def get_amberhome():
ambhome = os.getenv('AMBERHOME')
if ambhome == None:
GMXMMPBSA_ERROR('AMBERHOME is not set!')
return ambhome
def find_progs(INPUT):
""" Find the necessary programs based in the user INPUT """
# List all of the used programs with the conditions that they are needed
logging.info('Checking external programs...')
used_progs = {
'cpptraj':
True,
'tleap':
True,
'parmchk2':
True,
'mmpbsa_py_energy':
((INPUT['pbrun'] or INPUT['gbrun'])
and not (INPUT['use_sander'] or INPUT['decomprun'])),
'sander': (INPUT['decomprun'] or INPUT['use_sander']
or INPUT['ifqnt'] == 1),
'sander.APBS':
INPUT['sander_apbs'] == 1,
'mmpbsa_py_nabnmode':
INPUT['nmoderun'],
'rism3d.snglpnt':
INPUT['rismrun']
}
gro_exe = {
'gmx5': [
# look for any available gromacs executable
'gmx',
'gmx_mpi',
'gmx_d',
'gmx_mpi_d'
],
'gmx4': [
# look for gromacs 4.x
'make_ndx',
'trjconv',
'editconf'
]
}
# The returned dictionary:
my_progs = {}
search_path = True
force_path = INPUT['gmx_path']
for prog in list(used_progs.keys()):
my_progs[prog] = ExternProg(prog, used_progs[prog],
search_path).full_path
if used_progs[prog]:
if not my_progs[prog]:
GMXMMPBSA_ERROR('Could not find necessary program [%s]' % prog)
logging.info('%s found! Using %s' % (prog, str(my_progs[prog])))
if force_path:
search_path = False
g5 = False
for v in gro_exe:
if v == 'gmx5':
for prog in gro_exe[v]:
exe = ExternProg(prog, True, search_path, force_path)
if exe.full_path:
logging.info('Using GROMACS version > 5.x.x!')
my_progs['make_ndx'] = [exe.full_path, 'make_ndx']
my_progs['editconf'] = [exe.full_path, 'editconf']
my_progs['trjconv'] = [exe.full_path, 'trjconv']
g5 = True
logging.info('%s found! Using %s' % (prog, exe.full_path))
break
if g5:
break
else:
c = 0
logging.info('Using GROMACS version 4.x.x!')
for prog in gro_exe[v]:
exe = ExternProg(prog, True, search_path, force_path)
if exe.full_path:
c += 1
my_progs[prog] = [exe.full_path]
logging.info('%s found! Using %s' %
(prog, str(my_progs[prog])))
if 'make_ndx' not in my_progs or 'editconf' not in my_progs or 'trjconv' not in my_progs:
GMXMMPBSA_ERROR('Could not find necessary program [ GROMACS ]')
logging.info('Checking external programs...Done.\n')
return my_progs
def selector(selection: str):
string_list = selection.split()
dist = None
exclude = None
res_selections = []
if selection.startswith('within'):
try:
dist = float(string_list[1])
except:
GMXMMPBSA_ERROR(
f'Invalid dist, we expected a float value but we get "{string_list[1]}"'
)
if len(string_list) == 4:
if string_list[2] != 'not':
GMXMMPBSA_ERROR(
f'We expected "not" but we get {string_list[2]} instead')
if str(string_list[3]).lower() not in [
'receptor', 'ligand', 'rec', 'lig'
]:
GMXMMPBSA_ERROR(
f'We expected one of this values: "receptor", "rec", "ligand" or "lig" but we get'
f' {(string_list[3]).lower()} instead')
exclude = 'REC' if str(
string_list[3]).lower() in ['receptor', 'rec'] else 'LIG'
else:
# try to process residue selection
for s in string_list:
n = s.split('/')
if len(n) != 2 or n[0] not in ascii_letters:
GMXMMPBSA_ERROR(
f'We expected something like this: A/2-10,35,41 but we get {s} instead'
)
chain = n[0]
resl = n[1].split(',')
for r in resl:
rr = r.split('-')
if len(rr) == 1:
ci = rr[0].split(':')
ri = [chain, int(ci[0]), ''] if len(ci) == 1 else [
chain, int(ci[0]), ci[1]
]
if ri in res_selections:
GMXMMPBSA_WARNING(
'Found duplicated residue in selection: CHAIN:{} RES_NUM:{} ICODE: '
'{}'.format(*ri))
continue
res_selections.append(ri)
else:
try:
start = int(rr[0])
end = int(rr[1]) + 1
except:
GMXMMPBSA_ERROR(
f'When residues range is defined, start and end most be integer but we get'
f' {rr[0]} and {rr[1]}')
for cr in range(start, end):
if [chain, cr, ''] in res_selections:
GMXMMPBSA_WARNING(
'Found duplicated residue in selection: CHAIN:{} RES_NUM:{} ICODE: '
'{}'.format(chain, cr, ''))
continue
res_selections.append([chain, cr, ''])
return dist, exclude, res_selections