RNApolis 0.5.0__py3-none-any.whl → 0.6.0__py3-none-any.whl

rnapolis/aligner.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+import argparse
+import os
+import tempfile
+
+import pandas as pd
+
+from rnapolis.parser import is_cif
+from rnapolis.parser_v2 import parse_cif_atoms, parse_pdb_atoms, write_cif, write_pdb
+from rnapolis.tertiary_v2 import Structure
+
+
+def main():
+    """Main function to run the unifier tool."""
+    parser = argparse.ArgumentParser(description="Align two PDB or mmCIF files.")
+    parser.add_argument("--output", "-o", help="Output directory", required=True)
+    parser.add_argument(
+        "--format",
+        "-f",
+        help="Output format (possible values: PDB, mmCIF, keep. Default: keep)",
+        default="keep",
+    )
+    parser.add_argument("pdb1", help="First PDB or mmCIF file")
+    parser.add_argument("pdb2", help="Second PDB or mmCIF file")
+    args = parser.parse_args()
+
+    from pymol import cmd
+
+    cmd.load(args.pdb1, "pdb1")
+    cmd.load(args.pdb2, "pdb2")
+    cmd.align("pdb1", "pdb2", object="aligned", cycles=0)
+
+    pdb1_aligned = []
+    pdb2_aligned = []
+
+    with tempfile.NamedTemporaryFile("wt+", suffix=".aln") as f:
+        cmd.save(f.name, "aligned")
+        f.seek(0)
+
+        for line in f:
+            if line.startswith("pdb1"):
+                pdb1_aligned.append(line.split()[1])
+            elif line.startswith("pdb2"):
+                pdb2_aligned.append(line.split()[1])
+
+    pdb1_aligned = " ".join(pdb1_aligned)
+    pdb2_aligned = " ".join(pdb2_aligned)
+    residues_to_remove = {"pdb1": [], "pdb2": []}
+
+    for i, (c1, c2) in enumerate(zip(pdb1_aligned, pdb2_aligned)):
+        if c1 == c2:
+            continue
+        if c1 == "-":
+            residues_to_remove["pdb2"].append(i)
+        elif c2 == "-":
+            residues_to_remove["pdb1"].append(i)
+        elif c1 != c2:
+            residues_to_remove["pdb1"].append(i)
+            residues_to_remove["pdb2"].append(i)
+        else:
+            raise ValueError("This should not happen!")
+
+    if not residues_to_remove["pdb1"] and not residues_to_remove["pdb2"]:
+        print("Structures are already aligned")
+
+    structures = {}
+    for key, path in [("pdb1", args.pdb1), ("pdb2", args.pdb2)]:
+        with open(path) as f:
+            if is_cif(f):
+                atoms = parse_cif_atoms(f)
+            else:
+                atoms = parse_pdb_atoms(f)
+
+        structures[key] = Structure(atoms).residues
+
+    for key, residues in structures.items():
+        for i in sorted(residues_to_remove[key], reverse=True):
+            del residues[i]
+
+    # Write output
+    os.makedirs(args.output, exist_ok=True)
+
+    for (key, residues), path in zip(structures.items(), [args.pdb1, args.pdb2]):
+        base, _ = os.path.splitext(os.path.basename(path))
+
+        if args.format == "keep":
+            format = residues[0].atoms.attrs["format"]
+        else:
+            format = args.format
+
+        ext = ".pdb" if format == "PDB" else ".cif"
+
+        with open(f"{args.output}/{base}{ext}", "w") as f:
+            df = pd.concat([residue.atoms for residue in residues])
+
+            if format == "PDB":
+                write_pdb(df, f)
+            else:
+                write_cif(df, f)
+
+
+if __name__ == "__main__":
+    main()

rnapolis/clashfinder.py

@@ -179,20 +179,20 @@ def main():
         for ci, cj in sorted(clashing_chains):
             if ci == cj:
                 print(
-                    f"Clashes found in chain {ci} with maximum occupancy sum equal to {max_occupancy_chains[(ci,cj)]}"
+                    f"Clashes found in chain {ci} with maximum occupancy sum equal to {max_occupancy_chains[(ci, cj)]}"
                 )
             else:
                 print(
-                    f"Clashes found between chains {ci} and {cj} with maximum occupancy sum equal to {max_occupancy_chains[(ci,cj)]}"
+                    f"Clashes found between chains {ci} and {cj} with maximum occupancy sum equal to {max_occupancy_chains[(ci, cj)]}"
                 )
             for ri, rj in clashing_chains[(ci, cj)]:
                 if ri == rj:
                     print(
-                        f"    Clashes found in residue {ri} with maximum occupancy sum equal to {max_occupancy_residues[(ri,rj)]}"
+                        f"    Clashes found in residue {ri} with maximum occupancy sum equal to {max_occupancy_residues[(ri, rj)]}"
                     )
                 else:
                     print(
-                        f"    Clashes found between residues {ri} and {rj} with maximum occupancy sum equal to {max_occupancy_residues[(ri,rj)]}"
+                        f"    Clashes found between residues {ri} and {rj} with maximum occupancy sum equal to {max_occupancy_residues[(ri, rj)]}"
                     )
                 for ai, aj, occupancy in sorted(clashing_chains[(ci, cj)][(ri, rj)]):
                     print(

