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TooBBA
Commit 94aa95b9 authored by Stelios Karozis's avatar Stelios Karozis
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Add order parameter calculation, correction in whole workflow etc

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CHANGELOG
View file @ 94aa95b9
...@@ -6,6 +6,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ...@@ -6,6 +6,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased] ## [Unreleased]
## [0.0.9] - 2020-07-30
### Added
- calculate rdf profile for all combination of molecules
- create ndx for order parameter calculation
- calculate order parameter properties
- debug save function
### Changed
- text that is converted to unique hashed id, is now independent of group name and filename
- combine index and gmx ndx function
### Removed
- None
## [0.0.8] - 2020-07-17 ## [0.0.8] - 2020-07-17
### Added ### Added
- memory optimizations - memory optimizations
......
README.md
View file @ 94aa95b9
...@@ -2,4 +2,4 @@ ...@@ -2,4 +2,4 @@
## Tool for Bilayer in Blocks Analysis (TooBBA) ## Tool for Bilayer in Blocks Analysis (TooBBA)
It is an tool that reads .trr files, perform a domain decomposition (user defined) and analyzes each block in terms of lipids distribution. It is an tool that reads .trr files, perform a domain decomposition (user defined) and calculates structural properties for each block (domain). The final output constitute a domain dataset, aiming to feed Machine Learning (ML) algorithms and identify coherent groups of observations, sharing the same characteristics and properties.
main.py
View file @ 94aa95b9
...@@ -29,20 +29,33 @@ TPR=SYSTEM_NAME+'/eq_run.tpr' ...@@ -29,20 +29,33 @@ TPR=SYSTEM_NAME+'/eq_run.tpr'
# surf: Determine surface from atoms (ex. Head of lipid) # surf: Determine surface from atoms (ex. Head of lipid)
# vector: Determine vector that fits atoms (ex. Tail of lipid) # vector: Determine vector that fits atoms (ex. Tail of lipid)
# tilt: Use surf and vector result to calculate angle (if NAME is COMBINE) # tilt: Use surf and vector result to calculate angle (if NAME is COMBINE)
# index: Creates unique code (md5) for every subdomain to use in data saving process # index+FOLDER: Saves one ndx for every subdomain and creates unique code (md5)
# for every subdomain to use in data saving process
# index_order+FOLDER: Saves one ndx for order parameter calculations for every subdomain
# and creates unique code (md5) for every subdomain to use in data saving process
# density: Detrmine density profile of x,y,z and save peaks of directions with the least number # density: Detrmine density profile of x,y,z and save peaks of directions with the least number
# gmx_ndx: Saves one ndx for every subdomain # rdf: Calculate the 2D radial deistribution function g(r) and save peaks of directions with the least number
# [save, [type], save_name]: Save result of previous function, type: pkl, json # order: Calculate the order parameter of atom chain
# [save, [TYPE], SAVE_NAME]: Save result of previous function, type: pkl, json
# #
################################################### ###################################################
GROUPS={'ALL':['gmx_ndx','index',['save', ['pkl'],'index'],'density',['save', ['pkl'],'dens']], #todo save function faulty, save last result to existing pkl(s)
'HD_GROUP':['surf',['save', ['pkl', 'json'],'time_domain_c-normal-cg']], 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']],
'TL_GROUP':['vector',['save', ['pkl'],'vec']], 'TL_GROUP':['vector',['save', ['pkl'],'vec']],
'ORDER_NS_SPH':['index_order+ORDER_NS_SPH_ndx',['save', ['pkl'],'index'],'order',['save',['pkl'], 'order']],
'ORDER_NS_ACYL':['index_order+ORDER_NS_ACYL_ndx',['save', ['pkl'],'index'],'order',['save',['pkl'], 'order']],
'ORDER_FFA':['index_order+ORDER_FFA_ndx',['save', ['pkl'],'index'],'order',['save',['pkl'], 'order']],
