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Stelios Karozis
TooBBA
Commits
9ece9069
Commit
9ece9069
authored
Jul 31, 2020
by
Stelios Karozis
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Debug atomid_data function
parent
94aa95b9
Changes
3
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3 changed files
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12 additions
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2 deletions
+12
-2
CHANGELOG
CHANGELOG
+10
-0
main.py
main.py
+0
-1
tooba_f.py
tooba_f.py
+2
-1
No files found.
CHANGELOG
View file @
9ece9069
...
@@ -6,6 +6,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
...
@@ -6,6 +6,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
## [Unreleased]
## [0.1.0] - 2020-07-31
### Added
- None
### Changed
- In atomid_data function a extra check was added for residue type in order to avoid create dictionaries with empty values in keys
### Removed
- None
## [0.0.9] - 2020-07-30
## [0.0.9] - 2020-07-30
### Added
### Added
- calculate rdf profile for all combination of molecules
- calculate rdf profile for all combination of molecules
...
...
main.py
View file @
9ece9069
...
@@ -39,7 +39,6 @@ TPR=SYSTEM_NAME+'/eq_run.tpr'
...
@@ -39,7 +39,6 @@ TPR=SYSTEM_NAME+'/eq_run.tpr'
# [save, [TYPE], SAVE_NAME]: Save result of previous function, type: pkl, json
# [save, [TYPE], SAVE_NAME]: Save result of previous function, type: pkl, json
#
#
###################################################
###################################################
#todo save function faulty, save last result to existing pkl(s)
GROUPS
=
{
'ALL'
:[
'index+ALL_ndx'
,[
'save'
,
[
'pkl'
],
'index'
],
'density'
,[
'save'
,
[
'pkl'
],
'dens'
]],
GROUPS
=
{
'ALL'
:[
'index+ALL_ndx'
,[
'save'
,
[
'pkl'
],
'index'
],
'density'
,[
'save'
,
[
'pkl'
],
'dens'
]],
'HD_GROUP'
:[
'surf'
,[
'save'
,
[
'pkl'
,
'json'
],
'surf'
],
'index+HD_ndx'
,[
'save'
,
[
'pkl'
],
'index'
],
'rdf'
,[
'save'
,
[
'pkl'
],
'rdf'
]],
'HD_GROUP'
:[
'surf'
,[
'save'
,
[
'pkl'
,
'json'
],
'surf'
],
'index+HD_ndx'
,[
'save'
,
[
'pkl'
],
'index'
],
'rdf'
,[
'save'
,
[
'pkl'
],
'rdf'
]],
'TL_GROUP'
:[
'vector'
,[
'save'
,
[
'pkl'
],
'vec'
]],
'TL_GROUP'
:[
'vector'
,[
'save'
,
[
'pkl'
],
'vec'
]],
...
...
tooba_f.py
View file @
9ece9069
...
@@ -382,6 +382,7 @@ def atomid_data(res_num, res_type, atom_type, atom_num, group={}):
...
@@ -382,6 +382,7 @@ def atomid_data(res_num, res_type, atom_type, atom_num, group={}):
and correspond to the atom types in group list
and correspond to the atom types in group list
parameters: res_num=[]
parameters: res_num=[]
res_type=[]
atom_type=[]
atom_type=[]
atom_num=[]
atom_num=[]
group={}
group={}
...
@@ -396,7 +397,7 @@ def atomid_data(res_num, res_type, atom_type, atom_num, group={}):
...
@@ -396,7 +397,7 @@ def atomid_data(res_num, res_type, atom_type, atom_num, group={}):
for
res
,
atom
in
group
.
items
():
for
res
,
atom
in
group
.
items
():
res_ndx
[
res
]
=
[]
res_ndx
[
res
]
=
[]
for
element
in
atom
:
for
element
in
atom
:
tmp
=
[
res_num
[
i
]
.
strip
()
for
i
,
e
in
enumerate
(
atom_type
)
if
e
.
strip
()
==
element
.
strip
()]
tmp
=
[
res_num
[
i
]
.
strip
()
for
i
,
e
in
enumerate
(
atom_type
)
if
e
.
strip
()
==
element
.
strip
()
and
res
.
strip
()
==
res_type
[
i
]
.
strip
()]
res_ndx
[
res
]
.
append
(
tmp
)
res_ndx
[
res
]
.
append
(
tmp
)
#bar.next()
#bar.next()
#bar.finish()
#bar.finish()
...
...
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