New crystalform and assemblies documentation

xchem · Oct 23, 2023 · 52542f0 · 52542f0
1 parent 33962a7
commit 52542f0
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Showing 11 changed files with 10 additions and 25 deletions.
diff --git a/scripts/collate.py b/scripts/collate.py
@@ -1,7 +1,7 @@
 import argparse
 
-from xchemalign import utils
-from xchemalign.collator import Collator
+from xchemalign.xchemalign import utils
+from xchemalign.xchemalign.collator import Collator
 
 
 def main():

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -1,6 +1,6 @@
 import pytest
 
-from xchemalign.collator import Collator
+from xchemalign.xchemalign.collator import Collator
 from xchemalign.aligner import Aligner
 
 def test_collator_upload_1(

diff --git a/xchemalign/xchemalign/__init__.py b/xchemalign/xchemalign/__init__.py
diff --git a/xchemalign/aligner.py → xchemalign/xchemalign/aligner.py b/xchemalign/aligner.py → xchemalign/xchemalign/aligner.py
@@ -21,23 +21,6 @@
 # Local alignment imports
 from ligand_neighbourhood_alignment import constants as lna_constants
 from ligand_neighbourhood_alignment.align_xmaps import _align_xmaps
-from ligand_neighbourhood_alignment.data import (
-    CanonicalSites,
-    ChainOutput,
-    ConformerSites,
-    Dataset,
-    DatasetID,
-    DatasetOutput,
-    LigandBindingEvent,
-    LigandBindingEvents,
-    LigandID,
-    LigandNeighbourhoods,
-    LigandOutput,
-    Output,
-    SiteTransforms,
-    SystemData,
-    XtalForms,
-)
 
 # from ligand neighbourhood_alignment
 from ligand_neighbourhood_alignment import dt
@@ -73,7 +56,7 @@
     _update,
 )
 
-from . import utils
+from xchemalign.xchemalign import utils
 from .utils import Constants
 from .pdb_xtal import PDBXtal
 

diff --git a/xchemalign/collator.py → xchemalign/xchemalign/collator.py b/xchemalign/collator.py → xchemalign/xchemalign/collator.py
@@ -26,8 +26,9 @@
 
 from rdkit import Chem
 
-from xchemalign import utils, dbreader
-from xchemalign.utils import Constants
+from xchemalign import dbreader
+from xchemalign.xchemalign import utils
+from xchemalign.xchemalign.utils import Constants
 
 
 def generate_xtal_dir(input_path: Path, xtal_name: str):

diff --git a/xchemalign/copier.py → xchemalign/xchemalign/copier.py b/xchemalign/copier.py → xchemalign/xchemalign/copier.py
@@ -16,7 +16,8 @@
 
 import pandas as pd
 
-from . import collator, dbreader, utils
+from xchemalign import dbreader
+from xchemalign.xchemalign import collator, utils
 from .utils import Constants
 
 

diff --git a/xchemalign/dbreader.py → xchemalign/xchemalign/dbreader.py b/xchemalign/dbreader.py → xchemalign/xchemalign/dbreader.py
diff --git a/xchemalign/non_ligs.json → xchemalign/xchemalign/non_ligs.json b/xchemalign/non_ligs.json → xchemalign/xchemalign/non_ligs.json
diff --git a/xchemalign/pdb_xtal.py → xchemalign/xchemalign/pdb_xtal.py b/xchemalign/pdb_xtal.py → xchemalign/xchemalign/pdb_xtal.py
@@ -18,7 +18,7 @@
 from rdkit import Chem
 from rdkit import Geometry
 
-from . import utils
+from xchemalign.xchemalign import utils
 
 
 class PDBXtal:

diff --git a/xchemalign/rdkit_utils.py → xchemalign/xchemalign/rdkit_utils.py b/xchemalign/rdkit_utils.py → xchemalign/xchemalign/rdkit_utils.py
diff --git a/xchemalign/utils.py → xchemalign/xchemalign/utils.py b/xchemalign/utils.py → xchemalign/xchemalign/utils.py