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/
RNANet
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Authored by
Aglaé TABOT
2021-06-25 07:09:36 +0200
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Commit
e2b121cafc89755f63a8a863ffa96fea5706406f
e2b121ca
1 parent
51cf844e
Modification of the name and composition of nucleotide triphosphates (GTP etc.)
Former-commit-id:
5bd9fc11
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1 changed file
with
20 additions
and
3 deletions
RNAnet.py
RNAnet.py
View file @
e2b121c
...
...
@@ -148,7 +148,9 @@ class SelectivePortionSelector(object):
# Refuse hydrogens
if
self
.
hydrogen_regex
.
match
(
atom
.
get_id
()):
return
0
# Refuse the first two phosohate groups when residue is a triphosphate
if
atom
.
get_id
()
in
[
'O3B'
,
'O2B'
,
'O1B'
,
'PB'
,
'O3G'
,
'O2G'
,
'O1G'
,
'PG'
]:
return
0
# Accept all atoms otherwise.
return
1
...
...
@@ -295,10 +297,25 @@ class Chain:
res_id
[
2
]
=
' '
res_id
[
0
]
=
' '
res_id
=
tuple
(
res_id
)
if
nt
in
[
'ATP'
,
'GTP'
,
'CTP'
,
'UTP'
]:
res_name
=
res
.
get_resname
()[
0
]
else
:
res_name
=
res
.
get_resname
()
res_atoms
=
res
.
get_atoms
()
new_residu_t
=
pdb
.
Residue
.
Residue
(
res_id
,
res
.
get_resname
()
,
res
.
get_segid
())
new_residu_t
=
pdb
.
Residue
.
Residue
(
res_id
,
res
_name
,
res
.
get_segid
())
for
atom
in
list
(
res
.
get_atoms
()):
new_atom_t
=
atom
.
copy
()
if
atom
.
get_name
()
in
[
'PA'
,
'O1A'
,
'O2A'
,
'O3A'
]:
if
atom
.
get_name
()
==
'PA'
:
atom_name
=
'P'
if
atom
.
get_name
()
==
'O1A'
:
atom_name
=
'OP1'
if
atom
.
get_name
()
==
'O2A'
:
atom_name
=
'OP2'
if
atom
.
get_name
()
==
'O3A'
:
atom_name
=
'OP3'
new_atom_t
=
pdb
.
Atom
.
Atom
(
atom_name
,
atom
.
get_coord
(),
atom
.
get_bfactor
(),
atom
.
get_occupancy
(),
atom
.
get_altloc
(),
atom_name
,
atom
.
get_serial_number
())
else
:
new_atom_t
=
atom
.
copy
()
new_residu_t
.
add
(
new_atom_t
)
new_chain_t
.
add
(
new_residu_t
)
...
...
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