'ORDER_CHOL':['index_order+ORDER_CHOL_ndx',['save', ['pkl'],'index'],'order',['save',['pkl'], 'order']],
'COMBINE':[['HD_GROUP','surf'],['TL_GROUP','vector'],['COMB','tilt'],['save', ['pkl'],'tilt']] 'COMBINE':[['HD_GROUP','surf'],['TL_GROUP','vector'],['COMB','tilt'],['save', ['pkl'],'tilt']]
} }
ALL={'NS':['C6', 'Na', 'P4', 'P3', 'C7','C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['ROH','R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['AC','C1', 'C2', 'C3', 'C4']} ALL={'NS':['C1', 'C2', 'C3', 'C4', 'C5','C6', 'Na', 'P4', 'P3', 'C7','C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['ROH','R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['AC','C1', 'C2', 'C3', 'C4']}
HD_GROUP={'NS':['C6', 'Na', 'P4', 'P3', 'C7'], 'CHOL':['ROH'], 'FFA':['AC']} HD_GROUP={'NS':['C6', 'Na', 'P4', 'P3', 'C7'], 'CHOL':['ROH'], 'FFA':['AC']}
TL_GROUP={'NS':['C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['C1', 'C2', 'C3', 'C4']} TL_GROUP={'NS':['C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['C1', 'C2', 'C3', 'C4']}
ORDER_NS_SPH={'NS':['C1', 'C2', 'C3', 'C4', 'C5']} #propable problem with the same atomname of NS, FFA
ORDER_NS_ACYL={'NS':['C8', 'C9', 'C10']}
ORDER_FFA={'FFA':['C1', 'C2', 'C3', 'C4']}
ORDER_CHOL={'CHOL':['R2', 'R3', 'R4', 'R5']}
################################################### ###################################################
################################################### ###################################################
print(' ') print(' ')
...@@ -85,31 +98,44 @@ else: ...@@ -85,31 +98,44 @@ else:
#Check save files if exist in order to skip functions #Check save files if exist in order to skip functions
prev=0 prev=0
sv_index={} sv_index={}
ndx_fl={}
for i in GROUPS.keys(): for i in GROUPS.keys():
sv_index[i]={}
ndx_fl[i]={}
cnt_ndx=-1
for j in GROUPS[i]: for j in GROUPS[i]:
cnt_ndx=cnt_ndx+1
try: try:
sv_index[j]={} if j.split('+')[0]=='index' or j.split('+')[0]=='index_order':
sv_index[j]['status']='not exist' ndx_fl[i][j.split('+')[0]]=j.split('+')[1]
sv_index[j]['name']='None' j=j.split('+')[0] #generalize index function
GROUPS[i][cnt_ndx]=j
except:
pass
try:
sv_index[i][j]={}
sv_index[i][j]['status']='not exist'
sv_index[i][j]['name']='None'
except TypeError: except TypeError:
sv_index[str(j)]={} sv_index[i][str(j)]={}
sv_index[str(j)]['status']='not exist' sv_index[i][str(j)]['status']='not exist'
sv_index[str(j)]['name']='None' sv_index[i][str(j)]['name']='None'
if len(j)==3: if len(j)==3:
if j[0]=='save': if j[0]=='save':
for k in j[1]: for k in j[1]:
if k=='pkl': if k=='pkl':
if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl'): if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl'):
sv_index[prev]['status']='exist' sv_index[i][prev]['status']='exist'
sv_index[prev]['name']='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl' sv_index[i][prev]['name']='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl'
else: else:
sv_index[prev]['status']='not exist' sv_index[i][prev]['status']='not exist'
if k=='json': if k=='json':
if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl'): if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl'):
sv_index[prev]['status']='exist' sv_index[i][prev]['status']='exist'
sv_index[prev]['name']='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl' sv_index[i][prev]['name']='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]+'.pkl'
else: else:
sv_index[prev]['status']='not exist' sv_index[i][prev]['status']='not exist'
prev=str(j) prev=str(j)
################################################### ###################################################
#-------------------------------------------------- #--------------------------------------------------
...@@ -121,6 +147,9 @@ for i in GROUPS.keys(): ...@@ -121,6 +147,9 @@ for i in GROUPS.keys():
pass pass
else: else:
