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schwede
ma-wilkins-import
Commits
dbb0db78
Commit
dbb0db78
authored
3 years ago
by
Bienchen
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Add model, produce coordinates
parent
2a2b3b50
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translate2modelcif.py
+49
-7
49 additions, 7 deletions
translate2modelcif.py
with
49 additions
and
7 deletions
translate2modelcif.py
+
49
−
7
View file @
dbb0db78
...
...
@@ -10,6 +10,7 @@ import requests
import
ihm
import
modelcif
import
modelcif.dumper
import
modelcif.model
import
modelcif.reference
from
ost
import
io
...
...
@@ -41,6 +42,34 @@ def _parse_args():
return
opts
class
_OST2ModelCIF
(
modelcif
.
model
.
AbInitioModel
):
"""
Map OST entity elements to ihm.model
"""
def
__init__
(
self
,
*
args
,
**
kwargs
):
"""
Initialise a model
"""
# check that ost_entity exists, TypeError otherwise
self
.
ost_entity
=
kwargs
.
pop
(
"
ost_entity
"
)
self
.
asym
=
kwargs
.
pop
(
"
asym
"
)
super
().
__init__
(
*
args
,
**
kwargs
)
def
get_atoms
(
self
):
# ToDo [internal]: Take B-factor out since its not a B-factor?
for
atm
in
self
.
ost_entity
.
atoms
:
yield
modelcif
.
model
.
Atom
(
asym_unit
=
self
.
asym
[
atm
.
chain
.
name
],
seq_id
=
atm
.
residue
.
number
.
num
,
atom_id
=
atm
.
name
,
type_symbol
=
atm
.
element
,
x
=
atm
.
pos
[
0
],
y
=
atm
.
pos
[
1
],
z
=
atm
.
pos
[
2
],
het
=
atm
.
is_hetatom
,
biso
=
atm
.
b_factor
,
occupancy
=
atm
.
occupancy
,
)
def
_abort_msg
(
msg
,
exit_code
=
1
):
"""
Write error message and exit with exit_code.
"""
print
(
f
"
{
msg
}
\n
Aborting.
"
,
file
=
sys
.
stderr
)
...
...
@@ -227,10 +256,10 @@ def _get_entities(pdb_file, up_acs):
cif_ent
.
update
(
upkb
)
entities
.
append
(
cif_ent
)
return
entities
return
entities
,
ost_ent
def
_store_as_modelcif
(
interaction_name
,
data_json
,
file_prfx
):
def
_store_as_modelcif
(
interaction_name
,
data_json
,
ost_ent
,
file_prfx
):
"""
Mix all the data into a ModelCIF file.
"""
# create system to gather all the data
system
=
modelcif
.
System
(
...
...
@@ -280,11 +309,24 @@ def _store_as_modelcif(interaction_name, data_json, file_prfx):
assembly
=
modelcif
.
Assembly
(
asym_units
.
values
(),
name
=
"
ma_struct_assembly_details.assembly_name
"
)
system
.
assemblies
.
append
(
assembly
)
# audit_authors
system
.
authors
.
extend
(
data_json
[
"
audit_authors
"
])
# set up the model to produce coordinates
# ToDo [input]: Get ma_model_list.model_name
model
=
_OST2ModelCIF
(
assembly
=
assembly
,
asym
=
asym_units
,
ost_entity
=
ost_ent
,
name
=
"
ma_model_list.model_name
"
,
)
# ToDo [input]: Get name
model_group
=
modelcif
.
model
.
ModelGroup
(
[
model
],
name
=
"
ma_model_list.model_group_name
"
)
system
.
model_groups
.
append
(
model_group
)
# write modelcif System to file
with
open
(
f
"
{
file_prfx
}
.cif
"
,
"
w
"
,
encoding
=
"
utf8
"
)
as
mmcif_fh
:
modelcif
.
dumper
.
write
(
mmcif_fh
,
[
system
])
...
...
@@ -305,8 +347,8 @@ def _create_interaction_json():
def
_create_model_json
(
data
,
pdb_file
,
up_acs
):
"""
Create a dictionary (mimicking JSON) that contains all the data.
"""
data
[
"
target_entities
"
]
=
_get_entities
(
pdb_file
,
up_acs
)
return
data
data
[
"
target_entities
"
]
,
ost_ent
=
_get_entities
(
pdb_file
,
up_acs
)
return
ost_ent
def
_main
():
...
...
@@ -332,9 +374,9 @@ def _main():
fle
=
os
.
path
.
join
(
opts
.
model_dir
,
fle
)
# gather data into JSON-like structure
_create_model_json
(
mdlcf_json
,
fle
,
up_acs
)
ost_ent
=
_create_model_json
(
mdlcf_json
,
fle
,
up_acs
)
_store_as_modelcif
(
uid
,
mdlcf_json
,
file_prfx
)
_store_as_modelcif
(
uid
,
mdlcf_json
,
ost_ent
,
file_prfx
)
# ToDo [internal]: wipe data or is it overwritten in mdlcf_json?
print
(
f
"
... done with
{
opts
.
model_dir
}
.
"
)
...
...
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