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TooBBA
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Stelios Karozis
TooBBA
Commits
592ec4e6
Commit
592ec4e6
authored
May 14, 2020
by
Stelios Karozis
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Calculate Surface of HEADS & vector of each TAIL for every subdomain
parent
9b57904e
Changes
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4 changed files
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240 additions
and
56 deletions
+240
-56
.gitignore
.gitignore
+2
-0
CHANGELOG
CHANGELOG
+13
-0
main.py
main.py
+26
-5
tooba_f.py
tooba_f.py
+199
-51
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.gitignore
View file @
592ec4e6
...
...
@@ -2,3 +2,5 @@ FORTRAN_vscode/
__pycache__/
.venv/
.vscode/
*.png
*test*
CHANGELOG
View file @
592ec4e6
...
...
@@ -6,6 +6,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
## [0.0.3] - 2020-05-14
### Added
- code for assign coordinates to subdomain
- code for creating vectors for each tail of lipid in subdomain
- code for creating surface for heads of lipids in subdomain
### Changed
- change output in def atomid_data() to include resid
- adjust function that use def atomid_data() output accordigly
### Removed
- None
## [0.0.2] - 2020-05-11
### Added
- code for domain decomposition function
...
...
main.py
View file @
592ec4e6
...
...
@@ -10,9 +10,30 @@ data_all=tbf.fr_export(trajfile='traj.trr',num_frames=1)
_
,
data_num
,
_
,
res_num
,
res_type
,
atom_type
,
atom_num
,
_
=
tbf
.
read_gro
(
'initial.gro'
)
#Create subdomains coordinates
box_p
=
tbf
.
domain_decomposition
(
data
=
data_all
,
dx
=
2
,
dy
=
2
,
dz
=
2
)
#Find atom type index in lists created above
group_ndx
=
tbf
.
resid_data
(
atom_type
,
group
=
[
'C1'
])
#Assign desired atoms (from above function) to subdomains
_
,
box_res
=
tbf
.
res2grid
(
data_all
,
atom_num
,
box_p
,
group_ndx
)
print
(
box_res
)
\ No newline at end of file
###################################################
HEAD
=
False
if
HEAD
==
True
:
#Find atom type index in lists created above
group_ndx
=
tbf
.
atomid_data
(
res_num
,
atom_type
,
atom_num
,
group
=
{
'MMA'
:[
'C1'
,
'C2'
]})
#Assign desired atoms (from above function) to subdomains
##result1: {step:{res:{atom_type:{atom_num:(subX,subYsubZ)}}}}
##result2: {step:{res:{atom_type:{(subX,subYsubZ):[atom_num]}}}}
_
,
box_res
=
tbf
.
atom2grid
(
data_all
,
box_p
,
group_ndx
)
#Creates dictionary with coordinates per subdomain for each frame
coord_norm
,
_
=
tbf
.
sub_coord
(
box
=
box_res
,
data
=
data_all
,
res_num
=
res_num
)
#Creates dictionary with c, normal per subdomain for each frame
surf
=
tbf
.
coord2norm
(
coord_norm
,
img
=
True
)
###################################################
TAIL
=
True
if
TAIL
==
True
:
#Find atom type index in lists created above
group_ndx
=
tbf
.
atomid_data
(
res_num
,
atom_type
,
atom_num
,
group
=
{
'MMA'
:[
'C3'
,
'C4'
,
'C5'
]})
#Assign desired atoms (from above function) to subdomains
##result1: {step:{res:{atom_type:{atom_num:(subX,subYsubZ)}}}}
##result2: {step:{res:{atom_type:{(subX,subYsubZ):[atom_num]}}}}
_
,
box_res
=
tbf
.
atom2grid
(
data_all
,
box_p
,
group_ndx
)
#Creates dictionary with coordinates per subdomain for each frame
_
,
coord_vector
=
tbf
.
sub_coord
(
box
=
box_res
,
data
=
data_all
,
res_num
=
res_num
)
vector
=
tbf
.
coord2vector
(
coord_vector
)
\ No newline at end of file
tooba_f.py
View file @
592ec4e6
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