def test_parse_cg_files(cg_file):
data = li.parse_cgs_file(cg_file)
def charged_groups(cg_file):
return li.parse_cgs_file(cg_file)
def main():
########################### ARGUMENT PARSER ###########################
description = "Interaction calculator"
parser = argparse.ArgumentParser(description=description)
#------------------------------ Top/traj -----------------------------#
s_helpstr = "Topology file"
parser.add_argument("-s", "--top", \
action = "store", \
type = str, \
dest = "top", \
default = None, \
help = s_helpstr)
t_helpstr = "Trajectory file"
parser.add_argument("-t", "--trj", \
action = "store", \
type = str, \
dest = "trj", \
default = None, \
help = t_helpstr)
r_helpstr = "Reference structure"
parser.add_argument("-r", "--ref", \
action = "store", \
type = str, \
dest = "ref", \
default = None, \
help = r_helpstr)
#------------------------------ Analyses -----------------------------#
b_helpstr = "Analyze salt-bridges"
parser.add_argument("-b", "--salt-bridges", \
action = "store_true", \
dest = "do_sb", \
help = b_helpstr)
f_helpstr = "Analyze hydrophobic clusters"
parser.add_argument("-f","--hydrophobic", \
action = "store_true", \
dest = "do_hc", \
help = f_helpstr)
y_helpstr = "Analyze hydrogen bonds"
parser.add_argument("-y","--hydrogen-bonds", \
action = "store_true", \
dest = "do_hb", \
help = y_helpstr)
p_helpstr = \
"Analyze interactions using the knowledge-based potential"
parser.add_argument("-p","--potential", \
action = "store_true", \
dest = "do_kbp", \
help = p_helpstr)
#------------------------ Hydrophobic contacts -----------------------#
hc_reslist = ["ALA", "VAL", "LEU", "ILE", "PHE", "PRO", "TRP", "MET"]
hcres_helpstr = \
"comma-separated list of hydrophobic residues (default: {:s})"
parser.add_argument("--hc-residues", \
action = "store", \
type = str, \
dest = "hc_reslist", \
default = hc_reslist, \
help = hcres_helpstr.format(\
", ".join(hc_reslist)))
hcco_default = 5.0
hcco_helpstr = \
"Distance cut-off for side-chain interaction (default: {:f})"
parser.add_argument("--hc-co", "--hc-cutoff", \
action = "store", \
dest = "hc_co", \
type = float, \
default = hcco_default, \
help = hcco_helpstr.format(hcco_default))
hcperco_default = 0.0
hcperco_helpstr = "Minimum persistence for interactions (default: {:f})"
parser.add_argument("--hc-perco", "--hc-persistence-cutoff", \
action = "store", \
type = float, \
dest = "hc_perco", \
default = 0.0, \
help = hcperco_helpstr.format(hcperco_default))
hcdat_default = "hydrophobic-clusters.dat"
hcdat_helpstr = \
"Name of the file where to store the list of " \
"hydrophobic contacts found (default: {:s})"
parser.add_argument("--hc-dat", \
action = "store", \
type = str, \
dest = "hc_dat", \
default = hcdat_default, \
help = hcdat_helpstr.format(hcdat_default))
hcgraph_helpstr = \
"Name of the file where to store adjacency matrix " \
"for interaction graph (hydrophobic contacts)"
parser.add_argument("--hc-graph", \
action = "store", \
dest = "hc_graph", \
type = str, \
default = None, \
help = hcgraph_helpstr)
#---------------------------- Salt bridges ---------------------------#
sbco_default = 4.5
sbco_helpstr = \
"Distance cut-off for side-chain interaction (default: {:f})"
parser.add_argument("--sb-co", "--sb-cutoff", \
action = "store", \
type = float, \
dest = "sb_co", \
default = sbco_default, \
help = sbco_helpstr.format(sbco_default))
sbperco_default = 0.0
sbperco_helpstr = \
"Minimum persistence for interactions (default: {:f})"
parser.add_argument("--sb-perco", "--sb-persistence-cutoff", \
action = "store", \
type = float, \
dest = "sb_perco", \
default = sbperco_default, \
help = sbperco_helpstr.format(sbperco_default))
sbdat_default = "salt-bridges.dat"
sbdat_helpstr = \
"Name of the file where to store the list of " \
"salt bridges found (default: {:s})"
parser.add_argument("--sb-dat", \
action = "store", \
type = str, \
dest = "sb_dat", \
default = sbdat_default, \
help = sbdat_helpstr.format(sbdat_default))
sbgraph_helpstr = \
"Name of the file where to store adjacency matrix " \
"for interaction graph (salt bridges)"
parser.add_argument("--sb-graph", \
action = "store", \
type = str, \
dest = "sb_graph", \
default = None, \
help = sbgraph_helpstr)
sbcgfile_default = pkg_resources.resource_filename('pyinteraph',
"charged_groups.ini")
sbcgfile_helpstr = "Default charged groups file (default: {:s})"
parser.add_argument("--sb-cg-file", \
action = "store", \
type = str, \
dest = "cgs_file", \
default = sbcgfile_default, \
help = sbcgfile_helpstr.format(sbcgfile_default))
sbmode_choices = ["different_charge", "same_charge", "all"]
sbmode_default = "different_charge"
sbmode_helpstr = \
"Electrostatic interactions mode. Accepted modes are {:s} " \
"(default: {:s})"
parser.add_argument("--sb-mode", \
action = "store", \
type = str, \
dest = "sb_mode", \
choices = sbmode_choices, \
default = sbmode_default, \
help = sbmode_helpstr.format(\
", ".join(sbmode_choices), \
sbmode_default))
#--------------------------- Hydrogen bonds --------------------------#
hbco_default = 3.5
