Louis BECQUEY / RNANet

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cbd4fc82 1 parent 32e8cd93

management of special cases

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Showing 1 changed file with 14 additions and 5 deletions
......@@ -159,14 +159,14 @@ class SelectivePortionSelector(object):
_select=Select()
def save_mmcif(ioobj, out_file, select=_select, preserve_atom_numbering=False):
# reuse and modification of the source code of Biopython
# to have the 2 columns of numbering of residues numbered with the index_chain of DSSR
if isinstance(out_file, str):
fp = open(out_file, "w")
close_file = True
else:
fp = out_file
close_file = False
#fp = open(out_file, "w")
#close_file=True
atom_dict = defaultdict(list)
for model in ioobj.structure.get_list():
......@@ -188,7 +188,7 @@ def save_mmcif(ioobj, out_file, select=_select, preserve_atom_numbering=False):
chain_id = chain.get_id()
if chain_id == " ":
chain_id = "."
# This is used to write label_seq_id and increments from 1,
# This is used to write label_seq_id,
# remaining blank for hetero residues
prev_residue_type = ""
......@@ -404,7 +404,8 @@ class Chain:
index_chain=nums.at[i, "index_chain"]
nt=nums.at[i, "nt_name"]
if nt == 'A' or nt == 'G' or nt == 'C' or nt == 'U' or nt in ['DG', 'DU', 'DC', 'DA', 'DI', 'DT' ] or nt == 'N' or nt == 'I' :
# particular case 6n5s_1_A, residue 201 in the original cif file (resname = G and HETATM = H_G)
if nt == 'A' or (nt == 'G' and (self.chain_label != '6n5s_1_A' and resseq != 201)) or nt == 'C' or nt == 'U' or nt in ['DG', 'DU', 'DC', 'DA', 'DI', 'DT' ] or nt == 'N' or nt == 'I' :
res=chain[(' ', resseq, icode_res)]
else : #modified nucleotides (e.g. chain 5l4o_1_A)
het='H_' + nt
......@@ -422,7 +423,15 @@ class Chain:
res_atoms=res.get_atoms()
new_residu_t=pdb.Residue.Residue(res_id, res_name, res.get_segid())
for atom in list(res.get_atoms()):
if atom.get_name() in ['PA', 'O1A', 'O2A', 'O3A']:
# rename the remaining phosphate group to P, OP1, OP2, OP3
if atom.get_name() in ['PA', 'O1A', 'O2A', 'O3A'] and res_name != 'RIA':
# RIA is a residue made up of 2 riboses and 2 phosphates,
# so it has an O2A atom between the C2A and C1 'atoms,
# and it also has an OP2 atom attached to one of its phosphates
# (see chains 6fyx_1_1, 6zu9_1_1, 6fyy_1_1, 6gsm_1_1 , 3jaq_1_1 and 1yfg_1_A)
# we do not modify the atom names of RIA residue
if atom.get_name() == 'PA':
atom_name = 'P'
if atom.get_name() == 'O1A':
......