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from WaterNetworkAnalysis import align_trajectory
from WaterNetworkAnalysis import get_center_of_selection
from WaterNetworkAnalysis import get_selection_string_from_resnums
from WaterNetworkAnalysis import extract_waters_from_trajectory
from ConservedWaterSearch.water_clustering import WaterClustering
from ConservedWaterSearch.utils import get_orientations_from_positions

# MD trajectory filename
trajectory="1md_all_skip5_nojump_mol_fit_waters_ordered_whole.xtc"
# topology filename
topology="1md_all_skip5_nojump_mol_fit_waters_ordered_whole.gro"
# aligned trajectory filename
alignedtrj = "1md_all_skip5_nojump_mol_fit_waters_ordered_whole.xtc"
# aligned snapshot filename
aligned_snap = "1md_all_skip5_nojump_mol_fit_waters_ordered_whole.pdb"
# distance to select water molecules around
distance = 2.0
# align the trajectory and save the alignment reference configuration
###align_trajectory(
###    trajectory=trajectory,
###    topology=topology,
###    align_target_file_name=aligned_snap,
###    output_trj_file=alignedtrj,
###)
# define active site by aminoacid residue numbers
active_site_resnums = [293]
# find centre of the active site in aligned trajectory
selection_centre = get_center_of_selection(
    get_selection_string_from_resnums(active_site_resnums),
    trajectory=alignedtrj,
    topology=topology,
)
# extract water coordinates of interest around selection centre
coordO, coordH =  extract_waters_from_trajectory(
    trajectory=alignedtrj,
    topology=topology,
    selection_center=selection_centre,
    dist=distance
)
# start the clustering procedure
Nsnaps = 2
WC=WaterClustering(nsnaps= Nsnaps)
# perform multi stage reclustering
WC.multi_stage_reclustering(*get_orientations_from_positions(coordO,coordH))
# visualise results with pymol
WC.visualise_pymol(aligned_snap, active_site_ids=active_site_resnums, dist=distance)

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[3], line 46
     44 WC.multi_stage_reclustering(*get_orientations_from_positions(coordO,coordH))
     45 # visualise results with pymol
---> 46 WC.visualise_pymol(aligned_snap, active_site_ids=active_site_resnums, dist=distance)

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\ConservedWaterSearch\water_clustering.py:1024, in WaterClustering.visualise_pymol(self, aligned_protein, output_file, active_site_ids, crystal_waters, ligand_resname, dist, density_map)
    993 def visualise_pymol(
    994     self,
    995     aligned_protein: str = "aligned.pdb",
   (...)
   1001     density_map: str | None = None,
   1002 ) -> None:
   1003     """Visualise results using `pymol <[https://pymol.org/>`__](https://pymol.org/%3E%60__).
   1004 
   1005     Args:
   (...)
   1022             visualisation session (usually .dx file). Defaults to None.
   1023     """
-> 1024     visualise_pymol(
   1025         self._water_type,
   1026         self._waterO,
   1027         self._waterH1,
   1028         self._waterH2,
   1029         aligned_protein=aligned_protein,
   1030         output_file=output_file,
   1031         active_site_ids=active_site_ids,
   1032         crystal_waters=crystal_waters,
   1033         ligand_resname=ligand_resname,
   1034         dist=dist,
   1035         density_map=density_map,
   1036     )

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\ConservedWaterSearch\utils.py:356, in visualise_pymol(water_type, waterO, waterH1, waterH2, aligned_protein, output_file, active_site_ids, crystal_waters, ligand_resname, dist, density_map)
    354 if active_site_ids is not None:
    355     cmd.center(active_site_center)
--> 356 os.remove("hoh.cif")
    357 # save
    358 cmd.save(output_file)

FileNotFoundError: [WinError 2] The system cannot find the file specified: 'hoh.cif'

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[1], line 1
----> 1 from WaterNetworkAnalysis import align_and_extract_waters, get_center_of_selection,get_selection_string_from_resnums
      2 # MD trajectory filename
      3 trajectory="1md_all_skip5_nojump_mol_fit_waters_ordered_whole.xtc"

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\WaterNetworkAnalysis\__init__.py:6
      1 """
      2 WaterNetworkAnalysis
      3 Module for preparation of raw trajectories for analysis of conserved waters for ConservedWaterSearch
      4 """
----> 6 from .WaterNetworkAnalysis import (
      7     align_and_extract_waters,
      8     align_trajectory,
      9     calculate_oxygen_density_map,
     10     extract_waters_from_trajectory,
     11     get_center_of_selection,
     12     get_selection_string_from_resnums,
     13     make_results_pdb_MDA,
     14     read_results_and_make_pdb,
     15 )

