Converted to package. Changed all imports appropriately. Added README…

.gitignore

@@ -134,3 +134,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# MacOSX
+.DS_store

README.md

@@ -0,0 +1,23 @@
+# Protein holography
+
+Create the protein holography conda environment by running
+
+```bash
+conda env create -f env.yml
+```
+
+to install the necessary dependencies.
+Then run
+
+```bash
+pip install .
+```
+
+to install the `protein_holography` package.
+If you're going to make edits to the `protein_holography` package, run
+
+```bash
+pip install -e .
+```
+
+so you can test your changes.

env.yml

@@ -22,4 +22,3 @@ dependencies:
     - GitPython
     - freesasa
     - tensorflow-gpu==2.6
-

config.py → protein_holography/config.py

@@ -1,9 +1,10 @@
-import yaml
-import os
+from argparse import ArgumentParser
 import datetime
 import getpass
 import itertools
-from argparse import ArgumentParser
+import os
+
+import yaml
 
 class Config:
     def __parse_args(self):

config_sampler.py → protein_holography/config_sampler.py

@@ -1,10 +1,11 @@
-import yaml
-import os
+from argparse import ArgumentParser
 import datetime
 import getpass
 import itertools
-from argparse import ArgumentParser
+import os
+
 import numpy as np
+import yaml
 
 class Config:
     def __parse_args(self):

coordinates/SphericalChargeCalculation.py → protein_holography/coordinates/SphericalChargeCalculation.py

@@ -9,23 +9,23 @@
 #  - The neighborhood radius
 #  - "easy" flag to include central res
 #
-
-from preprocessorRosetta import PDBPreprocessor
-import pandas as pd
-import numpy as np
-import logging
+from argparse import ArgumentParser
 import itertools
+import logging
 import os
+import sys
+
 from Bio.PDB import Selection, NeighborSearch
-from argparse import ArgumentParser
-from progress.bar import Bar
-import coordinates as co
 import h5py
-import sys
-sys.path.append('/gscratch/spe/mpun/protein_holography/utils')
-from posterity import get_metadata,record_metadata
-import protein
-import charge
+import numpy as np
+import pandas as pd
+from progress.bar import Bar
+
+import protein_holography.coordinates.charge as charge
+import protein_holography.coordinates.coordinates as co
+from protein_holography.coordinates.preprocessorRosetta import PDBPreprocessor
+from protein_holography.utils.posterity import get_metadata, record_metadata
+import protein_holography.utils.protein as protein # Is this even used?
 
 def c(nb_list, pose, d, easy, COA=False):
     if pose is None:

coordinates/SphericalCoordCalculation.py → protein_holography/coordinates/SphericalCoordCalculation.py

@@ -9,22 +9,22 @@
 #  - The neighborhood radius
 #  - "easy" flag to include central res
 #
-
-from preprocessor import PDBPreprocessor
-import pandas as pd
-import numpy as np
-import logging
+from argparse import ArgumentParser
 import itertools
+import logging
 import os
+import sys
+
 from Bio.PDB import Selection, NeighborSearch
-from argparse import ArgumentParser
-from progress.bar import Bar
-import coordinates as co
 import h5py
-import sys
-sys.path.append('/gscratch/spe/mpun/protein_holography/utils')
-from posterity import get_metadata,record_metadata
-import protein
+import numpy as np
+import pandas as pd
+from progress.bar import Bar
+
+from protein_holography.coordinates.preprocessor import PDBPreprocessor
+import protein_holography.coordinates.coordinates as co
+from protein_holography.utils.posterity import get_metadata,record_metadata
+import protein_holography.coordinates.protein as protein
 
 
 def c(struct, res, d, easy, COA=False):

coordinates/coordinates.py → protein_holography/coordinates/coordinates.py

@@ -1,17 +1,17 @@
 #
 # File to take coordinates from list of neighborhoods
 #
-
-
-
-import COA_ref_frame as COA_calc
-import numpy as np
-import protein
-from geo import cartesian_to_spherical
-import Bio.PDB as pdb
 import sys
 sys.path.append('/gscratch/stf/mpun/software/freesasa-python')
+
+import Bio.PDB as pdb
 import freesasa
+import numpy as np
+
+
+import protein_holography.coordinates.COA_ref_frame as COA_calc
+from protein_holography.coordinates.geo import cartesian_to_spherical
+import protein_holography.utils.protein as protein
 
 # six channels for C,N,O,S,HOH,SASA
 EL_CHANNEL_NUM = 6

coordinates/coordinates_test.py → protein_holography/coordinates/coordinates_test.py

@@ -1,8 +1,9 @@
-import coordinates as co
 import Bio.PDB as pdb
-import protein
 import numpy as np
 
+import protein_holography.coordinates.coordinates as co
+import protein_holography.utils.protein as protein
+
 print('Program starting')
 
 parser = pdb.PDBParser(QUIET=True)

protein_holography/coordinates/geo.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""This module converts Cartesian coordinate arrays to spherical coordinate arrays.
+    Copyright (C) 2019 Pun, Michael
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+from typing import Tuple
+
+import numpy as np
+
+def cartesian_to_spherical(r: np.ndarray) -> Tuple[float]:
+    """
+    Convert Cartesian coordinates to spherical coorindates.
+
+    Parameters
+    ----------
+    r : numpy.ndarray
+        Array of Cartesian coordinates x, y, z.
+
+    Returns
+    -------
+    r_mag : float
+        Radial distance.
+    theta : float
+        Polar angle.
+    phi : float
+        Azimuthal angle.
+    """
+    x, y, z = *r,
+
+    r_mag = np.sqrt(np.sum(r**2))
+    theta = np.arccos(z / r_mag)
+    phi = np.arctan2(y, x)
+
+    return r_mag, theta , phi

coordinates/get_strucutral_info.py → protein_holography/coordinates/get_strucutral_info.py

@@ -9,18 +9,18 @@
 #  - The neighborhood radius
 #  - "easy" flag to include central res
 #
-
-from pyrosetta_hdf5_proteins import get_structural_info,pad_structural_info
-from preprocessor_pdbs import PDBPreprocessor
 from argparse import ArgumentParser
-import numpy as np
-import h5py
-import sys
-sys.path.append('/gscratch/spe/mpun/protein_holography/utils')
-from posterity import get_metadata,record_metadata
 import logging
+import sys
+
+import h5py
+import numpy as np
 from progress.bar import Bar
 
+from protein_holography.coordinates.pyrosetta_hdf5_proteins import get_structural_info,pad_structural_info
+from protein_holography.coordinates.preprocessor_pdbs import PDBPreprocessor
+from protein_holography.utils.posterity import get_metadata,record_metadata
+
 def c(pose):
 
     if pose is None: