From 258f724fabb3f59cb503214d972256198dc5b277 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 1 Feb 2024 13:37:38 +0100
Subject: [PATCH] refactor: use new CreateBU and SaveMMCIF functions
---
actions/ost-compare-structures | 140 ++++++++++++++-------------------
1 file changed, 57 insertions(+), 83 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 3f91c3de7..56c6087a8 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -80,11 +80,10 @@ ost compare-structures -m model.pdb -r reference.cif -c A:B B:A
import argparse
import os
import json
-import time
-import sys
import traceback
import math
+import ost
from ost import io
from ost.mol.alg import scoring
@@ -186,17 +185,17 @@ def _ParseArgs():
dest="dump_structures",
default=False,
action="store_true",
- help=("Dump cleaned structures used to calculate all the scores as "
- "PDB files using specified suffix. Files will be dumped to the "
- "same location as original files."))
+ help=("Dump cleaned structures used to calculate all the scores as PDB"
+ " or mmCIF files using specified suffix. Files will be dumped to"
+ " the same location and in the same format as original files."))
parser.add_argument(
"-ds",
"--dump-suffix",
dest="dump_suffix",
- default=".compare.structures.pdb",
+ default="_compare_structures",
help=("Use this suffix to dump structures.\n"
- "Defaults to .compare.structures.pdb."))
+ "Defaults to _compare_structures"))
parser.add_argument(
"-ft",
@@ -534,50 +533,19 @@ def _RoundOrNone(num, decimals = 3):
return None
return round(num, decimals)
-def _Rename(ent):
- """Revert chain names to original names.
-
- PDBize assigns chain name in order A,B,C,D... which does not allow to infer
- the original chain name. We do a renaming here:
- if there are two chains mapping to chain A the resulting
- chain names will be: A and A2.
+def _AddSuffix(filename, dump_suffix):
+ """Add dump_suffix to the file name.
"""
- new_chain_names = list()
- chain_indices = list() # the chains where we actually change the name
- suffix_indices = dict() # keep track of whats the current suffix index
- # for each original chain name
-
- for ch_idx, ch in enumerate(ent.chains):
- if not ch.HasProp("original_name"):
- # pdbize doesnt set this property for chain names in ['_', '-']
- continue
- original_name = ch.GetStringProp("original_name")
- if original_name in new_chain_names:
- new_name = original_name + str(suffix_indices[original_name])
- new_chain_names.append(new_name)
- suffix_indices[original_name] = suffix_indices[original_name] + 1
- else:
- new_chain_names.append(original_name)
- suffix_indices[original_name] = 2
- chain_indices.append(ch_idx)
- editor = ent.EditXCS()
- # rename to nonsense to avoid clashing chain names
- for ch_idx in chain_indices:
- editor.RenameChain(ent.chains[ch_idx], ent.chains[ch_idx].name+"_yolo")
- # and do final renaming
- for new_name, ch_idx in zip(new_chain_names, chain_indices):
- editor.RenameChain(ent.chains[ch_idx], new_name)
-
-def _LoadStructure(structure_path, sformat=None, fault_tolerant=False,
- bu_idx=None):
- """Read OST entity either from mmCIF or PDB.
-
- The returned structure has structure_path attached as structure name
+ root, ext = os.path.splitext(filename)
+ if ext == ".gz":
+ root, ext2 = os.path.splitext(root)
+ ext = ext2 + ext
+ return root + dump_suffix + ext
+
+def _GetStructureFormat(structure_path, sformat=None):
+ """Get the structure format and return it as "pdb" or "mmcif".
"""
- if not os.path.exists(structure_path):
- raise Exception(f"file not found: {structure_path}")
-
if sformat is None:
# Determine file format from suffix.
ext = structure_path.split(".")
@@ -587,11 +555,26 @@ def _LoadStructure(structure_path, sformat=None, fault_tolerant=False,
raise Exception(f"Could not determine format of file "
f"{structure_path}.")
sformat = ext[-1].lower()
+ if sformat in ["mmcif", "cif"]:
+ return "mmcif"
+ elif sformat == "pdb":
+ return sformat
+ else:
+ raise Exception(f"Unknown/unsupported file format found for "
+ f"file {structure_path}.")
+
+def _LoadStructure(structure_path, sformat, fault_tolerant, bu_idx):
+ """Read OST entity either from mmCIF or PDB.