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\WaterNetworkAnalysis\WaterNetworkAnalysis.py:10
      7 import MDAnalysis as mda
      8 import numpy as np
---> 10 from ConservedWaterSearch.utils import (
     11     get_orientations_from_positions,
     12     read_results,
     13 )
     16 def get_selection_string_from_resnums(
     17     resids: list[int], selection_type: str = "MDA"
     18 ) -> str:
     19     """Returns selection string for given residue ids.
     20 
     21     Returns the selection command string for different programs based on
   (...)
     38         "PYMOL")
     39     """

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\ConservedWaterSearch\utils.py:6
      3 import os
      4 import platform
----> 6 import nglview as ngl
      7 import numpy as np
      8 from nglview import NGLWidget

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\nglview\__init__.py:4
      1 import warnings
      3 # for doc
----> 4 from . import adaptor, datafiles, show, widget
      5 from ._version import get_versions
      6 from .adaptor import *

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\nglview\show.py:13
      3 from . import datafiles
      4 from .adaptor import (ASEStructure, ASETrajectory, BiopythonStructure,
      5                       FileStructure, HTMDTrajectory, IODataStructure,
      6                       IOTBXStructure, MDAnalysisTrajectory, MDTrajTrajectory,
   (...)
     11                       RdkitStructure,
     12                       TextStructure)
---> 13 from .widget import NGLWidget
     15 __all__ = [
     16     'demo',
     17     'show_pdbid',
   (...)
     40     'show_biopython',
     41 ]
     44 def show_pdbid(pdbid, **kwargs):

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\nglview\widget.py:19
     15 from traitlets import (Bool, CaselessStrEnum, Dict, Instance, Int, Integer,
     16                        List, Unicode, observe, validate)
     17 import traitlets
---> 19 from . import color, interpolate
     20 from .adaptor import Structure, Trajectory
     21 from .component import ComponentViewer

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\nglview\color.py:114
    110         else:
    111             raise ValueError(f"{obj} must be either list of list or string")
--> 114 ColormakerRegistry = _ColormakerRegistry()

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\nglview\base.py:10, in _singleton.<locals>.getinstance()
      8 def getinstance():
      9     if cls not in instances:
---> 10         instances[cls] = cls()
     11     return instances[cls]

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\nglview\color.py:47, in _ColormakerRegistry.__init__(self, *args, **kwargs)
     45 try:
     46     get_ipython() # only display in notebook
---> 47     self._ipython_display_()
     48 except NameError:
     49     pass

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\nglview\color.py:54, in _ColormakerRegistry._ipython_display_(self, **kwargs)
     52 if self._ready:
     53     return
---> 54 super()._ipython_display_(**kwargs)

AttributeError: 'super' object has no attribute '_ipython_display_'

start the clustering procedure
Nsnaps = 200
WC=WaterClustering(nsnaps= Nsnaps)
perform multi stage reclustering
WC.multi_stage_reclustering(*get_orientations_from_positions(coordO,coordH))
visualise results with pymol
WC.visualise_pymol(aligned_snap, active_site_ids=active_site_resnums, dist=distance)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[7], line 7
      5 WC.multi_stage_reclustering(*get_orientations_from_positions(coordO,coordH))
      6 # visualise results with pymol
----> 7 WC.visualise_pymol(aligned_snap, active_site_ids=active_site_resnums, dist=distance)

File ~/opt/miniconda3/envs/WaterNetworkAnalysis/lib/python3.11/site-packages/ConservedWaterSearch/water_clustering.py:1068, in WaterClustering.visualise_pymol(self, aligned_protein, output_file, active_site_ids, crystal_waters, ligand_resname, dist, density_map)
   1037 def visualise_pymol(
   1038     self,
   1039     aligned_protein: str = "aligned.pdb",
   (...)
   1045     density_map: str | None = None,
   1046 ) -> None:
   1047     """Visualise results using `pymol <[https://pymol.org/>`__](https://pymol.org/%3E%60__).
   1048 
   1049     Args:
   (...)
   1066             visualisation session (usually .dx file). Defaults to None.
   1067     """
-> 1068     visualise_pymol(
   1069         self._water_type,
   1070         self._waterO,
   1071         self._waterH1,
   1072         self._waterH2,
   1073         aligned_protein=aligned_protein,
   1074         output_file=output_file,
   1075         active_site_ids=active_site_ids,
   1076         crystal_waters=crystal_waters,
   1077         ligand_resname=ligand_resname,
   1078         dist=dist,
   1079         density_map=density_map,
   1080     )