#Find atom type index in lists created above #Find atom type index in lists created above
print('')
print('Group: ',i)
print('++++++++++++++++++++++++')
group_ndx=tbf.atomid_data(res_num, res_type, atom_type, atom_num, group=locals()[i]) group_ndx=tbf.atomid_data(res_num, res_type, atom_type, atom_num, group=locals()[i])
tbf.topickle(fl=group_ndx, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_ndx') tbf.topickle(fl=group_ndx, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_ndx')
del group_ndx del group_ndx
...@@ -156,7 +185,7 @@ for i in GROUPS.keys(): ...@@ -156,7 +185,7 @@ for i in GROUPS.keys():
################################################### ###################################################
for j in GROUPS[i]: for j in GROUPS[i]:
if len(j) > 1: if len(j) > 1:
if j=='surf' and sv_index[j]['status']=='not exist': if j=='surf' and sv_index[i][j]['status']=='not exist':
if j not in locals(): if j not in locals():
surf={} surf={}
#Creates dictionary with c, normal per subdomain for each frame #Creates dictionary with c, normal per subdomain for each frame
...@@ -164,34 +193,60 @@ for i in GROUPS.keys(): ...@@ -164,34 +193,60 @@ for i in GROUPS.keys():
surf[i]=tbf.coord2norm2cg(coord_vector,img=False) surf[i]=tbf.coord2norm2cg(coord_vector,img=False)
del coord_vector del coord_vector
sv_data=surf[i] sv_data=surf[i]
elif j=='surf' and sv_index[j]['status']=='exist': elif j=='surf' and sv_index[i][j]['status']=='exist':
if j not in locals(): if j not in locals():
surf={} surf={}
surf[i]=tbf.frompickle(sv_index[j]['name']) surf[i]=tbf.frompickle(sv_index[i][j]['name'])
#-------------------------------------------------- #--------------------------------------------------
if j=='vector' and sv_index[j]['status']=='not exist': if j=='vector' and sv_index[i][j]['status']=='not exist':
if j not in locals(): if j not in locals():
vector={} vector={}
coord_vector=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_FR'+str(NUM_FR)+'.pkl') coord_vector=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_FR'+str(NUM_FR)+'.pkl')
vector[i]=tbf.coord2vector(coord_vector) vector[i]=tbf.coord2vector(coord_vector)
del coord_vector del coord_vector
sv_data=vector[i] sv_data=vector[i]
elif j=='vector' and sv_index[j]['status']=='exist': elif j=='vector' and sv_index[i][j]['status']=='exist':
if j not in locals(): if j not in locals():
vector={} vector={}
vector[i]=tbf.frompickle(sv_index[j]['name']) vector[i]=tbf.frompickle(sv_index[i][j]['name'])
#--------------------------------------------------
#ToDo: make more generic file with ndx files and ndx for order parameter
#As for now the hash value is generic (system+domain coord), but needs to run for every input group
if j=='index' and sv_index[i][j]['status']=='not exist':
box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl')
tbf.togmxndx(box_res, fld='./'+SYSTEM_NAME+'/'+ndx_fl[i][j], sv_name=SYSTEM_NAME+'_'+i)
del box_res
uniq_id=tbgmx.ndx_index(SYSTEM_NAME,ndx_fl[i][j])
sv_data=uniq_id
elif j=='index' and sv_index[i][j]['status']=='exist':
box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl')
tbf.togmxndx(box_res, fld='./'+SYSTEM_NAME+'/'+ndx_fl[i][j], sv_name=SYSTEM_NAME+'_'+i)
del box_res
uniq_id=tbf.frompickle(sv_index[i][j]['name'])
#-------------------------------------------------- #--------------------------------------------------
if j=='index' and sv_index[j]['status']=='not exist': if j=='index_order' and sv_index[i][j]['status']=='not exist':
uniq_id=tbgmx.ndx_index(SYSTEM_NAME) box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl')
for mol, atoms in locals()[i].items():
tbgmx.order_ndx(box_res, fld='./'+SYSTEM_NAME+'/'+ndx_fl[i][j], atoms=atoms, sv_name=SYSTEM_NAME+'_'+i)
del box_res
uniq_id=tbgmx.ndx_index(SYSTEM_NAME,ndx_fl[i][j])
sv_data=uniq_id sv_data=uniq_id
elif j=='index' and sv_index[j]['status']=='exist': elif j=='index_order' and sv_index[i][j]['status']=='exist':
