pytme 0.1.2__cp311-cp311-macosx_13_0_arm64.whl → 0.1.3__cp311-cp311-macosx_13_0_arm64.whl

{pytme-0.1.2.dist-info → pytme-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pytme
-Version: 0.1.2
+Version: 0.1.3
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>

{pytme-0.1.2.dist-info → pytme-0.1.3.dist-info}/RECORD

@@ -1,10 +1,10 @@
-pytme-0.1.2.data/scripts/estimate_ram_usage.py,sha256=68P3cqtY74XmxUgp5MNks-13NEFAXbt3HWedQipNlQM,2095
-pytme-0.1.2.data/scripts/match_template.py,sha256=Yy4K6CewYfSHlPAt3yBsl8HqCCl-hUsAsGNiF1ixn6I,23491
-pytme-0.1.2.data/scripts/postprocess.py,sha256=3bWmXeyjx-nv5DfUC93WksRPvngKCNSexflm88c7jP4,9796
-pytme-0.1.2.data/scripts/preprocess.py,sha256=zog-l2Je-GeouJ6SnamOMuHgTn7fFPiGnO5X03y5qSY,2527
-pytme-0.1.2.data/scripts/preprocessor_gui.py,sha256=u1bRd40hLj-FbLe6FU7C8THW7fT0hl1MtHY7Va0nEIQ,23784
+pytme-0.1.3.data/scripts/estimate_ram_usage.py,sha256=68P3cqtY74XmxUgp5MNks-13NEFAXbt3HWedQipNlQM,2095
+pytme-0.1.3.data/scripts/match_template.py,sha256=Yy4K6CewYfSHlPAt3yBsl8HqCCl-hUsAsGNiF1ixn6I,23491
+pytme-0.1.3.data/scripts/postprocess.py,sha256=3bWmXeyjx-nv5DfUC93WksRPvngKCNSexflm88c7jP4,9796
+pytme-0.1.3.data/scripts/preprocess.py,sha256=zog-l2Je-GeouJ6SnamOMuHgTn7fFPiGnO5X03y5qSY,2527
+pytme-0.1.3.data/scripts/preprocessor_gui.py,sha256=u1bRd40hLj-FbLe6FU7C8THW7fT0hl1MtHY7Va0nEIQ,23784
 tme/__init__.py,sha256=NiPnYfrwb8e04ETubqwd3yzCGBliLBXRvCylD-T59jY,212
-tme/__version__.py,sha256=YvuYzWnKtqBb-IqG8HAu-nhIYAsgj9Vmc_b9o7vO-js,22
+tme/__version__.py,sha256=XEqb2aiIn8fzGE68Mph4ck1FtQqsR_am0wRWvrYPffQ,22
 tme/analyzer.py,sha256=_nWPqaTCvqa5fEk2VvEDFOHohSN5Vh03ilftWpSAL9g,38509
 tme/density.py,sha256=eAtUEykiWYAc5V_QVnJs0mwlsP_u_ObwZPem9h79BSM,67861
 tme/extensions.cpython-311-darwin.so,sha256=LGSXcU6cVE0zcIzoakOZ9E-VaHmUWHCOjl6c6IV0gXQ,395613
@@ -17,7 +17,7 @@ tme/matching_utils.py,sha256=xtNdn_kuYIAVxS5kkve47TDnGTZ-qYzy3QYEK_2dZUk,35708
 tme/parser.py,sha256=Tc7sLT5NsD4UqJearUqETStSWI-tNui1l9KG9CPaD2g,13847
 tme/preprocessor.py,sha256=5BT4JI3JgX57vIR11YY7Bb5_DZ1_W3f8Kf44inlpbPo,43198
 tme/scoring.py,sha256=xBDn3LdMyfNuwoug3X7L0lReTGrHmKntBinjFYA6iGo,23909
-tme/structure.py,sha256=wz1L77N-2ogeiCRGogFhmNoN6lGhI_1Nkh76OoF3rvI,54245
+tme/structure.py,sha256=fU_dMioPA0OSX6Pzsr01YJR4xV37MJPA5uIMirjwPts,54049
 tme/types.py,sha256=zEXAvmPegwFc5AAxoYmAZ6ZmSKk0ST6U3jVvPrQijac,258
 tme/backends/__init__.py,sha256=_5bg5jutlfejVdoDjReaYGviaCCtNPtvv0q0EuZICec,4330
 tme/backends/cupy_backend.py,sha256=eRReSzpbU1LDsEkQqRTroaHpVVoKznzvRlitzqFlx4M,10503
@@ -48,9 +48,9 @@ tme/data/c600vc.npy,sha256=Yht-GFXDSjjGvsjFBvyxxEZAI-ODADPd5gEgFNZQVTA,14528
 tme/data/metadata.yaml,sha256=fAgX-mEzB0QMHTEtYDG4cSMbJhYxBbDJH3sdvJvL7a8,750
 tme/data/quat_to_numpy.py,sha256=-gkDZb10fKBxwfYrSLCUWvMB76TzZWELCeKsYProwws,1333
 tme/data/scattering_factors.pickle,sha256=ZHktBc_AlS4H6uoER8AMmn5zOgjBwzgC92hUyww3Nik,38669
-pytme-0.1.2.dist-info/LICENSE,sha256=K1IUNSVAz8BXbpH5EA8y5FpaHdvFXnAF2zeK95Lr2bY,18467
-pytme-0.1.2.dist-info/METADATA,sha256=s_DMCBgJZN1oblaJ4vSjjCE9npi0MuZ03bLnsUbd1KQ,1653
-pytme-0.1.2.dist-info/WHEEL,sha256=I1hzfmF9bq6C1aO8MEzHd8iVHVAGAss0vqh7hMHqG50,110
-pytme-0.1.2.dist-info/entry_points.txt,sha256=lRC1XboB0_8nS3hzDyyhWkw32JDKZ0sAy8B_UsmHql0,236
-pytme-0.1.2.dist-info/top_level.txt,sha256=j63Mo93v1HYe3jaBesLoBssArSKOMkpf_aDObPfOkWo,4
-pytme-0.1.2.dist-info/RECORD,,
+pytme-0.1.3.dist-info/LICENSE,sha256=K1IUNSVAz8BXbpH5EA8y5FpaHdvFXnAF2zeK95Lr2bY,18467
+pytme-0.1.3.dist-info/METADATA,sha256=ZffsUYpOjjn6IPmo8P_CYc0gB6GKxYatnClkddPmGvM,1653
+pytme-0.1.3.dist-info/WHEEL,sha256=I1hzfmF9bq6C1aO8MEzHd8iVHVAGAss0vqh7hMHqG50,110
+pytme-0.1.3.dist-info/entry_points.txt,sha256=lRC1XboB0_8nS3hzDyyhWkw32JDKZ0sAy8B_UsmHql0,236
+pytme-0.1.3.dist-info/top_level.txt,sha256=j63Mo93v1HYe3jaBesLoBssArSKOMkpf_aDObPfOkWo,4
+pytme-0.1.3.dist-info/RECORD,,