hbco_helpstr = "Donor-acceptor distance cut-off (default: {:f})"
parser.add_argument("--hb-co", "--hb-cutoff", \
action = "store", \
type = float, \
dest = "hb_co", \
default = hbco_default, \
help = hbco_helpstr.format(hbco_default))
hbang_default = 120.0
hbang_helpstr = "Donor-acceptor angle cut-off (default: {:f})"
parser.add_argument("--hb-ang", "--hb-angle", \
action = "store", \
type = float, \
dest = "hb_angle", \
default = hbang_default, \
help = hbang_helpstr.format(hbang_default))
hbdat_default = "hydrogen-bonds.dat"
hbdat_helpstr = \
"Name of the file where to store the list of " \
"hydrogen bonds found (default: {:s})"
parser.add_argument("--hb-dat", \
action = "store", \
type = str, \
dest = "hb_dat", \
default = hbdat_default, \
help = hbdat_helpstr.format(hbdat_default))
hbgraph_helpstr = \
"Name of the file where to store adjacency matrix " \
"for interaction graph (hydrogen bonds)"
parser.add_argument("--hb-graph", \
action = "store", \
type = str, \
dest = "hb_graph", \
default = None, \
help = hbgraph_helpstr)
hbperco_default = 0.0
hbperco_helpstr = \
"Minimum persistence for hydrogen bonds (default: {:f})"
parser.add_argument("--hb-perco", \
action = "store", \
type = float, \
dest = "hb_perco", \
default = hbperco_default, \
help = hbperco_helpstr.format(hbperco_default))
hbclass_choices = ["all", "mc-mc", "mc-sc", "sc-sc", "custom"]
hbclass_default = "all"
hbclass_helpstr = \
"Class of hydrogen bonds to analyze. Accepted classes are {:s} " \
"(default: {:s})"
parser.add_argument("--hb-class", \
action = "store", \
type = str, \
dest = "hb_class", \
choices = hbclass_choices, \
default = hbclass_default, \
help = hbclass_helpstr.format(\
", ".join(hbclass_choices), \
hbclass_default))
hbadfile_default = pkg_resources.resource_filename('pyinteraph',
"hydrogen_bonds.ini")
hbadfile_helpstr = \
"File defining hydrogen bonds donor and acceptor atoms " \
"(default: {:s})"
parser.add_argument("--hb-ad-file", \
action = "store", \
type = str, \
dest = "hbs_file", \
default = hbadfile_default, \
help = hbadfile_helpstr.format(hbadfile_default))
hbcustom1_helpstr = "Custom group 1 for hydrogen bonds calculation"
parser.add_argument("--hb-custom-group-1", \
action = "store", \
type = str, \
dest = "hb_group1", \
default = None, \
help = hbcustom1_helpstr)
hbcustom2_helpstr = "Custom group 2 for hydrogen bonds calculation"
parser.add_argument("--hb-custom-group-2", \
action = "store", \
type = str, \
dest = "hb_group2", \
default = None, \
help = hbcustom2_helpstr)
#----------------------------- Potential -----------------------------#
kbpff_default = pkg_resources.resource_filename('pyinteraph',
"ff.S050.bin64")
kbpff_helpstr = "Statistical potential definition file (default: {:s})"
parser.add_argument("--kbp-ff", "--force-field", \
action = "store", \
type = str, \
dest = "kbp_ff", \
default = kbpff_default, \
help = kbpff_helpstr.format(kbpff_default))
kbpatom_default = pkg_resources.resource_filename('pyinteraph',
"kbp_atomlist")
kbpatom_helpstr = \
"Ordered, force-field specific list of atom names (default: {:s})"
parser.add_argument("--kbp-atomlist", \
action = "store", \
type = str, \
dest = "kbp_atomlist", \
default = kbpatom_default, \
help = kbpatom_helpstr.format(kbpatom_default))
kbpdat_default = "kb-potential.dat"
kbpdat_helpstr = \
"Name of the file where to store the results of " \
"the statistical potential analysis (default: {:s})"
parser.add_argument("--kbp-dat", \
action = "store", \
type = str, \
dest = "kbp_dat", \
default = kbpdat_default, \
help = kbpdat_helpstr.format(kbpdat_default))
kbpgraph_helpstr = \
"Name of the file where to store adjacency matrix " \
"for interaction graph (statistical potential)"
parser.add_argument('--kbp-graph', \
action = "store", \
type = str, \
dest = "kbp_graph", \
default = None, \
help = kbpgraph_helpstr)
kbpkbt_default = 1.0
kbpkbt_helpstr = \
"kb*T value used in the inverse-Boltzmann relation " \
"for the knowledge-based potential (default: {:f})"
parser.add_argument("--kbp-kbt", \
action = "store", \
type = float, \
dest = "kbp_kbt", \
default = kbpkbt_default, \
help = kbpkbt_helpstr.format(kbpkbt_default))
#---------------------------- Miscellanea ----------------------------#
ff_masses_dir = "ff_masses"
masses_dir = pkg_resources.resource_filename('pyinteraph', ff_masses_dir)
masses_files = os.listdir(masses_dir)
ffmasses_default = "charmm27"
ffmasses_helpstr = \
"Force field to be used (for masses calculation only). " \
"Accepted force fields are {:s} (default: {:s})"
parser.add_argument("--ff-masses", \
action = "store", \
type = str, \
choices = masses_files,
dest = "ffmasses", \
default = ffmasses_default, \
help = ffmasses_helpstr.format(\
", ".join(masses_files), \
ffmasses_default))
v_helpstr = "Verbose mode"
parser.add_argument("-v", "--verbose", \
action = "store_true", \
dest = "verbose", \
help = v_helpstr)
args = parser.parse_args()
############################ LOGGER SETUP #############################
# Logging format
LOGFMT = "%(levelname)s: %(message)s"