rnapolis/component_A.csv

@@ -0,0 +1,38 @@
+comp_id,atom_id,alt_atom_id,type_symbol,charge,pdbx_align,pdbx_aromatic_flag,pdbx_leaving_atom_flag,pdbx_stereo_config,model_Cartn_x,model_Cartn_y,model_Cartn_z,pdbx_model_Cartn_x_ideal,pdbx_model_Cartn_y_ideal,pdbx_model_Cartn_z_ideal,pdbx_component_atom_id,pdbx_component_comp_id,pdbx_ordinal
+A,OP3,O3P,O,0,1,N,Y,N,22.586,9.736,-6.030,2.135,-1.141,-5.313,OP3,A,1
+A,P,P,P,0,1,N,N,N,23.014,10.223,-7.491,1.024,-0.137,-4.723,P,A,2
+A,OP1,O1P,O,0,1,N,N,N,21.938,9.966,-8.412,1.633,1.190,-4.488,OP1,A,3
+A,OP2,O2P,O,0,1,N,N,N,24.378,9.686,-7.860,-0.183,0.005,-5.778,OP2,A,4
+A,O5',O5*,O,0,1,N,N,N,23.144,11.720,-7.092,0.456,-0.720,-3.334,O5',A,5
+A,C5',C5*,C,0,1,N,N,N,24.013,12.484,-7.839,-0.520,0.209,-2.863,C5',A,6
+A,C4',C4*,C,0,1,N,N,R,23.996,13.899,-7.276,-1.101,-0.287,-1.538,C4',A,7
+A,O4',O4*,O,0,1,N,N,N,24.523,13.928,-5.945,-0.064,-0.383,-0.538,O4',A,8
+A,C3',C3*,C,0,1,N,N,S,24.868,14.877,-8.041,-2.105,0.739,-0.969,C3',A,9
+A,O3',O3*,O,0,1,N,N,N,24.195,15.389,-9.178,-3.445,0.360,-1.287,O3',A,10
+A,C2',C2*,C,0,1,N,N,R,25.172,15.942,-7.004,-1.874,0.684,0.558,C2',A,11
+A,O2',O2*,O,0,1,N,N,N,24.060,16.759,-6.874,-3.065,0.271,1.231,O2',A,12
+A,C1',C1*,C,0,1,N,N,R,25.387,15.094,-5.814,-0.755,-0.367,0.729,C1',A,13
+A,N9,N9,N,0,1,Y,N,N,26.745,14.503,-5.630,0.158,0.029,1.803,N9,A,14
+A,C8,C8,C,0,1,Y,N,N,27.163,13.163,-5.773,1.265,0.813,1.672,C8,A,15
+A,N7,N7,N,0,1,Y,N,N,28.488,13.043,-5.514,1.843,0.963,2.828,N7,A,16
+A,C5,C5,C,0,1,Y,N,N,28.887,14.292,-5.222,1.143,0.292,3.773,C5,A,17
+A,C6,C6,C,0,1,Y,N,N,30.177,14.748,-4.871,1.290,0.091,5.156,C6,A,18
+A,N6,N6,N,0,1,N,N,N,31.245,13.997,-4.775,2.344,0.664,5.846,N6,A,19
+A,N1,N1,N,0,1,Y,N,N,30.286,16.119,-4.615,0.391,-0.656,5.787,N1,A,20
+A,C2,C2,C,0,1,Y,N,N,29.272,16.866,-4.702,-0.617,-1.206,5.136,C2,A,21
+A,N3,N3,N,0,1,Y,N,N,27.992,16.509,-5.030,-0.792,-1.051,3.841,N3,A,22
+A,C4,C4,C,0,1,Y,N,N,27.856,15.249,-5.271,0.056,-0.320,3.126,C4,A,23
+A,HOP3,3HOP,H,0,0,N,N,N,23.296,9.905,-5.422,2.448,-0.755,-6.142,HOP3,A,24
+A,HOP2,2HOP,H,0,0,N,N,N,25.088,9.855,-7.252,-0.552,-0.879,-5.902,HOP2,A,25
+A,H5',1H5*,H,0,1,N,N,N,25.039,12.050,-7.885,-1.319,0.301,-3.599,H5',A,26
+A,H5'',2H5*,H,0,0,N,N,N,23.788,12.450,-8.930,-0.052,1.182,-2.712,H5'',A,27
+A,H4',H4*,H,0,1,N,N,N,22.923,14.196,-7.338,-1.586,-1.254,-1.677,H4',A,28
+A,H3',H3*,H,0,1,N,N,N,25.794,14.420,-8.461,-1.890,1.736,-1.353,H3',A,29
+A,HO3',H3T,H,0,0,N,Y,N,24.741,16.001,-9.657,-4.024,1.035,-0.908,HO3',A,30
+A,H2',H2*,H,0,1,N,N,N,26.025,16.626,-7.219,-1.543,1.654,0.930,H2',A,31
+A,HO2',2HO*,H,0,0,N,N,N,24.250,17.425,-6.224,-3.740,0.936,1.037,HO2',A,32
+A,H1',H1*,H,0,1,N,N,N,25.197,15.783,-4.958,-1.185,-1.346,0.940,H1',A,33
+A,H8,H8,H,0,1,N,N,N,26.526,12.307,-6.055,1.611,1.246,0.745,H8,A,34
+A,H61,1H6,H,0,1,N,N,N,32.176,14.326,-4.521,2.432,0.522,6.801,H61,A,35
+A,H62,2H6,H,0,1,N,N,N,31.340,13.509,-5.666,2.996,1.205,5.374,H62,A,36
+A,H2,H2,H,0,1,N,N,N,29.524,17.915,-4.473,-1.325,-1.807,5.688,H2,A,37

