import nglview
import ipywidgets
import os

ligandCode = 'IBP'
mol_charge = 0
pH = 7.4

# Ligand: Download ligand structure from MMB PDB mirror REST API (https://mmb.irbbarcelona.org/api/)
# Import module
from biobb_io.api.ligand import ligand

# Create prop dict and inputs/outputs
input_structure = ligandCode + '.pdb'

prop = {
    'ligand_code' : ligandCode
}

#Create and launch bb
ligand(output_pdb_path=input_structure,
        properties=prop)

# Babel_add_hydrogens: add Hydrogen atoms to a small molecule
# Import module
from biobb_chemistry.babelm.babel_add_hydrogens import babel_add_hydrogens

# Create prop dict and inputs/outputs
output_babel_h = ligandCode + '.H.mol2' 

prop = {
    'ph' : pH,
    'input_format' : 'pdb',
    'output_format' : 'mol2'
}

#Create and launch bb
babel_add_hydrogens(input_path=input_structure,
                  output_path=output_babel_h,
                  properties=prop)

# Babel_minimize: Structure energy minimization of a small molecule after being modified adding hydrogen atoms
# Import module
from biobb_chemistry.babelm.babel_minimize import babel_minimize

# Create prop dict and inputs/outputs
output_babel_min = ligandCode + '.H.min.pdb'                              
prop = {
    'method' : 'sd',
    'criteria' : '1e-10',
    'force_field' : 'GAFF'
}


#Create and launch bb
babel_minimize(input_path=output_babel_h,
              output_path=output_babel_min,
              properties=prop)

# Acpype_params_gmx: Generation of topologies for GROMACS with ACPype
# Import module
from biobb_chemistry.acpype.acpype_params_gmx import acpype_params_gmx

# Create prop dict and inputs/outputs
output_acpype_gro = ligandCode + 'params.gro'
output_acpype_itp = ligandCode + 'params.itp'
output_acpype_top = ligandCode + 'params.top'
output_acpype = ligandCode + 'params'
prop = {
    'basename' : output_acpype,
    'charge' : mol_charge
}

#Create and launch bb
acpype_params_gmx(input_path=output_babel_min,
                output_path_gro=output_acpype_gro,
                output_path_itp=output_acpype_itp,
                output_path_top=output_acpype_top,
                properties=prop)