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Fix for Minor Issues with PDB <--> OxDNA Conversion #147

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Fix for Minor Issues with PDB <--> OxDNA Conversion #147

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fd49318
fixed PDB parsing where "TER" identifier is present but "END" identif…
Lucandia Dec 18, 2024
be15cff
Add "END" identifier at the end of each PDB file. Fixed filename with…
Lucandia Dec 18, 2024
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5 changes: 4 additions & 1 deletion analysis/src/oxDNA_analysis_tools/PDB_oxDNA.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,9 +206,12 @@ def end_system():
end_system()
continue

# Catch the case where there was no TER or END identifier
# Catch the case where there was no TER identifier
if len(strand) > 0:
end_strand()

# Catch the case where there was no END identifier
if len(sys) > 0:
end_system()

return configs, systems
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12 changes: 9 additions & 3 deletions analysis/src/oxDNA_analysis_tools/oxDNA_PDB.py
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Original file line number Diff line number Diff line change
Expand Up @@ -283,7 +283,7 @@ def oxDNA_PDB(conf:Configuration, system:System, out_basename:str, protein_pdb_f
atom_counter = 1

# Iterate over strands in the oxDNA file
for strand in system.strands:
for i, strand in enumerate(system.strands):
strand_pdb = []
nucleotides_in_strand = strand.monomers
sequence = [n.btype for n in nucleotides_in_strand]
Expand Down Expand Up @@ -381,11 +381,13 @@ def oxDNA_PDB(conf:Configuration, system:System, out_basename:str, protein_pdb_f
# Either open a new file or increment chain ID
# Chain ID can be any alphanumeric character. Convention is A-Z, a-z, 0-9
if one_file_per_strand:
print("END", file=out) # Add the END identifier
out.close()
log("Wrote strand {}'s data to {}".format (strand.id, out_name))
chain_id = 'A'
if strand != system.strands[-1]:
out_name = out_basename + "_{}.pdb".format(strand.id, )
if i < len(system) - 1:
next_strand = system.strands[i + 1]
out_name = out_basename + "_{}.pdb".format(next_strand.id, )
out = open(out_name, "w")
else:
chain_id = chr(ord(chain_id)+1)
Expand All @@ -396,6 +398,10 @@ def oxDNA_PDB(conf:Configuration, system:System, out_basename:str, protein_pdb_f
elif chain_id == chr(ord('0')+1):
log("More than 62 chains identified, looping chain identifier...", level='warning')
chain_id = 'A'

# Add the END identifier at the end of the file
if not one_file_per_strand:
print("END", file=out)
print()

log("Wrote data to '{}'".format(out_name))
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