"""This is PyMOL script generated by PPI3D webserver.
Run it with PyMOL and explore the structure of protein-protein interface.

Usage:
  pymol script.py

Commands:
  show_interface()
  show_hydrogen_bonds()
  show_interface_ligands()
"""

from pymol.wizard import Wizard

cmd.load('https://bioinformatics.lt/ppi3d/downloads/example1/pdb_files/1_3l2p_A_1-3l2p_D_B_C_1.pdb')
chain_A_color = 'carbon' # PyMOL default
chain_B_color = 'cyan' # PyMOL default
chain_A_residues_color = 'lightorange'
chain_B_residues_color = 'lightmagenta'
cmd.set('seq_view', 'on')
cmd.set('label_position', '(2, 1, 2)')


def start():
    cmd.hide('all')
    cmd.show('cartoon')
    util.cbc()
    util.cnc()


def visualize(selection, how, color, labels):
    if selection in cmd.get_names('selections'):
        cmd.show(how, selection)
        cmd.color(color, selection)
        if labels:
            label_selection = '%s and name ca' % selection
            cmd.set('label_color', color, label_selection)
            cmd.label(label_selection, '"%s-%s" % (resn, resi)')
    else:
        return


def visualize_interface(what, how='sticks', labels=False, distances=False):
    global chain_A_residues_color
    global chain_B_residues_color
    start()
    suffix = ('_%s' % what) if what else ''
    a = 'A_interface%s' % suffix
    b = 'B_interface%s' % suffix
    visualize(a, how, chain_A_residues_color, labels)
    visualize(b, how, chain_B_residues_color, labels)
    if distances:
        cmd.delete('_distances')
        cmd.distance('_distances', a, b, mode=2)
    util.cnc()
    cmd.deselect()


cmd.select('A_interface', 'chain A and resi 190+191+192+193+229+231+232+233+234+235+236+237+238+241+245+301+302+303+304+331+332+334+335+336+337+338+339+340+341+351+355+398+399+400+401+407+411+423+424+425+426+440+441+442+444+445+446+447+450+473+487+488+491+492+493+494+582+583+584+585+588+590+592+593+613+614+615+616+617+622+623+640+641+642+643+644+645+646+647+648+649+703+704+705+707+708+712+713+714+715+716+717+718+719+720')
cmd.select('B_interface', 'chain B and resi 4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+27+28+29+30+31+32+33+34+35+36+37+38+39+40+41+42')
cmd.select('interface', 'A_interface or B_interface')
cmd.select('A_interface_H_bonds', 'chain A and resi 191+192+193+193+233+235+238+301+303+336+338+341+351+440+441+442+493+494+583+588+593+614+616+616+622+640+641+641+648+703+703')
cmd.select('B_interface_H_bonds', 'chain B and resi 41+40+41+42+30+29+29+19+20+9+8+8+7+32+34+32+16+16+6+34+35+11+9+10+11+13+12+13+38+13+14')
cmd.select('interface_H_bonds', 'A_interface_H_bonds or B_interface_H_bonds')
cmd.select('A_interface_ligands', 'chain A and resi 901')
cmd.select('interface_ligands', 'A_interface_ligands')


class PPI3D_Interface(Wizard):
    def show_interface(self):
        visualize_interface('')

    def show_hydrogen_bonds(self):
        visualize_interface('H_bonds', labels=True, distances=True)

    def show_interface_ligands(self):
        visualize_interface('ligands', 'spheres')

    def clear_labels(self):
        cmd.label('all', '')

    def get_panel(self):
        return [['1', 'PPI3D Interface', ''], ['2', 'Interface', 'cmd.get_wizard().show_interface()'], ['2', 'H-bonds', 'cmd.get_wizard().show_hydrogen_bonds()'], ['2', 'Interface ligands', 'cmd.get_wizard().show_interface_ligands()'], ['2', 'Clear labels', 'cmd.get_wizard().clear_labels()']]


start()
interface = PPI3D_Interface()
cmd.set_wizard(interface)
interface.show_interface()
cmd.extend('show_interface', lambda: interface.show_interface())
cmd.extend('show_hydrogen_bonds', lambda: interface.show_hydrogen_bonds())
cmd.extend('show_interface_ligands', lambda: interface.show_interface_ligands())
cmd.extend('clear_labels', lambda: interface.clear_labels())