tme/__version__.py

@@ -1 +1 @@
-__version__ = "0.1.2"
+__version__ = "0.1.3"

tme/structure.py

@@ -793,7 +793,6 @@ class Structure:
         shape: Tuple[int],
         sampling_rate: Tuple[float],
         origin: Tuple[float],
-        chain: str,
     ) -> (NDArray, Tuple[str], Tuple[int], float, Tuple[float]):
         """
         Converts coordinates to positions.
@@ -808,16 +807,11 @@ class Structure:
 
         origin : Tuple[float,]
             The origin of the coordinate system.
-
-        chain : str
-            The chain identifier. If multiple chains should be selected they need
-            to be a comma separated string, e.g. 'A,B,CE'.
         Returns
         -------
         Tuple[NDArray, List[str], Tuple[int, ], float, Tuple[float,]]
             Returns positions, atom_types, shape, sampling_rate, and origin.
         """
-        temp = self.subset_by_chain(chain)
         coordinates = self.atom_coordinate.copy()
         atom_types = self.element_symbol.copy()
 
@@ -888,7 +882,6 @@ class Structure:
                 ).astype(int)
 
                 vdw_rad[atom_type] = atom_vdwr
-                print(atom_vdwr)
                 atom_slice = tuple(slice(-k, k + 1) for k in atom_vdwr)
                 distances = np.linalg.norm(
                     np.divide(
@@ -1076,8 +1069,11 @@ class Structure:
         if "source" not in scattering_args:
             scattering_args["source"] = "peng1995"
 
+        temp = self.copy()
+        self = self.subset_by_chain(chain = chain)
+
         positions, atoms, shape, sampling_rate, origin = self._coordinate_to_position(
-            shape=shape, sampling_rate=sampling_rate, origin=origin, chain=chain
+            shape=shape, sampling_rate=sampling_rate, origin=origin
         )
         volume = np.zeros(shape, dtype=np.float32)
         if weight_type in ("atomic_weight", "atomic_number"):
@@ -1104,6 +1100,7 @@ class Structure:
                 **scattering_args,
             )
 
+        self = temp
         return volume, origin, sampling_rate
 
     @classmethod
@@ -1231,10 +1228,10 @@ class Structure:
         query = structure2.atom_coordinate.copy()
         if sampling_rate is not None:
             reference, atoms1, shape, _, _ = structure1._coordinate_to_position(
-                shape=None, sampling_rate=sampling_rate, origin=origin, chain=None
+                shape=None, sampling_rate=sampling_rate, origin=origin
             )
             query, atoms2, shape, _, _ = structure2._coordinate_to_position(
-                shape=None, sampling_rate=sampling_rate, origin=origin, chain=None
+                shape=None, sampling_rate=sampling_rate, origin=origin
             )
 
         reference_mean = reference.mean(axis=0)