rnapolis/component_C.csv

@@ -0,0 +1,36 @@
+comp_id,atom_id,alt_atom_id,type_symbol,charge,pdbx_align,pdbx_aromatic_flag,pdbx_leaving_atom_flag,pdbx_stereo_config,model_Cartn_x,model_Cartn_y,model_Cartn_z,pdbx_model_Cartn_x_ideal,pdbx_model_Cartn_y_ideal,pdbx_model_Cartn_z_ideal,pdbx_component_atom_id,pdbx_component_comp_id,pdbx_ordinal
+C,OP3,O3P,O,0,1,N,Y,N,26.803,20.514,-11.017,2.147,-1.021,-4.678,OP3,C,1
+C,P,P,P,0,1,N,N,N,27.386,20.433,-12.503,1.049,-0.039,-4.028,P,C,2
+C,OP1,O1P,O,0,1,N,N,N,26.539,21.293,-13.322,1.692,1.237,-3.646,OP1,C,3
+C,OP2,O2P,O,0,1,N,N,N,27.570,19.015,-12.877,-0.116,0.246,-5.102,OP2,C,4
+C,O5',O5*,O,0,1,N,N,N,28.830,21.055,-12.361,0.415,-0.733,-2.721,O5',C,5
+C,C5',C5*,C,0,1,N,N,N,29.051,22.423,-11.973,-0.546,0.181,-2.193,C5',C,6
+C,C4',C4*,C,0,1,N,N,R,30.525,22.652,-11.850,-1.189,-0.419,-0.942,C4',C,7
+C,O4',O4*,O,0,1,N,N,N,30.993,22.001,-10.600,-0.190,-0.648,0.076,O4',C,8
+C,C3',C3*,C,0,1,N,N,S,31.457,22.096,-12.933,-2.178,0.583,-0.307,C3',C,9
+C,O3',O3*,O,0,1,N,N,N,31.346,22.915,-14.074,-3.518,0.283,-0.703,O3',C,10
+C,C2',C2*,C,0,1,N,N,R,32.751,22.157,-12.194,-2.001,0.373,1.215,C2',C,11
+C,O2',O2*,O,0,1,N,N,N,33.186,23.463,-12.031,-3.228,-0.059,1.806,O2',C,12
+C,C1',C1*,C,0,1,N,N,R,32.361,21.627,-10.851,-0.924,-0.729,1.317,C1',C,13
+C,N1,N1,N,0,1,N,N,N,32.476,20.131,-10.779,-0.036,-0.470,2.453,N1,C,14
+C,C2,C2,C,0,1,N,N,N,33.674,19.589,-10.493,0.652,0.683,2.514,C2,C,15
+C,O2,O2,O,0,1,N,N,N,34.680,20.354,-10.277,0.529,1.504,1.620,O2,C,16
+C,N3,N3,N,0,1,N,N,N,33.855,18.230,-10.434,1.467,0.945,3.535,N3,C,17
+C,C4,C4,C,0,1,N,N,N,32.804,17.495,-10.663,1.620,0.070,4.520,C4,C,18
+C,N4,N4,N,0,1,N,N,N,32.905,16.139,-10.606,2.464,0.350,5.569,N4,C,19
+C,C5,C5,C,0,1,N,N,N,31.488,18.044,-10.975,0.916,-1.151,4.483,C5,C,20
+C,C6,C6,C,0,1,N,N,N,31.389,19.360,-11.041,0.087,-1.399,3.442,C6,C,21
+C,HOP3,3HOP,H,0,0,N,N,N,27.354,19.953,-10.483,2.501,-0.569,-5.456,HOP3,C,22
+C,HOP2,2HOP,H,0,0,N,N,N,28.121,18.454,-12.343,-0.508,-0.608,-5.323,HOP2,C,23
+C,H5',1H5*,H,0,1,N,N,N,28.562,23.147,-12.665,-1.315,0.371,-2.941,H5',C,24
+C,H5'',2H5*,H,0,0,N,N,N,28.496,22.699,-11.045,-0.052,1.118,-1.933,H5'',C,25
+C,H4',H4*,H,0,1,N,N,N,30.596,23.763,-11.911,-1.699,-1.350,-1.188,H4',C,26
+C,H3',H3*,H,0,1,N,N,N,31.269,21.074,-13.339,-1.917,1.604,-0.586,H3',C,27
+C,HO3',H3T,H,0,0,N,Y,N,31.923,22.570,-14.745,-4.088,0.939,-0.278,HO3',C,28
+C,H2',H2*,H,0,1,N,N,N,33.568,21.607,-12.716,-1.653,1.290,1.689,H2',C,29
+C,HO2',2HO*,H,0,0,N,N,N,34.010,23.501,-11.560,-3.874,0.644,1.656,HO2',C,30
+C,H1',H1*,H,0,1,N,N,N,33.051,22.057,-10.088,-1.392,-1.708,1.418,H1',C,31
+C,H41,1H4,H,0,1,N,N,N,33.824,15.755,-10.388,2.950,1.189,5.590,H41,C,32
+C,H42,2H4,H,0,1,N,N,N,32.564,15.734,-11.478,2.571,-0.289,6.290,H42,C,33
+C,H5,H5,H,0,1,N,N,N,30.568,17.464,-11.160,1.030,-1.873,5.278,H5,C,34
+C,H6,H6,H,0,1,N,N,N,30.417,19.806,-11.309,-0.465,-2.326,3.393,H6,C,35

rnapolis/component_G.csv

@@ -0,0 +1,39 @@
+comp_id,atom_id,alt_atom_id,type_symbol,charge,pdbx_align,pdbx_aromatic_flag,pdbx_leaving_atom_flag,pdbx_stereo_config,model_Cartn_x,model_Cartn_y,model_Cartn_z,pdbx_model_Cartn_x_ideal,pdbx_model_Cartn_y_ideal,pdbx_model_Cartn_z_ideal,pdbx_component_atom_id,pdbx_component_comp_id,pdbx_ordinal
+G,OP3,O3P,O,0,1,N,Y,N,34.313,3.314,-0.422,-1.945,-1.360,5.599,OP3,G,1
+G,P,P,P,0,1,N,N,N,33.741,4.431,0.367,-0.911,-0.277,5.008,P,G,2
+G,OP1,O1P,O,0,1,N,N,N,33.537,5.671,-0.451,-1.598,1.022,4.844,OP1,G,3
+G,OP2,O2P,O,0,1,N,N,N,34.442,4.727,1.661,0.325,-0.105,6.025,OP2,G,4
+G,O5',O5*,O,0,1,N,N,N,32.289,3.932,0.811,-0.365,-0.780,3.580,O5',G,5
+G,C5',C5*,C,0,1,N,N,N,32.101,2.551,1.198,0.542,0.217,3.109,C5',G,6
+G,C4',C4*,C,0,1,N,N,R,30.760,2.450,1.879,1.100,-0.200,1.748,C4',G,7
+G,O4',O4*,O,0,1,N,N,N,30.797,3.202,3.104,0.033,-0.318,0.782,O4',G,8
+G,C3',C3*,C,0,1,N,N,S,29.597,3.022,1.070,2.025,0.898,1.182,C3',G,9
+G,O3',O3*,O,0,1,N,N,N,29.106,2.045,0.152,3.395,0.582,1.439,O3',G,10
+G,C2',C2*,C,0,1,N,N,R,28.603,3.421,2.118,1.741,0.884,-0.338,C2',G,11
+G,O2',O2*,O,0,1,N,N,N,27.930,2.319,2.657,2.927,0.560,-1.066,O2',G,12
+G,C1',C1*,C,0,1,N,N,R,29.487,3.936,3.170,0.675,-0.220,-0.507,C1',G,13
+G,N9,N9,N,0,1,Y,N,N,29.942,5.378,3.195,-0.297,0.162,-1.534,N9,G,14
+G,C8,C8,C,0,1,Y,N,N,31.187,5.907,3.065,-1.440,0.880,-1.334,C8,G,15
+G,N7,N7,N,0,1,Y,N,N,31.237,7.191,3.136,-2.066,1.037,-2.464,N7,G,16
+G,C5,C5,C,0,1,Y,N,N,29.896,7.536,3.341,-1.364,0.431,-3.453,C5,G,17
+G,C6,C6,C,0,1,N,N,N,29.331,8.813,3.503,-1.556,0.279,-4.846,C6,G,18
+G,O6,O6,O,0,1,N,N,N,29.901,9.926,3.495,-2.534,0.755,-5.397,O6,G,19
+G,N1,N1,N,0,1,N,N,N,27.948,8.749,3.683,-0.626,-0.401,-5.551,N1,G,20
+G,C2,C2,C,0,1,N,N,N,27.233,7.615,3.707,0.459,-0.934,-4.923,C2,G,21
+G,N2,N2,N,0,1,N,N,N,25.894,7.743,3.899,1.384,-1.626,-5.664,N2,G,22
+G,N3,N3,N,0,1,N,N,N,27.758,6.393,3.559,0.649,-0.800,-3.630,N3,G,23
+G,C4,C4,C,0,1,Y,N,N,29.079,6.431,3.382,-0.226,-0.134,-2.868,C4,G,24
+G,HOP3,3HOP,H,0,0,N,N,N,34.442,2.528,0.096,-2.247,-1.021,6.453,HOP3,G,25
+G,HOP2,2HOP,H,0,0,N,N,N,34.571,3.941,2.179,0.745,-0.973,6.104,HOP2,G,26
+G,H5',1H5*,H,0,1,N,N,N,32.209,1.841,0.344,1.362,0.327,3.820,H5',G,27
+G,H5'',2H5*,H,0,0,N,N,N,32.936,2.156,1.822,0.018,1.168,3.011,H5'',G,28
+G,H4',H4*,H,0,1,N,N,N,30.585,1.358,2.025,1.640,-1.144,1.833,H4',G,29
+G,H3',H3*,H,0,1,N,N,N,29.867,3.891,0.426,1.772,1.868,1.610,H3',G,30
+G,HO3',H3T,H,0,0,N,Y,N,28.382,2.400,-0.351,3.923,1.300,1.065,HO3',G,31
+G,H2',H2*,H,0,1,N,N,N,27.827,4.115,1.719,1.346,1.847,-0.662,H2',G,32
+G,HO2',2HO*,H,0,0,N,N,N,27.299,2.572,3.321,3.573,1.254,-0.871,HO2',G,33
+G,H1',H1*,H,0,1,N,N,N,28.814,3.801,4.048,1.148,-1.167,-0.769,H1',G,34
+G,H8,H8,H,0,1,N,N,N,32.110,5.323,2.909,-1.776,1.261,-0.381,H8,G,35
+G,H1,H1,H,0,1,N,N,N,27.411,9.607,3.808,-0.736,-0.518,-6.508,H1,G,36
+G,H21,1H2,H,0,1,N,N,N,25.350,6.880,3.917,2.165,-2.007,-5.232,H21,G,37
+G,H22,2H2,H,0,1,N,N,N,25.507,8.377,3.200,1.256,-1.736,-6.619,H22,G,38

