rna_tools/rna_torsions.py: add

rna_tools/rna_torsions.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Examples::
+
+    $ rna_torsions.py ./input/4GXY_min.pdb
+    f, alphaprime, beta
+    input ./input/4GXY_min.pdb <Residue G het=  resseq=2 icode= >, -64.20924484900823, -143.18546007904766
+    input ./input/4GXY_min.pdb <Residue C het=  resseq=3 icode= >, 2.3394112025736815, 70.4052871669199
+
+Comparison::
+
+    $ rna_x3dna.py input/4GXY_min.pdb -s
+    input: input/4GXY_min.pdb
+       nt id   res  alpha   beta  gamma  delta  epsilon  zeta      e-z           chi     phase-angle sugar-type  ssZp    Dp  splay     paired
+    0   1  G  A.G2    NaN -143.2  153.7   82.5    -92.3 -31.9  -60(..)  -179.0(anti)  19.5(C3'-endo)  ~C3'-endo  4.39  4.56  18.32  no paired
+    1   2  C  A.C3 -111.4   70.4  160.0   80.6      NaN   NaN      NaN  -177.6(anti)  11.1(C3'-endo)  ~C3'-endo   NaN   NaN    NaN  no paired
+
+"""
+from __future__ import print_function
+import argparse
+from icecream import ic
+import sys
+ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
+ic.configureOutput(prefix='> ')
+import math
+try:
+    from Bio import PDB
+except ImportError:
+    print("Biopython is not detected. It is required for some functions.")
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    #parser.add_argument('-', "--", help="", default="")
+
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    parser.add_argument("file", help="", default="") # nargs='+')
+    return parser
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    if list != type(args.file):
+        args.file = [args.file]
+
+
+    print(f'f, alphaprime, beta')    
+    for f in args.file:
+        #print(f'input {f}, ')
+
+        parser = PDB.PDBParser()
+        struct = parser.get_structure('', f)
+
+        for m in struct:
+              for c in m:
+                    for r in c:
+                        #print(r)#, end=' ')
+                        # check what residues is this one       
+                        x1, x2, x3, x4 = r["C5'"].get_vector(), r["O5'"].get_vector(), r['P'].get_vector(), r['OP1'].get_vector()
+                        a = PDB.vectors.calc_dihedral(x4, x3, x2, x1) # !!! order
+                        alphaprime = math.degrees(a)
+                        x1, x2, x3, x4 = r["C5'"].get_vector(), r["O5'"].get_vector(), r['P'].get_vector(), r["C4'"].get_vector()
+                        b = PDB.vectors.calc_dihedral(x3, x2, x1, x4)
+                        beta = math.degrees(b) # % 360
+                        print(f'input {f} {r}, {alphaprime}, {beta}')

setup.py

@@ -28,6 +28,8 @@
              'rna_tools/tools/rna_calc_rmsd/rna_calc_rmsd_all_vs_all.py',
              'rna_tools/tools/rna_calc_rmsd/rna_calc_rmsd_biopython.py',
 
+             'rna_tools/rna_torsions.py',
+
              'rna_tools/tools/diffpdb/diffpdb.py',
              'rna_tools/tools/clanstix/rna_clanstix.py',
              'rna_tools/rna_dot2ct.py',