RNApolis 0.4.17__py3-none-any.whl → 0.6.0__py3-none-any.whl

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-0.4.17.dist-info → rnapolis-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.4.17
+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-0.4.17.dist-info → rnapolis-0.6.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{RNApolis-0.4.17.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-0.4.17.dist-info/RECORD

@@ -1,18 +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/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
-rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
-rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
-rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.4.17.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.17.dist-info/METADATA,sha256=NXwscUxsO3lpMD3eukldViwH6JUSFlEC9ExXwirgfLM,54516
-RNApolis-0.4.17.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-RNApolis-0.4.17.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.17.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.17.dist-info/RECORD,,