rnapolis/component_U.csv

@@ -0,0 +1,35 @@
+comp_id,atom_id,alt_atom_id,type_symbol,charge,pdbx_align,pdbx_aromatic_flag,pdbx_leaving_atom_flag,pdbx_stereo_config,model_Cartn_x,model_Cartn_y,model_Cartn_z,pdbx_model_Cartn_x_ideal,pdbx_model_Cartn_y_ideal,pdbx_model_Cartn_z_ideal,pdbx_component_atom_id,pdbx_component_comp_id,pdbx_ordinal
+U,OP3,O3P,O,0,1,N,Y,N,29.106,2.045,0.152,-2.122,1.033,-4.690,OP3,U,1
+U,P,P,P,0,1,N,N,N,28.940,2.442,-1.379,-1.030,0.047,-4.037,P,U,2
+U,OP1,O1P,O,0,1,N,N,N,28.520,1.217,-2.078,-1.679,-1.228,-3.660,OP1,U,3
+U,OP2,O2P,O,0,1,N,N,N,30.133,3.129,-1.866,0.138,-0.241,-5.107,OP2,U,4
+U,O5',O5*,O,0,1,N,N,N,27.784,3.522,-1.387,-0.399,0.736,-2.726,O5',U,5
+U,C5',C5*,C,0,1,N,N,N,26.432,3.117,-1.047,0.557,-0.182,-2.196,C5',U,6
+U,C4',C4*,C,0,1,N,N,R,25.647,4.373,-0.834,1.197,0.415,-0.942,C4',U,7
+U,O4',O4*,O,0,1,N,N,N,26.122,5.093,0.327,0.194,0.645,0.074,O4',U,8
+U,C3',C3*,C,0,1,N,N,S,25.763,5.465,-1.895,2.181,-0.588,-0.301,C3',U,9
+U,O3',O3*,O,0,1,N,N,N,25.041,5.077,-3.062,3.524,-0.288,-0.686,O3',U,10
+U,C2',C2*,C,0,1,N,N,R,25.213,6.663,-1.148,1.995,-0.383,1.218,C2',U,11
+U,O2',O2*,O,0,1,N,N,N,23.829,6.500,-1.012,3.219,0.046,1.819,O2',U,12
+U,C1',C1*,C,0,1,N,N,R,25.917,6.524,0.133,0.922,0.723,1.319,C1',U,13
+U,N1,N1,N,0,1,N,N,N,27.224,7.194,0.137,0.028,0.464,2.451,N1,U,14
+U,C2,C2,C,0,1,N,N,N,27.201,8.578,0.406,-0.690,-0.671,2.486,C2,U,15
+U,O2,O2,O,0,1,N,N,N,26.156,9.121,0.619,-0.587,-1.474,1.580,O2,U,16
+U,N3,N3,N,0,1,N,N,N,28.408,9.189,0.403,-1.515,-0.936,3.517,N3,U,17
+U,C4,C4,C,0,1,N,N,N,29.660,8.606,0.152,-1.641,-0.055,4.530,C4,U,18
+U,O4,O4,O,0,1,N,N,N,30.676,9.330,0.195,-2.391,-0.292,5.460,O4,U,19
+U,C5,C5,C,0,1,N,N,N,29.604,7.215,-0.113,-0.894,1.146,4.502,C5,U,20
+U,C6,C6,C,0,1,N,N,N,28.447,6.605,-0.111,-0.070,1.384,3.459,C6,U,21
+U,HOP3,3HOP,H,0,0,N,N,N,29.377,2.835,0.603,-2.475,0.583,-5.470,HOP3,U,22
+U,HOP2,2HOP,H,0,0,N,N,N,30.404,3.919,-1.414,0.534,0.613,-5.325,HOP2,U,23
+U,H5',1H5*,H,0,1,N,N,N,25.974,2.434,-1.800,1.329,-0.373,-2.942,H5',U,24
+U,H5'',2H5*,H,0,0,N,N,N,26.387,2.417,-0.179,0.060,-1.117,-1.940,H5'',U,25
+U,H4',H4*,H,0,1,N,N,N,24.613,3.957,-0.795,1.712,1.345,-1.185,H4',U,26
+U,H3',H3*,H,0,1,N,N,N,26.782,5.677,-2.293,1.923,-1.609,-0.583,H3',U,27
+U,HO3',H3T,H,0,0,N,Y,N,25.113,5.756,-3.722,4.094,-0.926,-0.234,HO3',U,28
+U,H2',H2*,H,0,1,N,N,N,25.358,7.661,-1.622,1.643,-1.301,1.688,H2',U,29
+U,HO2',2HO*,H,0,0,N,N,N,23.484,7.251,-0.543,3.865,-0.657,1.671,HO2',U,30
+U,H1',H1*,H,0,1,N,N,N,25.312,6.996,0.941,1.392,1.700,1.423,H1',U,31
+U,H3,H3,H,0,1,N,N,N,28.370,10.187,0.610,-2.024,-1.762,3.528,H3,U,32
+U,H5,H5,H,0,1,N,N,N,30.486,6.589,-0.327,-0.982,1.863,5.305,H5,U,33
+U,H6,H6,H,0,1,N,N,N,28.506,5.526,-0.332,0.507,2.295,3.421,H6,U,34