# Verbose mode?
if args.verbose:
log.basicConfig(level=log.INFO, format=LOGFMT)
else:
log.basicConfig(level=log.WARNING, format=LOGFMT)
############################## ARGUMENTS ##############################
# input files
top = args.top
trj = args.trj
ref = args.ref
# hydrophobic contacts
do_hc = args.do_hc
if type(args.hc_reslist) is str:
hc_reslist = [l.strip() for l in args.hc_reslist.split(",")]
else:
hc_reslist = args.hc_reslist
hc_graph = args.hc_graph
hc_co = args.hc_co
hc_perco = args.hc_perco
hc_dat = args.hc_dat
# salt bridges
do_sb = args.do_sb
cgs_file = args.cgs_file
sb_mode = args.sb_mode
sb_graph = args.sb_graph
sb_co = args.sb_co
sb_perco = args.sb_perco
sb_dat = args.sb_dat
# hydrogen bonds
do_hb = args.do_hb
hbs_file = args.hbs_file
hb_group1 = args.hb_group1
hb_group2 = args.hb_group2
hb_class = args.hb_class
hb_graph = args.hb_graph
hb_co = args.hb_co
hb_perco = args.hb_perco
hb_angle = args.hb_angle
hb_dat = args.hb_dat
# potential
do_kbp = args.do_kbp
kbp_atomlist = args.kbp_atomlist
kbp_graph = args.kbp_graph
kbp_ff = args.kbp_ff
kbp_kbt = args.kbp_kbt
kbp_dat = args.kbp_dat
# miscellanea
ffmasses = os.path.join(masses_dir, args.ffmasses)
############################ CHECK INPUTS #############################
# top and trj must be present
if not top or not trj:
log.error("Topology and trajectory are required.")
exit(1)
# if no reference, topology is reference
if not ref:
ref = top
log.info("Using topology as reference structure.")
# Load systems
try:
pdb = mda.Universe(ref)
uni = mda.Universe(top, trj)
except ValueError:
logstr = \
"Could not read one of the input files, or trajectory " \
"and topology are not compatible."
log.error(logstr)
exit(1)
######################## HYDROPHOBIC CONTACTS #########################
if do_hc:
fmfunc = None if not hc_graph else li.calc_sc_fullmatrix
str_out, hc_mat_out = li.do_interact(li.generate_sc_identifiers,
pdb=pdb,
uni=uni,
co=hc_co,
perco=hc_perco,
ffmasses=ffmasses,
fullmatrixfunc=fmfunc,
mindist=False,
reslist=hc_reslist)
# Save .dat
with open(hc_dat, "w") as out:
out.write(str_out)
# Save .mat (if available)
if hc_mat_out is not None:
np.savetxt(hc_graph, hc_mat_out, fmt="%.1f")
############################ SALT BRIDGES #############################
if do_sb:
try:
cgs = li.parse_cgs_file(cgs_file)
except IOError:
logstr = f"Problems reading file {cgs_file}."
log.error(logstr, exc_info=True)
exit(1)
except:
logstr = \
f"Could not parse the charged groups file {cgs_file}. " \
f"Are there any inconsistencies?"
log.error(logstr, exc_info=True)
exit(1)
if sb_mode == "same_charge":
sb_mode = "same"
elif sb_mode == "different_charge":
sb_mode = "diff"
elif sb_mode == "all":
sb_mode = "both"
fmfunc = None if not sb_graph else li.calc_cg_fullmatrix
str_out, sb_mat_out = li.do_interact(li.generate_cg_identifiers,
pdb=pdb,
uni=uni,
co=sb_co,
perco=sb_perco,
ffmasses=ffmasses,
fullmatrixfunc=fmfunc,
mindist=True,
mindist_mode=sb_mode,
cgs=cgs)
# Save .dat
with open(sb_dat, "w") as out:
out.write(str_out)
# Save .mat (if available)
if sb_mat_out is not None:
np.savetxt(sb_graph, sb_mat_out, fmt="%.1f")
########################### HYDROGEN BONDS ############################
if args.do_hb:
# atom selection for main chain hydrogen bonds
mc_sel = "backbone or name H or name H1 or name H2 " \
"or name H3 or name O1 or name O2 or name OXT"
# atom selection for side chain hydrogen bonds
sc_sel = f"protein and (not {mc_sel})"
if (hb_group1 and hb_group2) and hb_class != "custom":
warnstr = \
"Hydrogen bond custom groups have been specified; " \
"they will be used. Please use --hb-class=custom to " \
"get rid of this warning!"
log.warning(warnstr)
hb_class = "custom"
if hb_class == "custom":
if not hb_group1 or not hb_group2:
errstr = \
"Hydrogen bond class 'custom' requires the " \
"definition of two interation groups. (see " \
"options --hb-custom-group1 and --hb-custom-group2)"
log.error(errstr)
exit(1)
elif hb_class == "all":
hb_group1 = "protein"
hb_group2 = "protein"
elif hb_class == "mc-mc":
hb_group1 = mc_sel
hb_group2 = mc_sel
elif hb_class == "sc-sc":
hb_group1 = sc_sel
hb_group2 = sc_sel
elif hb_class == "mc-sc":
hb_group1 = mc_sel
hb_group2 = sc_sel
# check if selection 1 is valid
try:
uni.select_atoms(hb_group1)
except:
log.error("Selection 1 is invalid", exc_info=True)
exit(1)
# check if selection 2 is valid
try:
uni.select_atoms(hb_group2)
except:
log.error("Selection 2 is invalid", exc_info=True)
exit(1)
# check the donors-acceptors file
try:
hbs = li.parse_hbs_file(hbs_file)
except IOError:
logstr = f"Problems reading {hbs_file}."