uniq_id=tbf.frompickle(sv_index[j]['name']) box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl')
for mol, atoms in locals()[i].items():
tbgmx.order_ndx(box_res, fld='./'+SYSTEM_NAME+'/'+ndx_fl[i][j], atoms=atoms, sv_name=SYSTEM_NAME+'_'+i)
del box_res
uniq_id=tbf.frompickle(sv_index[i][j]['name'])
#-------------------------------------------------- #--------------------------------------------------
if j=='density' and sv_index[j]['status']=='not exist': if j=='density' and sv_index[i][j]['status']=='not exist':
dens_dict={} dens_dict={}
for iidd in uniq_id.keys(): for iidd in uniq_id.keys():
dens_dict[iidd]={} dens_dict[iidd]={}
fl='./'+uniq_id[iidd]['system']+'/gmx_ndx/'+uniq_id[iidd]['ndx_file'] fl='./'+uniq_id[iidd]['system']+'/'+uniq_id[iidd]['fld']+'/'+uniq_id[iidd]['ndx_file']
cnt=-1 cnt=-1
for mol in locals()[i].keys(): for mol in locals()[i].keys():
ind=tbf.search_pattern(fl,mol) ind=tbf.search_pattern(fl,mol)
...@@ -199,11 +254,11 @@ for i in GROUPS.keys(): ...@@ -199,11 +254,11 @@ for i in GROUPS.keys():
break break
cnt=cnt+1 cnt=cnt+1
for d in ('x','y','z'): for d in ('x','y','z'):
peaks = tbgmx.density_picks(TRR=TRAJ,TPR=TPR,IND=fl,SLC=400,ST=time_index[ST_FR],EN=-1,normal=d,fld='./'+uniq_id[iidd]['system'],arg=cnt,dist_pk=20) peaks = tbgmx.density_peaks(TRR=TRAJ,TPR=TPR,IND=fl,SLC=400,ST=time_index[ST_FR],EN=-1,normal=d,fld='./'+uniq_id[iidd]['system'],arg=cnt,dist_pk=20)
if d=='x': if d=='x':
tmp=peaks tmp=peaks
else: else:
print(len(tmp),len(peaks)) #print(len(tmp),len(peaks))
if len(tmp)<len(peaks): if len(tmp)<len(peaks):
peaks=tmp peaks=tmp
tmp=peaks tmp=peaks
...@@ -212,14 +267,63 @@ for i in GROUPS.keys(): ...@@ -212,14 +267,63 @@ for i in GROUPS.keys():
sv_data=dens_dict sv_data=dens_dict
mrg_data[j]=[dens_dict,[]] mrg_data[j]=[dens_dict,[]]
del dens_dict del dens_dict
elif j=='density' and sv_index[j]['status']=='exist': elif j=='density' and sv_index[i][j]['status']=='exist':
dens_dict=tbf.frompickle(sv_index[j]['name']) dens_dict=tbf.frompickle(sv_index[i][j]['name'])
mrg_data[j]=[dens_dict,[]] mrg_data[j]=[dens_dict,[]]
del dens_dict del dens_dict
#-------------------------------------------------- #--------------------------------------------------
if j=='gmx_ndx': if j=='rdf' and sv_index[i][j]['status']=='not exist':
box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl') rdf_dict={}
tbf.togmxndx(box_res, fld='./'+SYSTEM_NAME, sv_name=SYSTEM_NAME+'_'+i) for iidd in uniq_id.keys():
rdf_dict[iidd]={}
fl='./'+uniq_id[iidd]['system']+'/'+uniq_id[iidd]['fld']+'/'+uniq_id[iidd]['ndx_file']
cnt1=-1
for mol1 in locals()[i].keys():
ind=tbf.search_pattern(fl,mol1)
if ind=='not exist':
break
cnt1=cnt1+1
cnt2=-1
for mol2 in locals()[i].keys():
ind=tbf.search_pattern(fl,mol2)
if ind=='not exist':
break
cnt2=cnt2+1
peaks = tbgmx.rdf_peaks(TRR=TRAJ,TPR=TPR,IND=fl,ST=time_index[ST_FR],EN=-1,fld='./'+uniq_id[iidd]['system'],arg1=cnt1,arg2=cnt2,dist_pk=20)
rdf_nm=mol1+'-'+mol2+'_rdf'
rdf_dict[iidd][rdf_nm]=peaks
sv_data=rdf_dict
mrg_data[j]=[rdf_dict,[]]
del rdf_dict
elif j=='rdf' and sv_index[i][j]['status']=='exist':
rdf_dict=tbf.frompickle(sv_index[i][j]['name'])
mrg_data[j]=[rdf_dict,[]]
del rdf_dict
#--------------------------------------------------
if j=='order' and sv_index[i][j]['status']=='not exist':
order_dict={}
for iidd in uniq_id.keys():
order_dict[iidd]={}
#fl='./'+uniq_id[iidd]['system']+'order_'+i+uniq_id[iidd]['ndx_file']
fl='./'+uniq_id[iidd]['system']+'/'+uniq_id[iidd]['fld']+'/'+uniq_id[iidd]['ndx_file']
for d in ('x','y','z'):
yy = tbgmx.order(TRR=TRAJ,TPR=TPR,IND=fl,ST=time_index[ST_FR],EN=-1,normal=d,fld='./'+uniq_id[iidd]['system'],dist_pk=1)
if d=='x':
tmp=yy
else:
#print(len(tmp),len(peaks))
if max(tmp)>max(yy):
yy=tmp
tmp=yy
order_nm=mol+'_order'
order_dict[iidd][order_nm]=yy
sv_data=order_dict
mrg_data[j]=[order_dict,[]]
del order_dict
