biotite 0.38.0__cp310-cp310-win_amd64.whl → 0.40.0__cp310-cp310-win_amd64.whl

biotite/structure/__init__.py

@@ -40,7 +40,7 @@ Category   Type         Examples           Description
 chain_id   string (U4)  'A','S','AB', ...  Polypeptide chain
 res_id     int          1,2,3, ...         Sequence position of residue
 ins_code   string (U1)  '', 'A','B',..     PDB insertion code (iCode)
-res_name   string (U3)  'GLY','ALA', ...   Residue name
+res_name   string (U5)  'GLY','ALA', ...   Residue name
 hetero     bool         True, False        False for ``ATOM``, true for ``HETATM``
 atom_name  string (U6)  'CA','N', ...      Atom name
 element    string (U2)  'C','O','SE', ...  Chemical Element

biotite/structure/atoms.py

@@ -39,7 +39,7 @@ class _AtomArrayBase(Copyable, metaclass=abc.ABCMeta):
         self.add_annotation("chain_id", dtype="U4")
         self.add_annotation("res_id", dtype=int)
         self.add_annotation("ins_code", dtype="U1")
-        self.add_annotation("res_name", dtype="U3")
+        self.add_annotation("res_name", dtype="U5")
         self.add_annotation("hetero", dtype=bool)
         self.add_annotation("atom_name", dtype="U6")
         self.add_annotation("element", dtype="U2")

biotite/structure/basepairs.py

@@ -15,7 +15,7 @@ import numpy as np
 import warnings
 from enum import IntEnum
 from .atoms import Atom, array
-from .superimpose import superimpose, superimpose_apply
+from .superimpose import superimpose
 from .filter import filter_nucleotides
 from .celllist import CellList
 from .hbond import hbond
@@ -386,7 +386,7 @@ def base_pairs_edge(atom_array, base_pairs):
 
     References
     ----------
-    
+
     .. footbibliography::
     """
     # Result-``ndarray`` matches the dimensions of the input array
@@ -537,7 +537,7 @@ def base_pairs_glycosidic_bond(atom_array, base_pairs):
 
     References
     ----------
-    
+
     .. footbibliography::
     """
     results = np.zeros(len(base_pairs), dtype='uint8')
@@ -679,7 +679,7 @@ def base_stacking(atom_array, min_atoms_per_base=3):
 
     References
     ----------
-    
+
     .. footbibliography::
     """
     # Get the stacking candidates according to a cutoff distance, where
@@ -846,7 +846,7 @@ def base_pairs(atom_array, min_atoms_per_base = 3, unique = True):
 
     References
     ----------
-    
+
     .. footbibliography::
     """
 
@@ -1190,12 +1190,7 @@ def _match_base(nucleotide, min_atoms_per_base):
 
     # Match the selected std_base to the base.
     _, transformation = superimpose(nucleotide_matched, std_base_matched)
-
-    # Transform the vectors
-    trans1, rot, trans2 = transformation
-    vectors += trans1
-    vectors  = np.dot(rot, vectors.T).T
-    vectors += trans2
+    vectors = transformation.apply(vectors)
     # Normalize the base-normal-vector
     vectors[1,:] = vectors[1,:]-vectors[0,:]
     norm_vector(vectors[1,:])
@@ -1255,7 +1250,7 @@ def map_nucleotide(residue, min_atoms_per_base=3, rmsd_cutoff=0.28):
 
     References
     ----------
-    
+
     .. footbibliography::
     """
     # Check if the residue is a 'standard' nucleotide