rnapolis/parser_v2.py

@@ -1,7 +1,10 @@
-from typing import IO, Union
+import io
+import tempfile
+from typing import IO, TextIO, Union
 
 import pandas as pd
 from mmcif.io.IoAdapterPy import IoAdapterPy
+from mmcif.io.PdbxReader import DataCategory, DataContainer
 
 
 def parse_pdb_atoms(content: Union[str, IO[str]]) -> pd.DataFrame:
@@ -200,3 +203,304 @@ def parse_cif_atoms(content: Union[str, IO[str]]) -> pd.DataFrame:
     df.attrs["format"] = "mmCIF"
 
     return df
+
+
+def write_pdb(
+    df: pd.DataFrame, output: Union[str, TextIO, None] = None
+) -> Union[str, None]:
+    """
+    Write a DataFrame of atom records to PDB format.
+
+    Parameters:
+    -----------
+    df : pd.DataFrame
+        DataFrame containing atom records, as created by parse_pdb_atoms or parse_cif_atoms
+    output : Union[str, TextIO, None], optional
+        Output file path or file-like object. If None, returns the PDB content as a string.
+
+    Returns:
+    --------
+    Union[str, None]
+        If output is None, returns the PDB content as a string. Otherwise, returns None.
+    """
+    # Create a buffer to store the PDB content
+    buffer = io.StringIO()
+
+    # Get the format of the DataFrame
+    format_type = df.attrs.get("format", "PDB")
+
+    # Process each row in the DataFrame
+    for _, row in df.iterrows():
+        # Initialize the line with spaces
+        line = " " * 80
+
+        # Set record type (ATOM or HETATM)
+        if format_type == "PDB":
+            record_type = row["record_type"]
+        else:  # mmCIF
+            record_type = row.get("group_PDB", "ATOM")
+        line = record_type.ljust(6) + line[6:]
+
+        # Set atom serial number
+        if format_type == "PDB":
+            serial = str(int(row["serial"]))
+        else:  # mmCIF
+            serial = str(int(row["id"]))
+        line = line[:6] + serial.rjust(5) + line[11:]
+
+        # Set atom name
+        if format_type == "PDB":
+            atom_name = row["name"]
+        else:  # mmCIF
+            atom_name = row.get("auth_atom_id", row.get("label_atom_id", ""))
+
+        # Right-justify atom name if it starts with a number
+        if atom_name and atom_name[0].isdigit():
+            line = line[:12] + atom_name.ljust(4) + line[16:]
+        else:
+            line = line[:12] + " " + atom_name.ljust(3) + line[16:]
+
+        # Set alternate location indicator
+        if format_type == "PDB":
+            alt_loc = row.get("altLoc", "")
+        else:  # mmCIF
+            alt_loc = row.get("label_alt_id", "")
+        line = line[:16] + alt_loc + line[17:]
+
+        # Set residue name
+        if format_type == "PDB":
+            res_name = row["resName"]
+        else:  # mmCIF
+            res_name = row.get("auth_comp_id", row.get("label_comp_id", ""))
+        line = line[:17] + res_name.ljust(3) + line[20:]
+
+        # Set chain identifier
+        if format_type == "PDB":
+            chain_id = row["chainID"]
+        else:  # mmCIF
+            chain_id = row.get("auth_asym_id", row.get("label_asym_id", ""))
+        line = line[:21] + chain_id + line[22:]
+
+        # Set residue sequence number
+        if format_type == "PDB":
+            res_seq = str(int(row["resSeq"]))
+        else:  # mmCIF
+            res_seq = str(int(row.get("auth_seq_id", row.get("label_seq_id", 0))))
+        line = line[:22] + res_seq.rjust(4) + line[26:]
+
+        # Set insertion code
+        if format_type == "PDB":
+            icode = row["iCode"] if pd.notna(row["iCode"]) else ""
+        else:  # mmCIF
+            icode = (
+                row.get("pdbx_PDB_ins_code", "")
+                if pd.notna(row.get("pdbx_PDB_ins_code", ""))
+                else ""
+            )
+        line = line[:26] + icode + line[27:]
+
+        # Set X coordinate
+        if format_type == "PDB":
+            x = float(row["x"])
+        else:  # mmCIF
+            x = float(row["Cartn_x"])
+        line = line[:30] + f"{x:8.3f}" + line[38:]
+
+        # Set Y coordinate
+        if format_type == "PDB":
+            y = float(row["y"])
+        else:  # mmCIF
+            y = float(row["Cartn_y"])
+        line = line[:38] + f"{y:8.3f}" + line[46:]
+
+        # Set Z coordinate
+        if format_type == "PDB":
+            z = float(row["z"])
+        else:  # mmCIF
+            z = float(row["Cartn_z"])
+        line = line[:46] + f"{z:8.3f}" + line[54:]
+
+        # Set occupancy
+        if format_type == "PDB":
+            occupancy = float(row["occupancy"])
+        else:  # mmCIF
+            occupancy = float(row.get("occupancy", 1.0))
+        line = line[:54] + f"{occupancy:6.2f}" + line[60:]
+
+        # Set temperature factor
+        if format_type == "PDB":
+            temp_factor = float(row["tempFactor"])
+        else:  # mmCIF
+            temp_factor = float(row.get("B_iso_or_equiv", 0.0))
+        line = line[:60] + f"{temp_factor:6.2f}" + line[66:]
+
+        # Set element symbol
+        if format_type == "PDB":
+            element = row["element"]
+        else:  # mmCIF
+            element = row.get("type_symbol", "")
+        line = line[:76] + element.rjust(2) + line[78:]
+
+        # Set charge
+        if format_type == "PDB":
+            charge = row["charge"]
+        else:  # mmCIF
+            charge = row.get("pdbx_formal_charge", "")
+            if charge and charge not in ["?", "."]:
+                # Convert numeric charge to PDB format (e.g., "1+" or "2-")
+                try:
+                    charge_val = int(charge)
+                    if charge_val != 0:
+                        charge = f"{abs(charge_val)}{'+' if charge_val > 0 else '-'}"
+                    else:
+                        charge = ""
+                except ValueError:
+                    pass
+        line = line[:78] + charge + line[80:]
+
+        # Write the line to the buffer
+        buffer.write(line.rstrip() + "\n")
+
+    # Add END record
+    buffer.write("END\n")
+
+    # Get the content as a string
+    content = buffer.getvalue()
+    buffer.close()
+
+    # Write to output if provided
+    if output is not None:
