fixed bug where strands would sometimes be backwards in converted PDB…

…s and fixed bug where the box center was incorrect during inboxing

analysis/src/oxDNA_analysis_tools/UTILS/RyeReader.py

@@ -466,13 +466,10 @@ def calc_PBC_COM(conf):
  cms = calc_PBC_COM(conf)
  positions = conf.positions + target - cms 
  new_poses = coord_in_box(positions)
- positions += (new_poses - conf.positions)
- #if center:
- # cms = np.mean(positions, axis=0)
- # positions -= cms
+
  return Configuration(
  conf.time, conf.box, conf.energy,
- positions, conf.a1s, conf.a3s
+ new_poses, conf.a1s, conf.a3s
  )
 
 ####################################################################################

analysis/src/oxDNA_analysis_tools/__init__.py

@@ -1 +1 @@
-__version__ = '2.3.4'
+__version__ = '2.3.5'

analysis/src/oxDNA_analysis_tools/oxDNA_PDB.py

@@ -388,10 +388,16 @@ def main():
  # end residue identifiers
  residue_type = ""
  if not uniform_residue_names:
- if nucleotide == strand.monomers[0] and not strand.is_circular():
- residue_type = "3"
- elif nucleotide == strand.monomers[-1]:
- residue_type = "5"
+ if strand.is_old():
+ if nucleotide == strand.monomers[0] and not strand.is_circular():
+ residue_type = "3"
+ elif nucleotide == strand.monomers[-1]:
+ residue_type = "5"
+ else:
+ if nucleotide == strand.monomers[0] and not strand.is_circular():
+ residue_type = "5"
+ elif nucleotide == strand.monomers[-1]:
+ residue_type = "3"
 
  nuc_data = {
  'pos' : conf.positions[nucleotide.id],