elif j=='order' and sv_index[i][j]['status']=='exist':
order_dict=tbf.frompickle(sv_index[i][j]['name'])
mrg_data[j]=[order_dict,[]]
del order_dict
#-------------------------------------------------- #--------------------------------------------------
# Save module # Save module
if len(j)==3: if len(j)==3:
...@@ -234,6 +338,7 @@ for i in GROUPS.keys(): ...@@ -234,6 +338,7 @@ for i in GROUPS.keys():
tbf.topickle(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]) tbf.topickle(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2])
if k=='json': if k=='json':
tbf.tojson(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]) tbf.tojson(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2])
del sv_data
################################################### ###################################################
#COMBINE section #COMBINE section
else: else:
...@@ -248,7 +353,7 @@ for i in GROUPS.keys(): ...@@ -248,7 +353,7 @@ for i in GROUPS.keys():
#del vector[j[0]] #del vector[j[0]]
#Calculate COMBINE property #Calculate COMBINE property
if j[0]=='COMB': if j[0]=='COMB':
if j[1]=='tilt' and sv_index[str(j)]['status']=='not exist': if j[1]=='tilt' and sv_index[i][str(j)]['status']=='not exist':
tilt=tbf.SurfVector_angle(surf,vector) tilt=tbf.SurfVector_angle(surf,vector)
del surf del surf
del vector del vector
...@@ -278,8 +383,8 @@ for i in GROUPS.keys(): ...@@ -278,8 +383,8 @@ for i in GROUPS.keys():
sv_data=tot_avg sv_data=tot_avg
mrg_data[j[1]]=[tot_avg,['Tilt[degrees]']] mrg_data[j[1]]=[tot_avg,['Tilt[degrees]']]
del tot_avg del tot_avg
elif j[1]=='tilt' and sv_index[str(j)]['status']=='exist': elif j[1]=='tilt' and sv_index[i][str(j)]['status']=='exist':
tot_avg=tbf.frompickle(sv_index[str(j)]['name']) tot_avg=tbf.frompickle(sv_index[i][str(j)]['name'])
mrg_data[j[1]]=[tot_avg,['Tilt[degrees]']] mrg_data[j[1]]=[tot_avg,['Tilt[degrees]']]
del tot_avg del tot_avg
#-------------------------------------------------- #--------------------------------------------------
...@@ -295,7 +400,8 @@ for i in GROUPS.keys(): ...@@ -295,7 +400,8 @@ for i in GROUPS.keys():
if k=='pkl': if k=='pkl':
tbf.topickle(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]) tbf.topickle(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2])
if k=='json': if k=='json':
tbf.tojson(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2]) tbf.tojson(fl=sv_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_'+j[2])
del sv_data
################################################### ###################################################
#Merge data #Merge data
tbf.topickle(fl=mrg_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_merge') tbf.topickle(fl=mrg_data, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_merge')
...@@ -313,5 +419,6 @@ for tp in mrg_data.keys(): ...@@ -313,5 +419,6 @@ for tp in mrg_data.keys():
data_df=df.copy() data_df=df.copy()
continue continue
tbf.topickle(fl=data_df, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_dataset') tbf.topickle(fl=data_df, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_dataset')
print(data_df.head())
################################################### ###################################################
################################################### ###################################################
\ No newline at end of file
tooba_f.py
View file @ 94aa95b9
...@@ -721,10 +721,10 @@ def SurfVector_angle(surf,vector): ...@@ -721,10 +721,10 @@ def SurfVector_angle(surf,vector):
def togmxndx(box_res, fld, sv_name): def togmxndx(box_res, fld, sv_name):
print(' ') print(' ')
print('Save to gmx_ndx progress:') print('Save to ndx progress:')
print('==============================') print('==============================')
cnt=0 cnt=0
fl_save=fld+'/gmx_ndx/' fl_save=fld+'/'
if not os.path.exists(fl_save): if not os.path.exists(fl_save):
os.makedirs(fl_save) os.makedirs(fl_save)
else: else:
......
