Collection of structures & TMAlign

.gitignore

@@ -4,6 +4,8 @@ docs/tutorials/Working_with_mmCIF_Structures_in_DataFrames_files/*
 docs/tutorials/Working_with_MOL2_Structures_in_DataFrames_files/*
 docs/tutorials/Working_with_PDB_Structures_in_DataFrames_files/*
 docs/tutorials/data/3eiy_stripped.pdb.gz
+docs/tutorials/data/*output/
+docs/tutorials/data/aligned_structures/
 docs/api_subpackages/
 docs/api_modules
 docs/py-docstring-parser/
@@ -35,3 +37,5 @@ doc/_build
 *ENV
 .DS_store
 .idea
+/biopandas/align/USalign.exe
+/biopandas/align/USalign

biopandas/__init__.py

@@ -24,5 +24,5 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = "0.5.1dev"
+__version__ = "0.6.0dev"
 __author__ = "Sebastian Raschka <[email protected]>"

biopandas/align/__init__.py

@@ -0,0 +1,15 @@
+# BioPandas
+# Author: Sebastian Raschka <[email protected]>
+# License: BSD 3 clause
+# Project Website: http://rasbt.github.io/biopandas/
+# Code Repository: https://github.com/rasbt/biopandas
+
+"""
+BioPandas module for working with a collection
+Protein Data Bank (PDB) files.
+"""
+
+from .align import Align
+from .tmalign import TMAlign
+
+__all__ = ['Align', 'TMAlign']

biopandas/align/align.py

@@ -0,0 +1,52 @@
+""" Class for aligning PDB structures"""
+
+# BioPandas
+# Author: Sebastian Raschka <[email protected]>
+# License: BSD 3 clause
+# Project Website: http://rasbt.github.io/biopandas/
+# Code Repository: https://github.com/rasbt/biopandas
+
+import tempfile
+from copy import deepcopy
+
+import numpy as np
+
+
+class Align():
+    def __init__(self):
+        pass
+
+    def write_pdb_to_temp_file(self, pdb):
+        """Write a PandasPdb object's data to a temporary PDB file and return the file handle.
+        :param pdb: the PandasPdb object to write to the file.
+
+        :return: file handle
+        """
+        temp_file = tempfile.NamedTemporaryFile(delete=False, suffix='.pdb')
+        pdb.to_pdb(path=temp_file.name, records=None, gz=False, append_newline=True)
+        return temp_file
+
+    def filter_and_validate_chain(self, pdb, chain_id):
+        """Filter the PandasPdb by chain_id and validate the presence of the chain.
+        :param pdb: the PandasPdb object to filter.
+        :param chain_id: the chain ID to filter by.
+
+        :return: filtered_pdb
+        """
+        filtered_pdb = deepcopy(pdb)
+        filtered_atoms = pdb.df['ATOM'][pdb.df['ATOM']['chain_id'].isin([chain_id])]
+        if filtered_atoms.empty:
+            raise ValueError(f"No such chain '{chain_id}' found in the structure.")
+        filtered_pdb.df['ATOM'] = filtered_atoms
+        return filtered_pdb
+
+    def transform(self, coords, matrix, translation):
+        """Apply the rotation matrix and translation vector to the structure.
+        :param coords: the coordinates to transform.
+        :param matrix: the rotation matrix.
+        :param translation: the translation vector.
+
+        :return: transformed coordinates as a numpy array.
+        """
+
+        return np.dot(coords, matrix.T) + translation

biopandas/align/tests/data/4eiy_anisouchunk.pdb

@@ -0,0 +1,10 @@
+HEADER    MEMBRANE PROTEIN                        06-APR-12   4EIY              
+ATOM    101  CG1 VAL A  12      -5.222   2.059   3.696  1.00 17.98           C  
+ANISOU  101  CG1 VAL A  12     2231   2335   2262    -42    326    285       C  
+ATOM    102  CG2 VAL A  12      -5.748   3.603   1.839  1.00 16.30           C  
+ANISOU  102  CG2 VAL A  12     2409   2061   1722     37    584    238       C  
+ATOM    103  N   GLU A  13      -8.338   2.518   5.470  1.00 16.24           N  
+ANISOU  103  N   GLU A  13     2362   2337   1469    -17      0      0       N  
+ATOM    104  CA  GLU A  13      -8.773   1.934   6.759  1.00 15.34           C  
+ANISOU  104  CA  GLU A  13     2354   2186   1285    -33    -18    -33       C  
+ATOM    105  C   GLU A  13      -9.966   1.026   6.560  1.00 16.90           C  

biopandas/align/tests/data/tmalign_output.txt

@@ -0,0 +1,13 @@
+------ The rotation matrix to rotate Structure_1 to Structure_2 ------
+m               t[m]        u[m][0]        u[m][1]        u[m][2]
+0      -7.8641206905   0.9999934600   0.0029980568  -0.0020227599
+1     -28.5356545158  -0.0030052335   0.9999891677  -0.0035542976
+2     -45.4038063602   0.0020120820   0.0035603533   0.9999916377
+
+Code for rotating Structure 1 from (x,y,z) to (X,Y,Z):
+for(i=0; i<L; i++)
+{
+   X[i] = t[0] + u[0][0]*x[i] + u[0][1]*y[i] + u[0][2]*z[i];
+   Y[i] = t[1] + u[1][0]*x[i] + u[1][1]*y[i] + u[1][2]*z[i];
+   Z[i] = t[2] + u[2][0]*x[i] + u[2][1]*y[i] + u[2][2]*z[i];
+}

biopandas/align/tests/test_align.py

@@ -0,0 +1,55 @@
+# BioPandas
+# Author: Sebastian Raschka <[email protected]>
+# License: BSD 3 clause
+# Project Website: http://rasbt.github.io/biopandas/
+# Code Repository: https://github.com/rasbt/biopandas
+
+from nose.tools import assert_raises
+from biopandas.pdb import PandasPdb
+from biopandas.align import Align
+import numpy as np
+import os
+
+TESTDATA_FILENAME = os.path.join(os.path.dirname(__file__), "data", "3eiy.pdb")
+TESTDATA_FILENAME2 = os.path.join(
+    os.path.dirname(__file__), "data", "4eiy_anisouchunk.pdb"
+)
+
+OUTFILE = os.path.join(os.path.dirname(__file__), "data", "tmp.pdb")
+
+def test_write_pdb_to_temp_file():
+    ppdb = PandasPdb()
+    ppdb.read_pdb(TESTDATA_FILENAME)
+
+    align = Align()
+
+    with align.write_pdb_to_temp_file(ppdb) as temp_file:
+        assert os.path.exists(temp_file.name)
+        assert temp_file.name.endswith('.pdb')
+
+        temp_content = open(temp_file.name, 'r').read()
+        assert temp_content == open(TESTDATA_FILENAME, 'r').read()
+
+def test_transform():
+    align = Align()
+    coords = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+    matrix = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
+    translation = np.array([3, 2, 1])
+
+    transformed_coords = align.transform(coords, matrix, translation)
+    target_coords = np.array([[4, 4, 4], [7, 7, 7], [10, 10, 10]])
+
+    assert np.array_equal(transformed_coords, target_coords)
+
+def test_filter_and_validate_chain():
+    ppdb = PandasPdb()
+    ppdb.read_pdb(TESTDATA_FILENAME)
+
+    align = Align()
+
+    filtered_pdb = align.filter_and_validate_chain(ppdb, 'A')
+    assert filtered_pdb.df['ATOM']['chain_id'].unique() == ['A']
+
+    assert_raises(ValueError, align.filter_and_validate_chain, ppdb, 'B')
+
+