refactor: Move PyMolecule into separate repo

.gitignore

@@ -11,3 +11,8 @@ public
 
 __pycache__
 .vscode
+
+# Coverage
+.coverage
+coverage.xml
+report.xml

pixi.toml

@@ -9,6 +9,8 @@ readme = "README.md"
 
 [pypi-dependencies]
 povme = { path = ".", editable = true }
+pymolecule = { git = "https://github.com/durrantlab/pymolecule.git", rev = "main" }
+
 
 [system-requirements]
 linux = "3.10.0"

povme/hull.py

@@ -5,9 +5,9 @@
 import numpy as np
 import numpy.typing as npt
 from loguru import logger
+from pymolecule import Molecule
 from scipy.spatial.distance import cdist, pdist, squareform
 
-from . import pymolecule
 from .io import gzopenfile, numpy_to_pdb, openfile, write_to_file
 from .parallel import MultithreadingTaskGeneral
 
@@ -394,8 +394,8 @@ def value_func(self, item, results_queue):
         # you may need to load it from disk if the user so specified
         if config.use_disk_not_memory:  # so you need to load it from disk
             pym_filename = pdb
-            pdb = pymolecule.Molecule()
-            pdb.fileio.load_pym_into(pym_filename)
+            pdb = Molecule()
+            pdb.io.load_pym_into(pym_filename)
 
         # remove the points that are far from the points region anyway
         min_pts = np.min(pts, 0) - config.distance_cutoff - 1

povme/pocket_id.py

@@ -2,14 +2,14 @@
 
 import numpy as np
 from loguru import logger
+from pymolecule import Molecule
 from scipy.cluster.vq import kmeans2
 from scipy.spatial.distance import cdist
 
 from .config import PocketIDConfig
 from .hull import ConvexHull
 from .io import openfile, write_pdbs
 from .pocket import BoxOfPoints
-from .pymolecule import Molecule
 
 
 class PocketDetector:
@@ -43,7 +43,7 @@ def run(self, path_pdb: str, output_prefix: str = "") -> None:
 
         logger.info("Step 1. Loading the PDB file " + path_pdb + "...")
         molecule = Molecule()
-        molecule.fileio.load_pdb_into(path_pdb)
+        molecule.io.load_pdb_into(path_pdb)
 
         # Step 2: Get rid of hydogen atoms. They just slow stuff down.
 

povme/povme.py

@@ -8,9 +8,9 @@
 
 import numpy as np
 from loguru import logger
+from pymolecule import Molecule
 from scipy.spatial.distance import cdist
 
-from . import pymolecule
 from .config import POVMEConfig
 from .hull import MultithreadingCalcVolumeTask
 from .io import dx_freq, gzopenfile, numpy_to_pdb, openfile, write_to_file
@@ -54,8 +54,8 @@ def value_func(self, item, results_queue):
 
         # make the pdb object
         str_obj = StringIO(pdb_string)
-        tmp = pymolecule.Molecule()
-        tmp.fileio.load_pdb_into_using_file_object(str_obj, False, False, False)
+        tmp = Molecule()
+        tmp.io.load_pdb_into_using_file_object(str_obj, False, False, False)
 
         logger.debug("\tFurther processing frame " + str(index))
 
@@ -64,7 +64,7 @@ def value_func(self, item, results_queue):
             self.results.append((index, tmp))
         else:  # save to disk, record filename
             pym_filename = f"./.povme_tmp/frame_{str(index)}.pym"
-            tmp.fileio.save_pym(pym_filename, False, False, False, False, False)
+            tmp.io.save_pym(pym_filename, False, False, False, False, False)
             self.results.append((index, pym_filename))