapped_within_watermap=None,
hydration_sites_to_color=None,
workspace_vm=None,
sketcher=None) |
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| LigandInteractionDiagram_from_split_file(file_name) |
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| LigandInteractionDiagram_from_complex(complex_st,
app=None,
chooseLigandCallback=None) |
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| LigandInteractionDiagram_from_complex_file(file_name,
app=None,
chooseLigandCallback=None) |
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| LigandInteractionDiagram_from_either(file_name,
app=None,
chooseLigandCallback=None) |
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| LigandInteractionDiagram_from_either_ct(cts,
app=None,
chooseLigandCallback=None) |
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__doc__ = ... |
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_version = '$Revision: 1.0 $' |
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usage = '\nligand_interaction_diagram.py\n$Revision: 1.0 $\n\n... |
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_canvas_license = <C ChmLicenseShared instance at _9059bb0f000...
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handler = logging.StreamHandler(sys.stdout)
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epsilon = 1e-15
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epsilons = 1e-05
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red = [255, 0, 0, 255] |
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keep_center = False
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relative_to_ligand_scale = False
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move_and_scale = True
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pipi_c = [[QtGui.QColor(0, 140, 70, 255), QtGui.QColor(128, 19...
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pipi_c_bw = convert_color_list_to_bw(pipi_c)
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picat_c = [[QtGui.QColor(224, 143, 26, 255), QtGui.QColor(234,...
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picat_c_bw = convert_color_list_to_bw(pipi_c)
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pipi_colors = [pipi_c, pipi_c_bw]
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picat_colors = [picat_c, picat_c_bw]
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need_next_arg = {'-background': 'white|black|trans', '-docsize... |
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no_next_arg = set(['-1letter', '-bw', '-legacy', '-pwhbonds', ... |
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__package__ = 'schrodinger.application.lid' |