log.error(logstr, exc_info=True)
exit(1)
except:
logstr = f"Could not parse {hbs_file}."
log.error(logstr, exc_info=True)
exit(1)
do_fullmatrix = True if hb_graph else False
perresidue = False
str_out, hb_mat_out = li.do_hbonds(sel1 = hb_group1, \
sel2 = hb_group2, \
pdb = pdb, \
uni = uni, \
distance = hb_co, \
angle = hb_angle, \
perco = hb_perco, \
do_fullmatrix = do_fullmatrix, \
other_hbs = hbs, \
perresidue = perresidue)
# Save .dat
with open(hb_dat, "w") as out:
out.write(str_out)
# Save .mat (if available)
if hb_mat_out is not None:
np.savetxt(hb_graph, hb_mat_out, fmt="%.1f")
######################## STATISTICAL POTENTIAL ########################
if do_kbp:
# Residue list for potential calculation - all canonical but GLY
kbp_reslist = \
["ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "HIS", \
"ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", \
"TRP", "TYR", "VAL"]
kbp_atomlist = li.parse_atomlist(kbp_atomlist)
do_fullmatrix = True if kbp_graph else False
str_out, kbp_mat_out = li.do_potential(kbp_atomlist = kbp_atomlist, \
residues_list = kbp_reslist, \
potential_file = kbp_ff, \
uni = uni, \
pdb = pdb, \
do_fullmatrix = do_fullmatrix, \
kbT = kbp_kbt, \
seq_dist_co = 0)
# Save .dat
with open(kbp_dat, "w") as out:
out.write(str_out)
# Save .mat (if available)
if kbp_mat_out is not None:
np.savetxt(kbp_graph, kbp_mat_out, fmt="%.3f")
def main():
######################### ARGUMENT PARSER #########################
description = "Interaction calculator"
parser = argparse.ArgumentParser(description=description)
#---------------------------- Top/traj ---------------------------#
s_helpstr = "Topology file"
parser.add_argument("-s",
"--top",
action="store",
type=str,
dest="top",
default=None,
help=s_helpstr)
t_helpstr = "Trajectory file"
parser.add_argument("-t",
"--trj",
action="store",
type=str,
dest="trj",
default=None,
help=t_helpstr)
r_helpstr = "Reference structure"
parser.add_argument("-r",
"--ref",
action="store",
type=str,
dest="ref",
default=None,
help=r_helpstr)
#---------------------------- Analyses ---------------------------#
m_helpstr = "Analyze side-chain centers-of-mass contacts (cmPSN)"
parser.add_argument("-m",
"--cmpsn",
action="store_true",
dest="do_cmpsn",
help=m_helpstr)
a_helpstr = "Analyze atomic contacts (acPSN)"
parser.add_argument("-a",
"--acpsn",
action="store_true",
dest="do_acpsn",
help=a_helpstr)
f_helpstr = "Analyze hydrophobic clusters"
parser.add_argument("-f",
"--hydrophobic",
action="store_true",
dest="do_hc",
help=f_helpstr)
b_helpstr = "Analyze salt bridges"
parser.add_argument("-b",
"--salt-bridges",
action="store_true",
dest="do_sb",
help=b_helpstr)
y_helpstr = "Analyze hydrogen bonds"
parser.add_argument("-y",
"--hydrogen-bonds",
action="store_true",
dest="do_hb",
help=y_helpstr)
p_helpstr = \
"Analyze interactions using the knowledge-based potential"
parser.add_argument("-p",
"--potential",
action="store_true",
dest="do_kbp",
help=p_helpstr)
#----------------------------- cmPSN -----------------------------#
cmpsnco_default = 5.0
cmpsnco_helpstr = \
f"Distance cut-off for the cmPSN (default: {cmpsnco_default})"
parser.add_argument("--cmpsn-co",
"--cmpsn-cutoff",
action="store",
dest="cmpsn_co",
type=float,
default=cmpsnco_default,
help=cmpsnco_helpstr)
cmpsnperco_default = 0.0
cmpsnperco_helpstr = \
f"Minimum persistence for the cmPSN (default: " \
f"{cmpsnperco_default})"
parser.add_argument("--cmpsn-perco",
"--cmpsn-persistence-cutoff",
action="store",
type=float,
dest="cmpsn_perco",
default=cmpsnperco_default,
help=cmpsnperco_helpstr)
cmpsn_reslist = \
["ALA", "CYS", "ASP", "GLU", "PHE", "HIS", "ILE", "LYS", "LEU",
"MET", "ASN", "PRO", "GLN", "ARG", "SER", "THR", "VAL", "TRP",
"TYR"]
cmpsnres_helpstr = \
f"Comma-separated list of residues to be used when " \
f"calculating the cmPSN (default: {', '.join(cmpsn_reslist)})"
parser.add_argument("--cmpsn-residues",
action="store",
type=str,
dest="cmpsn_reslist",
default=cmpsn_reslist,
help=cmpsnres_helpstr)
cmpsn_correction_choices = ["null", "rg"]
cmpsn_correction_default = "null"
cmpsn_correction_helpstr = \
f"Correction to be applied to the cmPSN (default: " \
f"{cmpsn_correction_default}"
parser.add_argument("--cmpsn-correction",
action="store",
dest="cmpsn_correction",
type=str,
choices=cmpsn_correction_choices,
default=cmpsn_correction_default,
help=cmpsn_correction_helpstr)
cmpsncsv_default = "cmpsn.csv"
cmpsncsv_helpstr = \
f"Name of the CSV file where to store the list of contacts " \