+
+ The returned structure has structure_path attached as structure name
+ """
+ if not os.path.exists(structure_path):
+ raise Exception(f"file not found: {structure_path}")
# increase loglevel, as we would pollute the info log with weird stuff
ost.PushVerbosityLevel(ost.LogLevel.Error)
# Load the structure
- if sformat in ["mmcif", "cif"]:
+ if sformat == "mmcif":
if bu_idx is not None:
cif_entity, cif_seqres, cif_info = \
io.LoadMMCIF(structure_path, info=True, seqres=True,
@@ -600,28 +583,31 @@ def _LoadStructure(structure_path, sformat=None, fault_tolerant=False,
raise RuntimeError(f"Invalid biounit index - requested {bu_idx} "
f"must be < {len(cif_info.biounits)}.")
biounit = cif_info.biounits[bu_idx]
- entity = biounit.PDBize(cif_entity, min_polymer_size=0)
+ entity = ost.mol.alg.CreateBU(cif_entity, biounit)
if not entity.IsValid():
raise IOError(
"Provided file does not contain valid entity.")
- _Rename(entity)
else:
entity = io.LoadMMCIF(structure_path,
fault_tolerant = fault_tolerant)
if len(entity.residues) == 0:
raise Exception(f"No residues found in file: {structure_path}")
- elif sformat == "pdb":
+ else:
entity = io.LoadPDB(structure_path, fault_tolerant = fault_tolerant)
if len(entity.residues) == 0:
raise Exception(f"No residues found in file: {structure_path}")
- else:
- raise Exception(f"Unknown/ unsupported file extension found for "
- f"file {structure_path}.")
+
# restore old loglevel and return
ost.PopVerbosityLevel()
entity.SetName(structure_path)
return entity
+def _DumpStructure(entity, structure_path, sformat):
+ if sformat == "mmcif":
+ io.SaveMMCIF(entity, structure_path)
+ else:
+ io.SavePDB(entity, structure_path)
+
def _AlnToFastaStr(aln):
""" Returns alignment as fasta formatted string
"""
@@ -714,7 +700,7 @@ def _GetAlignedResidues(aln):
"reference": ref_dct})
return aligned_residues
-def _Process(model, reference, args):
+def _Process(model, reference, args, model_format, reference_format):
mapping = None
if args.chain_mapping is not None:
@@ -855,32 +841,16 @@ def _Process(model, reference, args):
out["usalign_mapping"] = scorer.usalign_mapping
if args.dump_structures:
- try:
- io.SavePDB(scorer.model, model.GetName() + args.dump_suffix)
- except Exception as e:
- if "single-letter" in str(e) and args.model_biounit is not None:
- raise RuntimeError("Failed to dump processed model. PDB "
- "format only supports single character "
- "chain names. This is likely the result of "
- "chain renaming when constructing a user "
- "specified biounit. Dumping structures "
- "fails in this case.")
- else:
- raise
- try:
- io.SavePDB(scorer.target, reference.GetName() + args.dump_suffix)
- except Exception as e:
- if "single-letter" in str(e) and args.reference_biounit is not None:
- raise RuntimeError("Failed to dump processed reference. PDB "
- "format only supports single character "
- "chain names. This is likely the result of "
- "chain renaming when constructing a user "
- "specified biounit. Dumping structures "
- "fails in this case.")
- else:
- raise
+ # Dump model
+ model_dump_filename = _AddSuffix(model.GetName(), args.dump_suffix)
+ _DumpStructure(model, model_dump_filename, model_format)
+ # Dump reference
+ reference_dump_filename = _AddSuffix(reference.GetName(), args.dump_suffix)
+ _DumpStructure(reference, reference_dump_filename, reference_format)
+
return out
+
def _Main():
args = _ParseArgs()
@@ -890,15 +860,19 @@ def _Main():
raise RuntimeError("Only support CAD score when residue numbers in "
"model and reference match. Use -rna flag if "
"this is the case.")
+ reference_format = _GetStructureFormat(args.reference,
+ sformat=args.reference_format)
reference = _LoadStructure(args.reference,
- sformat=args.reference_format,
+ sformat=reference_format,
bu_idx=args.reference_biounit,
fault_tolerant = args.fault_tolerant)
+ model_format = _GetStructureFormat(args.model,
+ sformat=args.model_format)
model = _LoadStructure(args.model,
- sformat=args.model_format,
+ sformat=model_format,
bu_idx=args.model_biounit,
fault_tolerant = args.fault_tolerant)
- out = _Process(model, reference, args)
+ out = _Process(model, reference, args, model_format, reference_format)
# append input arguments
out["model"] = args.model
--
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