+        if isinstance(output, str):
+            with open(output, "w") as f:
+                f.write(content)
+        else:
+            output.write(content)
+        return None
+
+    # Return the content as a string
+    return content
+
+
+def write_cif(
+    df: pd.DataFrame, output: Union[str, TextIO, None] = None
+) -> Union[str, None]:
+    """
+    Write a DataFrame of atom records to mmCIF format.
+
+    Parameters:
+    -----------
+    df : pd.DataFrame
+        DataFrame containing atom records, as created by parse_pdb_atoms or parse_cif_atoms
+    output : Union[str, TextIO, None], optional
+        Output file path or file-like object. If None, returns the mmCIF content as a string.
+
+    Returns:
+    --------
+    Union[str, None]
+        If output is None, returns the mmCIF content as a string. Otherwise, returns None.
+    """
+    # Get the format of the DataFrame
+    format_type = df.attrs.get("format", "PDB")
+
+    # Create a new DataContainer
+    data_container = DataContainer("data_structure")
+
+    # Define the attributes for atom_site category
+    if format_type == "mmCIF":
+        # Use existing mmCIF attributes
+        attributes = list(df.columns)
+    else:  # PDB format
+        # Map PDB columns to mmCIF attributes
+        attributes = [
+            "group_PDB",  # record_type
+            "id",  # serial
+            "type_symbol",  # element
+            "label_atom_id",  # name
+            "label_alt_id",  # altLoc
+            "label_comp_id",  # resName
+            "label_asym_id",  # chainID
+            "label_entity_id",  # (generated)
+            "label_seq_id",  # resSeq
+            "pdbx_PDB_ins_code",  # iCode
+            "Cartn_x",  # x
+            "Cartn_y",  # y
+            "Cartn_z",  # z
+            "occupancy",  # occupancy
+            "B_iso_or_equiv",  # tempFactor
+            "pdbx_formal_charge",  # charge
+            "auth_seq_id",  # resSeq
+            "auth_comp_id",  # resName
+            "auth_asym_id",  # chainID
+            "auth_atom_id",  # name
+            "pdbx_PDB_model_num",  # (generated)
+        ]
+
+    # Prepare rows for the atom_site category
+    rows = []
+
+    for _, row in df.iterrows():
+        if format_type == "mmCIF":
+            # Use existing mmCIF data
+            row_data = [str(row.get(attr, "?")) for attr in attributes]
+        else:  # PDB format
+            # Map PDB data to mmCIF format
+            entity_id = "1"  # Default entity ID
+            model_num = "1"  # Default model number
+
+            row_data = [
+                str(row["record_type"]),  # group_PDB
+                str(int(row["serial"])),  # id
+                str(row["element"]),  # type_symbol
+                str(row["name"]),  # label_atom_id
+                str(row.get("altLoc", "")),  # label_alt_id
+                str(row["resName"]),  # label_comp_id
+                str(row["chainID"]),  # label_asym_id
+                entity_id,  # label_entity_id
+                str(int(row["resSeq"])),  # label_seq_id
+                str(row["iCode"])
+                if pd.notna(row["iCode"])
+                else "?",  # pdbx_PDB_ins_code
+                f"{float(row['x']):.3f}",  # Cartn_x
+                f"{float(row['y']):.3f}",  # Cartn_y
+                f"{float(row['z']):.3f}",  # Cartn_z
+                f"{float(row['occupancy']):.2f}",  # occupancy
+                f"{float(row['tempFactor']):.2f}",  # B_iso_or_equiv
+                str(row.get("charge", "")) or "?",  # pdbx_formal_charge
+                str(int(row["resSeq"])),  # auth_seq_id
+                str(row["resName"]),  # auth_comp_id
+                str(row["chainID"]),  # auth_asym_id
+                str(row["name"]),  # auth_atom_id
+                model_num,  # pdbx_PDB_model_num
+            ]
+
+        rows.append(row_data)
+
+    # Create the atom_site category
+    atom_site_category = DataCategory("atom_site", attributes, rows)
+
+    # Add the category to the data container
+    data_container.append(atom_site_category)
+
+    # Create an IoAdapter for writing
+    adapter = IoAdapterPy()
+
+    # Handle output
+    if output is None:
+        # Return as string - write to a temporary file and read it back
+        with tempfile.NamedTemporaryFile(mode="w+", suffix=".cif") as temp_file:
+            adapter.writeFile(temp_file.name, [data_container])
+            temp_file.flush()
+            temp_file.seek(0)
+            return temp_file.read()
+    elif isinstance(output, str):
+        # Write to a file path
+        adapter.writeFile(output, [data_container])
+        return None
+    else:
+        # Write to a file-like object
+        with tempfile.NamedTemporaryFile(mode="w+", suffix=".cif") as temp_file:
+            adapter.writeFile(temp_file.name, [data_container])
+            temp_file.flush()
+            temp_file.seek(0)
+            output.write(temp_file.read())
+        return None

rnapolis/tertiary_v2.py

@@ -379,7 +379,7 @@ class Residue:
         self.atoms = residue_df
         self.format = residue_df.attrs.get("format", "unknown")
 
-    @cached_property
+    @property
     def chain_id(self) -> str:
         """Get the chain identifier for this residue."""
         if self.format == "PDB":
@@ -391,7 +391,18 @@ class Residue:
                 return self.atoms["label_asym_id"].iloc[0]
         return ""
 
-    @cached_property
+    @chain_id.setter
+    def chain_id(self, value: str) -> None:
+        """Set the chain identifier for this residue."""
+        if self.format == "PDB":
+            self.atoms["chainID"] = value
+        elif self.format == "mmCIF":
+            if "auth_asym_id" in self.atoms.columns:
+                self.atoms["auth_asym_id"] = value
+            if "label_asym_id" in self.atoms.columns:
+                self.atoms["label_asym_id"] = value
+
+    @property
     def residue_number(self) -> int:
         """Get the residue sequence number."""
         if self.format == "PDB":
@@ -403,7 +414,18 @@ class Residue:
                 return int(self.atoms["label_seq_id"].iloc[0])
         return 0
 