File ~/opt/miniconda3/envs/WaterNetworkAnalysis/lib/python3.11/site-packages/ConservedWaterSearch/utils.py:352, in visualise_pymol(water_type, waterO, waterH1, waterH2, aligned_protein, output_file, active_site_ids, crystal_waters, ligand_resname, dist, density_map)
    350     os.remove("hoh.cif")
    351 # save
--> 352 cmd.save(output_file)
    353 cmd.reinitialize()

File ~/opt/miniconda3/envs/WaterNetworkAnalysis/lib/python3.11/site-packages/pymol/exporting.py:834, in save(filename, selection, state, format, ref, ref_state, quiet, partial, _self)
    832 # analyze filename
    833 from pymol.importing import filename_to_format, _eval_func
--> 834 _, _, format_guessed, zipped = filename_to_format(filename)
    835 filename = _self.exp_path(filename)
    837 # file format

File ~/opt/miniconda3/envs/WaterNetworkAnalysis/lib/python3.11/site-packages/pymol/importing.py:42, in filename_to_format(filename)
     41 def filename_to_format(filename):
---> 42     filename = os.path.basename(filename)
     43     pre, delim, ext = filename.rpartition('.')
     45     if ext in ('gz', 'bz2',):

File <frozen posixpath>:142, in basename(p)

TypeError: expected str, bytes or os.PathLike object, not NoneType

---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
Cell In[2], line 19
     17 distance = 2.0
     18 # align the trajectory and save the alignment reference configuration
---> 19 align_trajectory(
     20     trajectory=trajectory,
     21     topology=topology,
     22     align_target_file_name=aligned_snap,
     23     output_trj_file=alignedtrj,
     24 )
     25 # define active site by aminoacid residue numbers
     26 active_site_resnums = [293]

File ~\anaconda3\envs\ConservedWaterSearch\lib\site-packages\WaterNetworkAnalysis\WaterNetworkAnalysis.py:649, in align_trajectory(trajectory, output_trj_file, align_target_file_name, topology, every, align_mode, align_target, align_selection, probis_exec)
    647     mob.trajectory.add_transformations(*transforms2)
    648 else:
--> 649     raise Exception("cannot center the protein")
    650 ref.select_atoms(align_selection).segments.segids = "A"
    651 ref.add_TopologyAttr("chainIDs")

Exception: cannot center the protein

  File "/home/greg/Desktop/wolf/WNA.py", line 43, in <module>
    coordO, coordH =  extract_waters_from_trajectory(
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/greg/mambaforge/envs/WNA/lib/python3.11/site-packages/WaterNetworkAnalysis/WaterNetworkAnalysis.py", line 401, in extract_waters_from_trajectory
    Opos, H1, H2 = get_orientations_from_positions(Odata, coordsH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/greg/mambaforge/envs/WNA/lib/python3.11/site-packages/ConservedWaterSearch/utils.py", line 101, in get_orientations_from_positions
    raise ValueError(
ValueError: ('bad input HO bonds in water longer than 1.2A; value:', 0.8907369, 79.257034)

from WaterNetworkAnalysis import align_and_extract_waters, get_center_of_selection,get_selection_string_from_resnums
# MD trajectory filename
trajectory="md.xtc"
# topology filename
topology="md.gro"
# aligned trajectory filename
alignedtrj = "aligned_trj.xtc"
# aligned snapshot filename
aligned_snap = "aligned.pdb"
# distance to select water molecules around
distance = 12.0
# name of water density map file
watdens_fname = 'water.dx'
# define active site by aminoacid residue numbers
active_site_resnums = [111, 112, 113, 122, 133, 138, 139, 142, 143, 157, 166, 167, 169, 170, 203, 231, 232, 238]
# find centre of the active site in aligned trajectory
selection_centre = get_center_of_selection(
    get_selection_string_from_resnums(active_site_resnums),
    trajectory=alignedtrj,
    topology=topology,
)
calculate_oxygen_density_map(
    selection_center=selection_centre,
    trajectory=alignedtrj,
    topology=topology,
    dist=distance,
    output_name=watdens_fname,
)