f"found in the cmPSN (default: {cmpsncsv_default})"
parser.add_argument("--cmpsn-csv",
action="store",
type=str,
dest="cmpsn_csv",
default=cmpsncsv_default,
help=cmpsncsv_helpstr)
cmpsngraph_helpstr = \
"File where to store the adjacency matrix for the " \
"interaction graph (cmPSN)"
parser.add_argument("--cmpsn-graph",
action="store",
dest="cmpsn_graph",
type=str,
default=None,
help=cmpsngraph_helpstr)
#----------------------------- acPSN -----------------------------#
acpsnco_default = 4.5
acpsnco_helpstr = \
f"Distance cut-off for the acPSN (default: {acpsnco_default})"
parser.add_argument("--acpsn-co",
"--acpsn-cutoff",
action="store",
dest="acpsn_co",
type=float,
default=acpsnco_default,
help=acpsnco_helpstr)
acpsnperco_default = 0.0
acpsnperco_helpstr = \
f"Minimum persistence for the acPSN (default: " \
f"{acpsnperco_default})"
parser.add_argument("--acpsn-perco",
"--acpsn-persistence-cutoff",
action="store",
type=float,
dest="acpsn_perco",
default=acpsnperco_default,
help=acpsnperco_helpstr)
acpsnproxco_default = 1
acpsnproxco_helpstr = \
f"Minimum sequence distance for the acPSN (default: " \
f"{acpsnproxco_default})"
parser.add_argument("--acpsn-proxco",
"--acpsn-sequence-cutoff",
action="store",
type=int,
dest="acpsn_proxco",
default=acpsnproxco_default,
help=acpsnproxco_helpstr)
acpsnimin_default = 3.0
acpsnimin_helpstr = \
f"Minimum interaction strength value for the acPSN " \
f"(default: {acpsnimin_default})"
parser.add_argument("--acpsn-imin",
"--acpsn-imin-cutoff",
action="store",
type=float,
dest="acpsn_imin",
default=acpsnimin_default,
help=acpsnimin_helpstr)
acpsnew_choices = ["strength", "persistence"]
acpsnew_default = "strength"
acpsnew_helpstr = \
f"Edge weighting method for the acPSN (default: " \
f"{acpsnew_default})"
parser.add_argument("--acpsn-ew",
"--acpsn-edge-weights",
action="store",
type=str,
dest="acpsn_ew",
choices=acpsnew_choices,
default=acpsnew_default,
help=acpsnew_helpstr)
acpsnnffile_default = \
pkg_resources.resource_filename("pyinteraph",
"normalization_factors.ini")
acpsnnffile_helpstr = \
f"File with normalization factors to be used " \
f"in the calculation of the acPSN (default: " \
f"{acpsnnffile_default})"
parser.add_argument("--acpsn-nf-file",
action="store",
type=str,
dest="nf_file",
default=acpsnnffile_default,
help=acpsnnffile_helpstr)
acpsnnf_default = 999.9
acpsnnfpermissive_helpstr = \
f"Permissive mode. If a residue with no associated " \
f"normalization factor is found, the default normalization " \
f"factor {acpsnnf_default} will be used, and no error will " \
f"be thrown"
parser.add_argument("--acpsn-nf-permissive",
action="store_true",
dest="nf_permissive",
help=acpsnnfpermissive_helpstr)
acpsnnf_helpstr = \
f"Default normalization factor to be used when running in " \
f"permissive mode (default: {acpsnnf_default})"
parser.add_argument("--acpsn-nf-default",
action="store",
type=str,
dest="nf_default",
default=acpsnnf_default,
help=acpsnnf_helpstr)
acpsncsv_default = "acpsn.csv"
acpsncsv_helpstr = \
f"Name of the CSV file where to store the list of contacts " \
f"found in the acPSN (default: {acpsncsv_default})"
parser.add_argument("--acpsn-csv",
action="store",
type=str,
dest="acpsn_csv",
default=acpsncsv_default,
help=acpsncsv_helpstr)
acpsngraph_helpstr = \
"File where to store the adjacency matrix for the " \
"interaction graph (acPSN)"
parser.add_argument("--acpsn-graph",
action="store",
dest="acpsn_graph",
type=str,
default=None,
help=acpsngraph_helpstr)
#---------------------- Hydrophobic contacts ---------------------#
hcco_default = 5.0
hcco_helpstr = \
f"Distance cut-off for hydrophobic contacts (default: " \
f"{hcco_default})"
parser.add_argument("--hc-co",
"--hc-cutoff",
action="store",
dest="hc_co",
type=float,
default=hcco_default,
help=hcco_helpstr)
hcperco_default = 0.0
hcperco_helpstr = \
f"Minimum persistence for hydrophobic contacts (default: " \
f"{hcperco_default})"
parser.add_argument("--hc-perco",
"--hc-persistence-cutoff",
action="store",
type=float,
dest="hc_perco",
default=hcperco_default,
help=hcperco_helpstr)
hc_reslist = \
["ALA", "VAL", "LEU", "ILE", "PHE", "PRO", "TRP", "MET"]
hcres_helpstr = \
f"Comma-separated list of hydrophobic residues (default: " \
f"{', '.join(hc_reslist)})"
parser.add_argument("--hc-residues",
action="store",
type=str,
dest="hc_reslist",
default=hc_reslist,
help=hcres_helpstr)
hccsv_default = "hydrophobic-clusters.csv"
hccsv_helpstr = \
f"Name of the CSV file where to store the list of " \
