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Merge pull request #19 from hernanchavezthielemann/beta_beta
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Beta beta
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@hernanchavezthielemann
hernanchavezthielemann committed May 22, 2019
2 parents 361d011 + 23841a1 commit 7cde8ac
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Showing 2 changed files with 53 additions and 21 deletions.
61 changes: 40 additions & 21 deletions lib/handling/gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from lib.misc.warn import wrg_1, wrg_3, pop_err_1, pop_wrg_1
from lib.misc.file import check_file, debugger_file, fileseeker
from lib.misc.geometry import rotate, arcos, raiz
from lib.misc.data import isnot_num
from sys import exit


Expand Down Expand Up @@ -162,7 +163,7 @@ def extract_gromacs_data( _data_files_, _autoload_):
###########################################################################
section = '''---------- .SIDE MOLE FILES. -------------'''
#=========================================================================#
#### research in topology for new molecules / side molecules
#### re-search in topology for new molecules / side molecules
if _autoload_:
data_container, ok_flag, _sidemol_f_ = sidemol_data( filename_top,
data_container)
Expand Down Expand Up @@ -227,7 +228,7 @@ def extract_gromacs_data( _data_files_, _autoload_):
aux_here = {}

if filename_nb <> filename_ff and filename_nb <> filename_bon:
# it is GROMOS there ??
# Is it GROMOS there ??
aux_here = get_gromos_define( filename_bon)

for key_ in aux_here.keys():
Expand Down Expand Up @@ -282,7 +283,8 @@ def extract_gromacs_data( _data_files_, _autoload_):

if _sidemol_f_:

# A_02 maths
### A_02 maths
# "previewing / preallocating" // computing side mol size
sidemol = data_container['sidemol']
side_bonds_n = 0
side_angles_n = 0
Expand All @@ -301,30 +303,35 @@ def extract_gromacs_data( _data_files_, _autoload_):
side_dihed_n += sm_quantity * dihedr_x_mol
side_improp_n += sm_quantity * improp_x_mol

n_bondsnew = n_bonds + side_bonds_n
n_anglesnew = n_angles + side_angles_n
n_dihednew = n_dihedrals + side_dihed_n
n_impropnew = n_impropers + side_improp_n
#print n_bonds, side_bonds_n, n_bonds + side_bonds_n
#print n_angles, side_angles_n, n_angles + side_angles_n

### A_03
# tester in case is an asigment for define ore something like that
contentkey = [ 'bond', 'angle', 'improper', 'dihedral']
for cont_k in contentkey:
# memorandum:
# 'define' stores in a contentkey dictionary each define key:value
cddd = data_container[ 'define'][ cont_k]

if cddd.keys() <> []:
for sb in range( len( sidemol['tag'])):
datacont = sidemol['data'][sb][cont_k+'s']
for dc in range( len(datacont)):
if not datacont[dc][-1].isdigit():
for sb in range( len( sidemol['tag'])): # in each side mol
datacont = sidemol['data'][sb][cont_k+'s']# in its cont-key
for dc in range( len( datacont)):# lets look their content
if isnot_num( datacont[dc][-1]):#
#print( '{} {} {}'.format( cont_k+'s', dc,
# datacont[dc][-1]))
aux = datacont[dc][:-1] + cddd[ datacont[dc][-1]]
sidemol['data'][sb][cont_k+'s'][dc] = aux
#elif 'gb_33' in datacont[dc]:
#else:
#print datacont[dc]

n_bondsnew = n_bonds + side_bonds_n
n_anglesnew = n_angles + side_angles_n
n_dihednew = n_dihedrals + side_dihed_n
n_impropnew = n_impropers + side_improp_n

#print n_bonds, side_bonds_n, n_bonds + side_bonds_n
#print n_angles, side_angles_n, n_angles + side_angles_n

#######################################################################
### A_04
# I think that this part is deprecated... however I am not sure
# Regarding the itp format:
# charges index 6 in data-atoms
# opls names in index 1
Expand All @@ -344,9 +351,11 @@ def extract_gromacs_data( _data_files_, _autoload_):

data_container['S_charge'] = _charge_
data_container['S_translation'] = _conv_dict_

#######################################################################
### A_05
############ Esoteric part ;) ###############
####----------- DEFINING BONDED INTERACTIONS ----------####
#### ----------- DEFINING BONDED INTERACTIONS ---------- ####
# load the side molecules data if exist
#sidemol = _topodata_['sidemol']
smol_extra_bondtypes = []
Expand Down Expand Up @@ -460,7 +469,13 @@ def extract_gromacs_data( _data_files_, _autoload_):
return data_container, [ ok_flag, _sidemol_f_]

def sidemol_data( _file_top_, data_container):
''' getter of the side molecules data'''
''' -- getter of the side molecules data --
Per each side mole returns a dictionary with:
tag : side mole tag
num : number in this instance of this kind of side mol
data : dictionary with topology data
{atoms bonds angles dihedrals impropers}
'''

sidemol = {'tag': [],'num':[], 'data':[] }# Tag # mol_number
sm_flag = False
Expand All @@ -473,7 +488,7 @@ def sidemol_data( _file_top_, data_container):
non_sm = [non_sm[i][0] for i in range(len(non_sm))]
_buffer_ = ''
else:
# non conventional case
# non conventional case // the one in the main top
non_sm = ['']
_buffer_ = '0'

Expand Down Expand Up @@ -536,10 +551,11 @@ def sidemol_data_gatherer( _sm_files_, _sm_):
''' collects all the data related with one kind of side molecule
the data types are specified in startstrings
'''
print 'Search for: ', _sm_, ' in: ' ,_sm_files_
print( '\nSearching for: {}'.format( _sm_ ))#, ' in: ' ,_sm_files_
_flag_ = True
_file_ = ''
_sm_data_c_ = {}

# is sm in sm_file?? in cases with more than one file
for smfile in _sm_files_:
with open( smfile, 'r') as sm_data:
Expand Down Expand Up @@ -570,6 +586,7 @@ def sidemol_data_gatherer( _sm_files_, _sm_):
pop_err_1('Error!! side molecule {} not found in itp -- '.format( _sm_))
_flag_ = False
else:
print( 'Succes!, found in : {}\n'.format( _file_))
tag_str = [ 'atoms', 'bonds', 'angles', 'dihedrals','fin']
_sm_data_c_ = { x:[] for x in tag_str if x <> 'fin'}
read_flag = False
Expand All @@ -591,6 +608,7 @@ def sidemol_data_gatherer( _sm_files_, _sm_):
i = tag_str.index( j_line[1])
cd_tag = tag_str[i]
iner_flag = True
print( '** Gathering {} data'.format( cd_tag))
elif j_line[1] == 'moleculetype':
break
else:
Expand All @@ -599,6 +617,7 @@ def sidemol_data_gatherer( _sm_files_, _sm_):
iner_flag = False
else :
cd_tag = tag_str[i]
print( '* Gathering {} data'.format( cd_tag))
iner_flag = True

elif iner_flag:
Expand Down
13 changes: 13 additions & 0 deletions lib/misc/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -213,3 +213,16 @@ def check_vars( _vars_, _varstype_, _endtext_ = 'Input script not created!'):


return _flag_c_

def isnot_num( _string_):
''' return True if the string is not numeric
'''
_flag_ = True
try:
float( _string_)
_flag_ = False
except ValueError:
pass
return _flag_

# vim:tw=80

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