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Stelios Karozis
TooBBA
Commits
1d83dc7f
Commit
1d83dc7f
authored
Jul 03, 2020
by
Stelios Karozis
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Unified I/O + checking if save exists
parent
f8332608
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4 changed files
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139 additions
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28 deletions
+139
-28
CHANGELOG
CHANGELOG
+13
-0
main.py
main.py
+117
-26
tooba_f.py
tooba_f.py
+7
-1
tooba_gmx.py
tooba_gmx.py
+2
-1
No files found.
CHANGELOG
View file @
1d83dc7f
...
@@ -6,6 +6,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
...
@@ -6,6 +6,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
## [Unreleased]
## [0.0.7] - 2020-07-03
### Added
- unified properties output
- Add 'if file exist' universal fuction
- debug main.py
### Changed
- None
### Removed
- None
## [0.0.6] - 2020-07-02
## [0.0.6] - 2020-07-02
### Added
### Added
- Initial support for gmx commands
- Initial support for gmx commands
...
...
main.py
View file @
1d83dc7f
This diff is collapsed.
Click to expand it.
tooba_f.py
View file @
1d83dc7f
...
@@ -677,11 +677,14 @@ def SurfVector_angle(surf,vector):
...
@@ -677,11 +677,14 @@ def SurfVector_angle(surf,vector):
bar
=
Bar
(
'Step: '
+
step
,
max
=
len
(
surf
[
step
]
.
keys
()))
bar
=
Bar
(
'Step: '
+
step
,
max
=
len
(
surf
[
step
]
.
keys
()))
for
sudomain
in
surf
[
step
]
.
keys
():
for
sudomain
in
surf
[
step
]
.
keys
():
angle
[
step
][
sudomain
]
=
{}
angle
[
step
][
sudomain
]
=
{}
tot
=
[]
for
resid
in
vector
[
step
][
sudomain
]
.
keys
():
for
resid
in
vector
[
step
][
sudomain
]
.
keys
():
P1
=
tuple
(
surf
[
step
][
sudomain
][
'normal'
])
P1
=
tuple
(
surf
[
step
][
sudomain
][
'normal'
])
P2
=
tuple
(
vector
[
step
][
sudomain
][
resid
])
P2
=
tuple
(
vector
[
step
][
sudomain
][
resid
])
#print(tbf.angle_between3D(P1,P2))
#print(tbf.angle_between3D(P1,P2))
angle
[
step
][
sudomain
][
resid
]
=
angle_between3D
(
P1
,
P2
)
angle
[
step
][
sudomain
][
resid
]
=
angle_between3D
(
P1
,
P2
)
tot
.
append
(
angle_between3D
(
P1
,
P2
))
angle
[
step
][
sudomain
][
'avg/frame'
]
=
sum
(
tot
)
/
len
(
tot
)
bar
.
next
()
bar
.
next
()
bar
.
finish
()
bar
.
finish
()
return
angle
return
angle
...
@@ -694,6 +697,9 @@ def togmxndx(box_res, fld, sv_name):
...
@@ -694,6 +697,9 @@ def togmxndx(box_res, fld, sv_name):
fl_save
=
fld
+
'/gmx_ndx/'
fl_save
=
fld
+
'/gmx_ndx/'
if
not
os
.
path
.
exists
(
fl_save
):
if
not
os
.
path
.
exists
(
fl_save
):
os
.
makedirs
(
fl_save
)
os
.
makedirs
(
fl_save
)
else
:
print
(
'WARNING: .ndx files exists. Nothing to do!'
)
return
ndx
=
{}
ndx
=
{}
for
step
in
box_res
.
keys
():
for
step
in
box_res
.
keys
():
...
...
tooba_gmx.py
View file @
1d83dc7f
...
@@ -23,8 +23,9 @@ def ndx_index(SYSTEM_NAME):
...
@@ -23,8 +23,9 @@ def ndx_index(SYSTEM_NAME):
for
f
in
os
.
listdir
(
path
):
for
f
in
os
.
listdir
(
path
):
text
=
SYSTEM_NAME
+
'_'
+
f
text
=
SYSTEM_NAME
+
'_'
+
f
iidd
=
hashlib
.
md5
(
text
.
encode
(
'utf-8'
))
.
hexdigest
()
iidd
=
hashlib
.
md5
(
text
.
encode
(
'utf-8'
))
.
hexdigest
()
dom
=
f
.
split
(
'_'
)[
2
]
.
split
(
'.'
)[
0
]
uniq_id
[
iidd
]
=
{}
uniq_id
[
iidd
]
=
{}
uniq_id
[
iidd
]
=
{
'system'
:
SYSTEM_NAME
,
'
domain'
:
f
}
uniq_id
[
iidd
]
=
{
'system'
:
SYSTEM_NAME
,
'
ndx_file'
:
f
,
'domain'
:
dom
}
return
uniq_id
return
uniq_id
def
read_xvg
(
XVG
):
def
read_xvg
(
XVG
):
...
...
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