tooba_gmx.py
View file @ 94aa95b9
...@@ -4,6 +4,8 @@ import numpy as np ...@@ -4,6 +4,8 @@ import numpy as np
from scipy.signal import find_peaks from scipy.signal import find_peaks
from scipy.signal import savgol_filter from scipy.signal import savgol_filter
import hashlib import hashlib
from progress.bar import Bar
#cmd="gmx covar -s test/eq_run.tpr -f test/eq_traj.trr -n test/gmx_ndx/test_\(1\,\ 0\,\ 3\).ndx" #cmd="gmx covar -s test/eq_run.tpr -f test/eq_traj.trr -n test/gmx_ndx/test_\(1\,\ 0\,\ 3\).ndx"
#os.system(cmd) #os.system(cmd)
...@@ -17,15 +19,18 @@ import hashlib ...@@ -17,15 +19,18 @@ import hashlib
#os.system(cmd) #os.system(cmd)
def ndx_index(SYSTEM_NAME): def ndx_index(SYSTEM_NAME, pth):
uniq_id={} uniq_id={}
path='./'+SYSTEM_NAME+'/gmx_ndx/' path='./'+SYSTEM_NAME+'/'+pth+'/'
for f in os.listdir(path): for f in os.listdir(path):
text=SYSTEM_NAME+'_'+f dom=f.split('(')[1].split(')')[0]
dom='('+dom+')'
#dom=f.split('_')[2].split('.')[0]
text=SYSTEM_NAME+'_'+dom
iidd=hashlib.md5(text.encode('utf-8')).hexdigest() iidd=hashlib.md5(text.encode('utf-8')).hexdigest()
dom=f.split('_')[2].split('.')[0] #dom=f.split('_')[2].split('.')[0]
uniq_id[iidd]={} uniq_id[iidd]={}
uniq_id[iidd]={'system':SYSTEM_NAME,'ndx_file':f,'domain':dom} uniq_id[iidd]={'system':SYSTEM_NAME,'fld':pth,'ndx_file':f,'domain':dom}
return uniq_id return uniq_id
def read_xvg(XVG): def read_xvg(XVG):
...@@ -43,7 +48,7 @@ def read_xvg(XVG): ...@@ -43,7 +48,7 @@ def read_xvg(XVG):
y = np.asarray(y) y = np.asarray(y)
return x,y return x,y
def density_picks(TRR,TPR,IND,SLC,ST,EN,normal,fld,arg,dist_pk=1): def density_peaks(TRR,TPR,IND,SLC,ST,EN,normal,fld,arg,dist_pk=1):
cmd=str(arg)+'\n'+str(arg)+'\n' cmd=str(arg)+'\n'+str(arg)+'\n'
if EN==-1: if EN==-1:
...@@ -54,7 +59,7 @@ def density_picks(TRR,TPR,IND,SLC,ST,EN,normal,fld,arg,dist_pk=1): ...@@ -54,7 +59,7 @@ def density_picks(TRR,TPR,IND,SLC,ST,EN,normal,fld,arg,dist_pk=1):
'-o', fld+'/tmp.xvg'], '-o', fld+'/tmp.xvg'],
stdin=subprocess.PIPE) stdin=subprocess.PIPE)
else: else:
p = subprocess.Popen(['gmx', 'density', '-symm', '-b', str(ST), '-e', str(EN),'-sl',str(SLC), '-d', normal, p = subprocess.Popen(['gmx', 'density', '-symm', '-b', str(ST), '-e', str(EN), '-sl',str(SLC), '-d', normal,
'-f', TRR, '-f', TRR,
'-s',TPR, '-s',TPR,
'-n',IND, '-n',IND,
...@@ -70,4 +75,119 @@ def density_picks(TRR,TPR,IND,SLC,ST,EN,normal,fld,arg,dist_pk=1): ...@@ -70,4 +75,119 @@ def density_picks(TRR,TPR,IND,SLC,ST,EN,normal,fld,arg,dist_pk=1):
pathname = os.path.abspath(os.path.join(fld, 'tmp.xvg')) pathname = os.path.abspath(os.path.join(fld, 'tmp.xvg'))
os.remove(pathname) os.remove(pathname)
return peaks #res return peaks
\ No newline at end of file
def rdf_peaks(TRR,TPR,IND,ST,EN,fld,arg1,arg2,dist_pk):
cmd=str(arg1)+'\n'+str(arg2)+'\n'