f"hydrophobic contacts found (default: {hccsv_default})"
parser.add_argument("--hc-csv",
action="store",
type=str,
dest="hc_csv",
default=hccsv_default,
help=hccsv_helpstr)
hcgraph_helpstr = \
"File where to store the adjacency matrix for the " \
"interaction graph (hydrophobic contacts)"
parser.add_argument("--hc-graph",
action="store",
dest="hc_graph",
type=str,
default=None,
help=hcgraph_helpstr)
#-------------------------- Salt bridges -------------------------#
sbco_default = 4.5
sbco_helpstr = \
f"Distance cut-off for salt bridges (default: {sbco_default})"
parser.add_argument("--sb-co",
"--sb-cutoff",
action="store",
type=float,
dest="sb_co",
default=sbco_default,
help=sbco_helpstr)
sbperco_default = 0.0
sbperco_helpstr = \
f"Minimum persistence for salt bridges (default: " \
f"{sbperco_default})"
parser.add_argument("--sb-perco",
"--sb-persistence-cutoff",
action="store",
type=float,
dest="sb_perco",
default=sbperco_default,
help=sbperco_helpstr)
sbmode_choices = ["different_charge", "same_charge", "all"]
sbmode_default = "different_charge"
sbmode_helpstr = \
f"Electrostatic interactions mode (default: {sbmode_default})"
parser.add_argument("--sb-mode",
action="store",
type=str,
dest="sb_mode",
choices=sbmode_choices,
default=sbmode_default,
help=sbmode_helpstr)
sbcgfile_default = \
pkg_resources.resource_filename("pyinteraph",
"charged_groups.ini")
sbcgfile_helpstr = \
f"File with charged groups to be used to find " \
f"salt bridges (default: {sbcgfile_default})"
parser.add_argument("--sb-cg-file",
action="store",
type=str,
dest="cgs_file",
default=sbcgfile_default,
help=sbcgfile_helpstr)
sbcsv_default = "salt-bridges.csv"
sbcsv_helpstr = \
f"Name of the CSV file where to store the list of " \
f"salt bridges found (default: {sbcsv_default})"
parser.add_argument("--sb-csv",
action="store",
type=str,
dest="sb_csv",
default=sbcsv_default,
help=sbcsv_helpstr)
sbgraph_helpstr = \
"File where to store the adjacency matrix for the " \
"interaction graph (salt bridges)"
parser.add_argument("--sb-graph",
action="store",
type=str,
dest="sb_graph",
default=None,
help=sbgraph_helpstr)
#------------------------- Hydrogen bonds ------------------------#
hbco_default = 3.5
hbco_helpstr = \
f"Donor-acceptor distance cut-off for hydrogen bonds " \
f"(default: {hbco_default})"
parser.add_argument("--hb-co",
"--hb-cutoff",
action="store",
type=float,
dest="hb_co",
default=hbco_default,
help=hbco_helpstr)
hbang_default = 120.0
hbang_helpstr = \
f"Donor-acceptor angle cut-off for hydrogen bonds " \
f"(default: {hbang_default})"
parser.add_argument("--hb-ang",
"--hb-angle",
action="store",
type=float,
dest="hb_angle",
default=hbang_default,
help=hbang_helpstr)
hbperco_default = 0.0
hbperco_helpstr = \
f"Minimum persistence for hydrogen bonds (default: " \
f"{hbperco_default})"
parser.add_argument("--hb-perco",
action="store",
type=float,
dest="hb_perco",
default=hbperco_default,
help=hbperco_helpstr)
hbclass_choices = ["all", "mc-mc", "mc-sc", "sc-sc", "custom"]
hbclass_default = "all"
hbclass_helpstr = \
f"Class of hydrogen bonds to analyze (default: " \
f"{hbclass_default})"
parser.add_argument("--hb-class",
action="store",
type=str,
dest="hb_class",
choices=hbclass_choices,
default=hbclass_default,
help=hbclass_helpstr)
hbcustom1_helpstr = "Custom group 1 for hydrogen bonds calculation"
parser.add_argument("--hb-custom-group-1",
action="store",
type=str,
dest="hb_group1",
default=None,
help=hbcustom1_helpstr)
hbcustom2_helpstr = "Custom group 2 for hydrogen bonds calculation"
parser.add_argument("--hb-custom-group-2",
action="store",
type=str,
dest="hb_group2",
default=None,
help=hbcustom2_helpstr)
hbadfile_default = \
pkg_resources.resource_filename("pyinteraph",
"hydrogen_bonds.ini")
hbadfile_helpstr = \
f"File defining hydrogen bonds donor and acceptor atoms " \
f"(default: {hbadfile_default})"
parser.add_argument("--hb-ad-file",
action="store",
type=str,
dest="hbs_file",
default=hbadfile_default,
help=hbadfile_helpstr)
hbcsv_default = "hydrogen-bonds.csv"
hbcsv_helpstr = \
f"Name of the CSV file where to store the list of hydrogen " \
f"bonds found (default: {hbcsv_default})"
parser.add_argument("--hb-csv",
action="store",
type=str,
dest="hb_csv",
default=hbcsv_default,
help=hbcsv_helpstr)
hbgraph_helpstr = \
"File where to store the adjacency matrix for the " \
"interaction graph (hydrogen bonds)"
parser.add_argument("--hb-graph",
action="store",
type=str,
dest="hb_graph",
default=None,