-    @cached_property
+    @residue_number.setter
+    def residue_number(self, value: int) -> None:
+        """Set the residue sequence number."""
+        if self.format == "PDB":
+            self.atoms["resSeq"] = value
+        elif self.format == "mmCIF":
+            if "auth_seq_id" in self.atoms.columns:
+                self.atoms["auth_seq_id"] = value
+            if "label_seq_id" in self.atoms.columns:
+                self.atoms["label_seq_id"] = value
+
+    @property
     def insertion_code(self) -> Optional[str]:
         """Get the insertion code, if any."""
         if self.format == "PDB":
@@ -415,6 +437,15 @@ class Residue:
                 return icode if pd.notna(icode) else None
         return None
 
+    @insertion_code.setter
+    def insertion_code(self, value: Optional[str]) -> None:
+        """Set the insertion code."""
+        if self.format == "PDB":
+            self.atoms["iCode"] = value
+        elif self.format == "mmCIF":
+            if "pdbx_PDB_ins_code" in self.atoms.columns:
+                self.atoms["pdbx_PDB_ins_code"] = value
+
     @cached_property
     def residue_name(self) -> str:
         """Get the residue name (e.g., 'A', 'G', 'C', 'U', etc.)."""
@@ -494,10 +525,11 @@ class Residue:
     def __str__(self) -> str:
         """String representation of the residue."""
         # Start with chain ID and residue name
-        if self.chain_id.isspace() or not self.chain_id:
+        chain = self.chain_id
+        if chain.isspace() or not chain:
             builder = f"{self.residue_name}"
         else:
-            builder = f"{self.chain_id}.{self.residue_name}"
+            builder = f"{chain}.{self.residue_name}"
 
         # Add a separator if the residue name ends with a digit
         if len(self.residue_name) > 0 and self.residue_name[-1] in string.digits:
@@ -507,8 +539,9 @@ class Residue:
         builder += f"{self.residue_number}"
 
         # Add insertion code if present
-        if self.insertion_code is not None:
-            builder += f"^{self.insertion_code}"
+        icode = self.insertion_code
+        if icode is not None:
+            builder += f"^{icode}"
 
         return builder
 

rnapolis/unifier.py

@@ -0,0 +1,153 @@
+#!/usr/bin/env python3
+import argparse
+import os
+import sys
+from collections import Counter
+
+import pandas as pd
+
+from rnapolis.parser import is_cif
+from rnapolis.parser_v2 import parse_cif_atoms, parse_pdb_atoms, write_cif, write_pdb
+from rnapolis.tertiary_v2 import Structure
+
+
+def load_components():
+    result = {}
+    for residue in "ACGU":
+        component = os.path.join(
+            os.path.abspath(os.path.dirname(__file__)), f"component_{residue}.csv"
+        )
+        result[residue] = pd.read_csv(component)
+    return result
+
+
+def main():
+    """Main function to run the unifier tool."""
+    parser = argparse.ArgumentParser(
+        description="Unify content of a set of PDB or mmCIF files."
+    )
+    parser.add_argument("--output", "-o", help="Output directory", required=True)
+    parser.add_argument(
+        "--format",
+        "-f",
+        help="Output format (possible values: PDB, mmCIF, keep. Default: keep)",
+        default="keep",
+    )
+    parser.add_argument("files", nargs="+", help="PDB or mmCIF files to compare")
+    args = parser.parse_args()
+
+    components = load_components()
+    structures = []
+
+    for path in args.files:
+        with open(path) as f:
+            if is_cif(f):
+                atoms = parse_cif_atoms(f)
+            else:
+                atoms = parse_pdb_atoms(f)
+
+        residues = []
+
+        for residue in Structure(atoms).residues:
+            if residue.residue_name not in "ACGU":
+                continue
+
+            component = components[residue.residue_name]
+            mapping_dict = dict(
+                [row["alt_atom_id"], row["atom_id"]] for _, row in component.iterrows()
+            )
+            valid_names = component["atom_id"]
+            valid_names = valid_names[~valid_names.str.startswith("H")]
+            valid_order = {value: idx for idx, value in enumerate(valid_names.tolist())}
+            column = "name" if residue.format == "PDB" else "auth_atom_id"
+
+            # Replace alternative name with standard name
+            residue.atoms[column] = residue.atoms[column].replace(mapping_dict)
+            # Leave only standard, non-hydrogen atoms
+            residue.atoms = residue.atoms[residue.atoms[column].isin(valid_names)]
+            # Reorder atoms
+            residue.atoms = residue.atoms.sort_values(
+                by=[column], key=lambda col: col.map(valid_order)
+            )
+            residues.append(residue)
+
+        structures.append((path, residues))
+
+    for path, residues in structures:
+        ref_path, ref_residues = structures[0]
+
+        # Validity check 1: residue count must be equal
+        if len(residues) != len(ref_residues):
+            print(
+                f"Number of residues in {path} does not match {ref_path}, cannot continue"
+            )
+            sys.exit(1)
+
+        # Validity check 2: residue names must be equal
+        for i, (residue, ref_residue) in enumerate(zip(residues, ref_residues)):
+            if residue.residue_name != ref_residue.residue_name:
+                print(
+                    f"Residue {str(residue)} in {path} does not match {str(ref_residue)} in {ref_path}, cannot continue"
+                )
+                sys.exit(1)
+
+        # Find residues with different number of atoms
+        residues_to_remove = set()
+        for i, (residue, ref_residue) in enumerate(zip(residues, ref_residues)):
+            if len(residue.atoms) != len(ref_residue.atoms):
+                print(
+                    f"Number of atoms in {str(residue)} in {path} does not match {str(ref_residue)} in {ref_path}, will unify this"
+                )
+                residues_to_remove.add(i)
+
+    # Remove residues with different number of atoms
+    for _, residues in structures:
+        for i in sorted(residues_to_remove, reverse=True):
+            del residues[i]
+
+    # Find most common residue identifiers for each residue
+    n = len(structures[0][1])
+    counters = [Counter() for _ in range(n)]
+    for _, residues in structures:
+        for i, residue in enumerate(residues):
+            counters[i].update(
+                [(residue.chain_id, residue.residue_number, residue.insertion_code)]
+            )
+
+    # If any residue has different identifiers, use the most common one in all structures
+    for i, counter in enumerate(counters):
+        (chain_id, residue_number, insertion_code), count = counter.most_common(1)[0]
+        if count != len(structures):
+            print(
+                f"Residue {i + 1} has different identifiers in different structures, will unify this"
+            )
+            for _, residues in structures:
+                residue = residues[i]
+                residue.chain_id = chain_id
+                residue.residue_number = residue_number
+                residue.insertion_code = insertion_code
+
+    # Write output
+    os.makedirs(args.output, exist_ok=True)
+
+    for path, residues in structures:
+        base, _ = os.path.splitext(os.path.basename(path))
+
+        if args.format == "keep":
+            format = residues[0].atoms.attrs["format"]
+        else:
+            format = args.format
+
+        ext = ".pdb" if format == "PDB" else ".cif"
+
+        with open(f"{args.output}/{base}{ext}", "w") as f:
+            df = pd.concat([residue.atoms for residue in residues])
+
+            if format == "PDB":
+                write_pdb(df, f)
+            else:
+                write_cif(df, f)
+
+
+if __name__ == "__main__":
+    main()