if EN==-1:
p = subprocess.Popen(['gmx', 'rdf', '-b', str(ST), '-selrpos', 'mol_com',
'-f', TRR,
'-s',TPR,
'-n',IND,
'-o', fld+'/tmp.xvg'],
stdin=subprocess.PIPE)
else:
p = subprocess.Popen(['gmx', 'rdf', '-b', str(ST), '-e', str(EN), '-selrpos', 'mol_com',
'-f', TRR,
'-s',TPR,
'-n',IND,
'-o', fld+'/tmp.xvg'],
stdin=subprocess.PIPE)
p.communicate(cmd.encode('UTF-8'))
p.send_signal('<Ctrl>-D')
p.wait()
x,y=read_xvg(XVG=fld+'/tmp.xvg')
yhat = savgol_filter(y, 15, 4) # window size 15, polynomial order 4
peaks, _ = find_peaks(yhat, distance=dist_pk)
pathname = os.path.abspath(os.path.join(fld, 'tmp.xvg'))
os.remove(pathname)
return peaks
def order_ndx(box_res,fld,atoms,sv_name):
#def togmxndx(box_res, fld, sv_name):
print(' ')
print('Save to order_ndx progress:')
print('==============================')
cnt=0
fl_save=fld+'/'
if not os.path.exists(fl_save):
os.makedirs(fl_save)
else:
print('WARNING: .ndx files exists. Nothing to do!')
return
ndx={}
for step in box_res.keys():
if cnt==1:
break
for resid in box_res[step].keys():
for res in box_res[step][resid].keys():
for subdomain in box_res[step][resid][res].keys():
ndx[subdomain]={}
rs=[]
bar = Bar('Create format: ', max=len(box_res[step].keys()))
for resid in box_res[step].keys():
for res in box_res[step][resid].keys():
for subdomain in box_res[step][resid][res]:
posl=-1
for at in atoms:
posl=posl+1
if (at,subdomain) not in rs:
rs.append((at,subdomain))
ndx[subdomain][at]=[]
posf=-1
for atomnum in box_res[step][resid][res][subdomain]:
posf=posf+1
if posl==posf:
ndx[subdomain][at].append(atomnum)
bar.next()
bar.finish()
cnt=cnt+1
bar = Bar('Save file: ', max=len(ndx.keys()))
for subdomain in ndx.keys():
save=fl_save+sv_name+'_'+str(subdomain)+'.ndx'
with open(save, "a") as myfile:
for res in ndx[subdomain].keys():
myfile.write("["+res+"]\n")
for atomnum in ndx[subdomain][res]:
myfile.write(atomnum+'\n')
bar.next()
bar.finish()
def order(TRR,TPR,IND,ST,EN,normal,fld,dist_pk=1):
if EN==-1:
p = subprocess.Popen(['gmx', 'order', '-b', str(ST), '-d', normal,
'-f', TRR,
'-s',TPR,
'-n',IND,
'-o', fld+'/tmp1.xvg',
'-od', fld+'/tmp2.xvg'],
stdin=subprocess.PIPE)
else:
p = subprocess.Popen(['gmx', 'order', '-b', str(ST), '-e', str(EN), '-d', normal,
'-f', TRR,
'-s',TPR,
'-n',IND,
'-o', fld+'/tmp1.xvg',
'-od', fld+'/tmp2.xvg'],
stdin=subprocess.PIPE)
p.wait()
x,y=read_xvg(XVG=fld+'/tmp1.xvg')
#yhat = savgol_filter(y, 15, 4) # window size 15, polynomial order 4
#peaks, _ = find_peaks(yhat, distance=dist_pk)
#exit()
pathname = os.path.abspath(os.path.join(fld, 'tmp1.xvg'))
os.remove(pathname)
pathname = os.path.abspath(os.path.join(fld, 'tmp2.xvg'))
os.remove(pathname)
return y
\ No newline at end of file
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GitLab - Multiscale Simulation Group - NCSR Demokritos