help=hbgraph_helpstr)
#--------------------------- Potential ---------------------------#
kbpkbt_default = 1.0
kbpkbt_helpstr = \
f"kb*T value used in the inverse-Boltzmann relation for the " \
f"knowledge-based potential (default: {kbpkbt_default})"
parser.add_argument("--kbp-kbt",
action="store",
type=float,
dest="kbp_kbt",
default=kbpkbt_default,
help=kbpkbt_helpstr)
kbpff_default = \
pkg_resources.resource_filename("pyinteraph", "ff.S050.bin64")
kbpff_helpstr = \
f"Statistical potential definition file (default: " \
f"{hbperco_default})"
parser.add_argument("--kbp-ff",
"--force-field",
action="store",
type=str,
dest="kbp_ff",
default=kbpff_default,
help=kbpff_helpstr)
kbpatom_default = \
pkg_resources.resource_filename("pyinteraph", "kbp_atomlist")
kbpatom_helpstr = \
f"Ordered, force-field specific list of atom names " \
f"(default: {kbpatom_default})"
parser.add_argument("--kbp-atomlist",
action="store",
type=str,
dest="kbp_atomlist",
default=kbpatom_default,
help=kbpatom_helpstr)
kbpcsv_default = "kb-potential.csv"
kbpcsv_helpstr = \
f"File where to store the results of the statistical " \
f"potential analysis (default: {kbpcsv_default})"
parser.add_argument("--kbp-csv",
action="store",
type=str,
dest="kbp_csv",
default=kbpcsv_default,
help=kbpcsv_helpstr)
kbpgraph_helpstr = \
"File where to store the adjacency matrix for the " \
"interaction graph (statistical potential)"
parser.add_argument("--kbp-graph",
action="store",
type=str,
dest="kbp_graph",
default=None,
help=kbpgraph_helpstr)
#-------------------------- Miscellanea --------------------------#
ffmasses_dir = "ff_masses"
ffmasses_dir = \
pkg_resources.resource_filename("pyinteraph", ffmasses_dir)
ffmasses_choices = os.listdir(ffmasses_dir)
ffmasses_default = "charmm27"
ffmasses_helpstr = \
f"Force field to be used (for masses calculation only) " \
f"(default: {ffmasses_default})"
parser.add_argument("--ff-masses",
action="store",
type=str,
dest="ffmasses",
choices=ffmasses_choices,
default=ffmasses_default,
help=ffmasses_helpstr)
v_helpstr = "Verbose mode"
parser.add_argument("-v",
"--verbose",
action="store_true",
dest="verbose",
help=v_helpstr)
args = parser.parse_args()
########################## LOGGER SETUP ###########################
# Logging format
LOGFMT = "%(levelname)s: %(message)s"
# Verbose mode?
if args.verbose:
log.basicConfig(level=log.INFO, format=LOGFMT)
else:
log.basicConfig(level=log.WARNING, format=LOGFMT)
############################ ARGUMENTS ############################
# Input files
top = args.top
trj = args.trj
ref = args.ref
# cmPSN
do_cmpsn = args.do_cmpsn
cmpsn_co = args.cmpsn_co
cmpsn_perco = args.cmpsn_perco
if type(args.cmpsn_reslist) is str:
cmpsn_reslist = [l.strip() for l in args.cmpsn_reslist.split(",")]
else:
cmpsn_reslist = args.cmpsn_reslist
cmpsn_correction = args.cmpsn_correction
cmpsn_csv = args.cmpsn_csv
cmpsn_graph = args.cmpsn_graph
# acPSN
do_acpsn = args.do_acpsn
acpsn_co = args.acpsn_co
acpsn_perco = args.acpsn_perco
acpsn_proxco = args.acpsn_proxco
acpsn_imin = args.acpsn_imin
acpsn_ew = args.acpsn_ew
nf_file = args.nf_file
nf_permissive = args.nf_permissive
nf_default = args.nf_default
acpsn_csv = args.acpsn_csv
acpsn_graph = args.acpsn_graph
# Hydrophobic contacts
do_hc = args.do_hc
hc_co = args.hc_co
hc_perco = args.hc_perco
if type(args.hc_reslist) is str:
hc_reslist = [l.strip() for l in args.hc_reslist.split(",")]
else:
hc_reslist = args.hc_reslist
hc_csv = args.hc_csv
hc_graph = args.hc_graph
# Salt bridges
do_sb = args.do_sb
sb_co = args.sb_co
sb_perco = args.sb_perco
sb_mode = args.sb_mode
cgs_file = args.cgs_file
sb_csv = args.sb_csv
sb_graph = args.sb_graph
# Hydrogen bonds
do_hb = args.do_hb
hb_angle = args.hb_angle
hb_co = args.hb_co
hb_perco = args.hb_perco
hb_class = args.hb_class
hb_group1 = args.hb_group1
hb_group2 = args.hb_group2
hbs_file = args.hbs_file
hb_csv = args.hb_csv
hb_graph = args.hb_graph
# Statistical potential
do_kbp = args.do_kbp
kbp_kbt = args.kbp_kbt
kbp_atomlist = args.kbp_atomlist
kbp_ff = args.kbp_ff
kbp_csv = args.kbp_csv
kbp_graph = args.kbp_graph
# Miscellanea
ffmasses = os.path.join(ffmasses_dir, args.ffmasses)
########################## CHECK INPUTS ###########################
# Topology and trajectory must be present
if not top or not trj:
log.error("Topology and trajectory are required.")
exit(1)
# If no reference structure is passed, the topology will be
# the reference
if not ref:
ref = top
log.info("Using topology as reference structure.")
