# :noTabs=true:
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
# (c) addressed to University of Washington CoMotion, email: license@uw.edu.

## @author Sergey Lyskov

from __future__ import print_function

import pyrosetta
from pyrosetta import *

pyrosetta.init(extra_options = "-constant_seed")  # WARNING: option '-constant_seed' is for testing only! MAKE SURE TO REMOVE IT IN PRODUCTION RUNS!!!!!
import os; os.chdir('.test.output')


print('General testing ----------------------------------------------')

print('Creating Pose object...')
pose = Pose()

print('Pose from PDB...')
pose = pose_from_file("../test/data/test_in.pdb")

# TODO: rename pose_from_file or make_pose_from_sequence to be parallel

print('Building Pose from sequence...')
pose3 = Pose()
make_pose_from_sequence(pose3, "DSEEKFLRRIGRFGYGYGPYE",'centroid')
print(pose3)

pose4 = Pose()
make_pose_from_sequence(pose4, "ARNDCEQGHILKMFPSTWYV", 'fa_standard')


print('Dump PDB...')
dump_pdb(pose, "T110_Basic._.pdb")

print('accessing pose attributes')
print(pose)
# TODO: remove extra blank lines at end
print('there are ', pose.total_residue(), 'residues in this pose object')
print('phi of residue 5 is ', pose.phi(5) )
print('psi of residue 5 is ', pose.psi(5) )

print('set phi of residue 5 to -60')
pose.set_phi(1, -60)
print('set psi of residue 5 to -50')
pose.set_psi(1, -50)

print('accessing residue 5 from pose')
res5 = pose.residue(5)
print(res5)

print('accessing atoms from residue 5')
at5N  = res5.atom('N')
at5CA = res5.atom("CA")
at5C  = res5.atom("C")

print(at5N)
# TODO: above should print atom type key not magic number
# 2/23/9: hm, not sure this is possible b/c atom does not know which AtomTypeSet to use!

print('xyz of at5N:', at5N.xyz().x, at5N.xyz().y, at5N.xyz().z)
print('norm of xyz at5N:', at5N.xyz().norm)

print( res5.atoms() )  # <-- Still missing

atomN = AtomID(1,5)
atomCA = AtomID(2,5)
atomC = AtomID(3,5)
print('bond length of N-CA in residue 5 is ')
print( pose.conformation().bond_length(atomN, atomCA) )
print('bond angle of N-CA-C in residue 5 is ')
print( pose.conformation().bond_angle(atomN, atomCA, atomC) )
print('setting bond length of N-CA in residue 5 to 1.5A ')
pose.conformation().set_bond_length(atomN, atomCA, 1.5)
print('setting bond angle of N-CA-C in residue 5 to 90 ')
pose.conformation().set_bond_angle(atomN, atomCA, atomC, 90)
# TODO: make the above work with atom objects instead of atomIDs


print('pose was generated from this pdb file: ', pose.pdb_info().name() )
print('pose numbering for chain A, residue 5, is ', pose.pdb_info().pdb2pose('A',5) )
print('pdb chain letter and residue number for residue 5, is ', pose.pdb_info().pose2pdb(5) )
# TODO: pdb_info.* does not tab-complete


# Creating residue example
chm = rosetta.core.chemical.ChemicalManager.get_instance()
rts = chm.residue_type_set('fa_standard')
ala = rosetta.core.conformation.ResidueFactory.create_residue( rts.name_map('ALA') )
print(ala)