{rnapolis-0.5.0.dist-info → rnapolis-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.5.0
+Version: 0.6.0
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok
@@ -32,6 +32,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: project-url
 Dynamic: requires-dist
 Dynamic: summary

rnapolis-0.6.0.dist-info/RECORD

@@ -0,0 +1,26 @@
+rnapolis/aligner.py,sha256=oJ81FrjlEEzqJcYJdZUE1PrPjabIOT7j0idwAHXVQMI,3156
+rnapolis/annotator.py,sha256=hRRzRmneYxbg2tvwVHMWLfzmJb4szV0JL_6EOC09Gwg,22101
+rnapolis/clashfinder.py,sha256=AC9_tIx7QIk57sELq_aKfU1u3UMOXbgcccQeGHhMR6c,8517
+rnapolis/common.py,sha256=LY6Uz96Br8ki_gA8LpfatgtvVbt9jOTkwgagayqTgf8,31251
+rnapolis/component_A.csv,sha256=koirS-AwUZwoYGItT8yn3wS6Idvmh2FANfTQcOS_xh8,2897
+rnapolis/component_C.csv,sha256=NtvsAu_YrUgTjzZm3j4poW4IZ99x3dPARB09XVIiMCc,2803
+rnapolis/component_G.csv,sha256=Z5wl8OnHRyx4XhTyBiWgRZiEvmZXhoxtVRH8bn6Vxf0,2898
+rnapolis/component_U.csv,sha256=8BUoU1m2YzGmi8_kw1xdpf3pucszHjFEtTex87CuXiE,2645
+rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
+rnapolis/mmcif_pdbx_v50.dic,sha256=5QFx1ssDaehR4_DQ-tS9VQux262SiLXaqcwmwwejF5c,5744659
+rnapolis/molecule_filter.py,sha256=jgcpJxx_oXEBX0d30v4k_FdwRouRUPUsEtCYWgLGpD4,7310
+rnapolis/motif_extractor.py,sha256=Lfn1iEkhkP9eZD3GPEWNAfy00QO7QPCc8wM_XS1ory8,1147
+rnapolis/parser.py,sha256=3g4mtFvpiEENFcSBBtx_E_x1vJPF9BujWnts0kb9XjE,16340
+rnapolis/parser_v2.py,sha256=ltesVKBiIKk9JlM02ttTJzLm1g5MHdPzDgQTcl40GP8,16257
+rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
+rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
+rnapolis/tertiary_v2.py,sha256=I1uyHWIUePNGO5m-suoL4ibtz02qAJUMvYm0BUKUygY,22480
+rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
+rnapolis/unifier.py,sha256=bXscX3lxeSxT4K1fm2UEURcU9_0JA0HdTbd8ZoHZFAY,5442
+rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
+rnapolis-0.6.0.dist-info/licenses/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+rnapolis-0.6.0.dist-info/METADATA,sha256=TcGmjLlYH8jPvWJr48a2ce-UhIIl_dAO_wygm4ZPrKY,54537
+rnapolis-0.6.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+rnapolis-0.6.0.dist-info/entry_points.txt,sha256=kS_Ji3_6UaomxkOaYpGHh4aZKaIh9CAfzoexbaS3y50,372
+rnapolis-0.6.0.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+rnapolis-0.6.0.dist-info/RECORD,,

{rnapolis-0.5.0.dist-info → rnapolis-0.6.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.0.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{rnapolis-0.5.0.dist-info → rnapolis-0.6.0.dist-info}/entry_points.txt

@@ -1,4 +1,5 @@
 [console_scripts]
+aligner = rnapolis.aligner:main
 annotator = rnapolis.annotator:main
 clashfinder = rnapolis.clashfinder:main
 metareader = rnapolis.metareader:main
@@ -6,3 +7,4 @@ molecule-filter = rnapolis.molecule_filter:main
 motif-extractor = rnapolis.motif_extractor:main
 rfam-folder = rnapolis.rfam_folder:main
 transformer = rnapolis.transformer:main
+unifier = rnapolis.unifier:main

rnapolis-0.5.0.dist-info/RECORD

@@ -1,20 +0,0 @@
-rnapolis/annotator.py,sha256=hRRzRmneYxbg2tvwVHMWLfzmJb4szV0JL_6EOC09Gwg,22101
-rnapolis/clashfinder.py,sha256=i95kp0o6OWNqmJDBr-PbsZd7RY2iJtBDr7QqolJSuAQ,8513
-rnapolis/common.py,sha256=LY6Uz96Br8ki_gA8LpfatgtvVbt9jOTkwgagayqTgf8,31251
-rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
-rnapolis/mmcif_pdbx_v50.dic,sha256=5QFx1ssDaehR4_DQ-tS9VQux262SiLXaqcwmwwejF5c,5744659
-rnapolis/molecule_filter.py,sha256=jgcpJxx_oXEBX0d30v4k_FdwRouRUPUsEtCYWgLGpD4,7310
-rnapolis/motif_extractor.py,sha256=Lfn1iEkhkP9eZD3GPEWNAfy00QO7QPCc8wM_XS1ory8,1147
-rnapolis/parser.py,sha256=3g4mtFvpiEENFcSBBtx_E_x1vJPF9BujWnts0kb9XjE,16340
-rnapolis/parser_v2.py,sha256=L85dRYlh_aOcSvt2ZtRJYFhYa0bwvYgoTQi9kUSqDGQ,5803
-rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
-rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
-rnapolis/tertiary_v2.py,sha256=GuTSEtbkMlYks6XA-P8pbLaT4M1cVS1T8gb8zcaGRzQ,21250
-rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
-rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-rnapolis-0.5.0.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-rnapolis-0.5.0.dist-info/METADATA,sha256=gq8j-Oln2H84wuzLZNvilJ5m1dPYtvm7vX2cpEunHYg,54515
-rnapolis-0.5.0.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
-rnapolis-0.5.0.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-rnapolis-0.5.0.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-rnapolis-0.5.0.dist-info/RECORD,,