# Load systems
try:
pdb = mda.Universe(ref)
uni = mda.Universe(top, trj)
except ValueError:
logstr = \
"Could not read one of the input files, or trajectory " \
"and topology are not compatible."
log.error(logstr)
exit(1)
###################### HYDROPHOBIC CONTACTS #######################
if do_hc:
# Function to compute the full matrix
hc_fmfunc = \
None if hc_graph is None else li.calc_sc_fullmatrix
# Compute the table and the matrix
hc_table_out, hc_mat_out = \
li.do_interact(identfunc = li.generate_sc_identifiers,
pdb = pdb,
uni = uni,
co = hc_co,
perco = hc_perco,
ffmasses = ffmasses,
fullmatrixfunc = hc_fmfunc,
mindist = False,
reslist = hc_reslist,
correction_func = li.null_correction)
# Save .csv
hc_table_dict = li.create_dict_tables(hc_table_out)
li.save_output_dict(hc_table_dict, hc_csv)
# Save .dat (if available) (hc_graph being not None has
# been checked already)
if hc_mat_out is not None:
hc_mat_dict = \
li.create_dict_matrices(hc_mat_out,
hc_table_dict,
pdb)
li.save_output_dict(hc_mat_dict, hc_graph)
############################## cmPSN ##############################
if do_cmpsn:
# Function to compute the full matrix
cmpsn_fmfunc = \
None if not cmpsn_graph else li.calc_sc_fullmatrix
# Select the appropriate correction function
if cmpsn_correction == "null":
selected_func = li.null_correction
elif cmpsn_correction == "rg":
selected_func = li.rg_correction
# Compute the table and the matrix
cmpsn_table_out, cmpsn_mat_out = \
li.do_interact(identfunc = li.generate_sc_identifiers,
pdb = pdb,
uni = uni,
co = cmpsn_co,
perco = cmpsn_perco,
ffmasses = ffmasses,
fullmatrixfunc = cmpsn_fmfunc,
mindist = False,
reslist = cmpsn_reslist,
correction_func = selected_func)
# Save .csv
cmpsn_table_dict = li.create_dict_tables(cmpsn_table_out)
li.save_output_dict(cmpsn_table_dict, cmpsn_csv)
# Save .dat (if available)
if cmpsn_mat_out is not None and cmpsn_graph is not None:
cmpsn_mat_dict = \
li.create_dict_matrices(cmpsn_mat_out,
cmpsn_table_dict,
pdb)
li.save_output_dict(cmpsn_mat_dict, cmpsn_graph)
############################## acPSN ##############################
if do_acpsn:
# Try to parse the charged groups definitions file
try:
norm_facts = li.parse_nf_file(nf_file)
except IOError:
logstr = f"Problems reading file {nf_file}."
log.error(logstr, exc_info=True)
exit(1)
except:
logstr = \
f"Could not parse the normalization factors file " \
f"{nf_file}. Are there any inconsistencies?"
log.error(logstr, exc_info=True)
exit(1)
# Try to compute the table of contacts and the matrix
try:
acpsn_table_out, acpsn_mat_out = \
li.do_acpsn(pdb = pdb,
uni = uni,
co = acpsn_co,
perco = acpsn_perco,
proxco = acpsn_proxco,
imin = acpsn_imin,
edge_weight = acpsn_ew,
norm_facts = norm_facts,
nf_permissive = nf_permissive,
nf_default = nf_default)
# In case something went wront, report it and exit
except Exception as e:
logstr = \
f"Could not compute the table of contacts and the " \
f"matrix for acPSN: {e}"
log.error(logstr)
exit(1)
# Save .csv
acpsn_table_dict = li.create_dict_tables(acpsn_table_out)
li.save_output_dict(acpsn_table_dict, acpsn_csv)
# Save .dat (if available)
if acpsn_mat_out is not None and acpsn_graph is not None:
acpsn_mat_dict = \
li.create_dict_matrices(acpsn_mat_out,
acpsn_table_dict,
pdb)
li.save_output_dict(acpsn_mat_dict, acpsn_graph)
########################## SALT BRIDGES ###########################
if do_sb:
# Try to parse the charged groups definitions file
try:
cgs = li.parse_cgs_file(cgs_file)
except IOError:
logstr = f"Problems reading file {cgs_file}."
log.error(logstr, exc_info=True)
exit(1)
except:
logstr = \
f"Could not parse the charged groups file " \
f"{cgs_file}. Are there any inconsistencies?"
log.error(logstr, exc_info=True)
exit(1)
if sb_mode == "same_charge":
sb_mode = "same"
elif sb_mode == "different_charge":
sb_mode = "diff"
elif sb_mode == "all":
sb_mode = "both"
# Function to compute the full matrix
sb_fmfunc = None if not sb_graph else li.calc_cg_fullmatrix
# Compute the table and the matrix
sb_table_out, sb_mat_out = \
li.do_interact(identfunc = li.generate_cg_identifiers,
pdb = pdb,
uni = uni,
co = sb_co,
perco = sb_perco,
ffmasses = ffmasses,
fullmatrixfunc = sb_fmfunc,
mindist = True,
mindist_mode = sb_mode,
cgs = cgs)
# Save .csv
sb_table_dict = li.create_dict_tables(sb_table_out)
li.save_output_dict(sb_table_dict, sb_csv)
# Save .dat (if available)
if sb_mat_out is not None and sb_graph is not None:
sb_mat_dict = \
li.create_dict_matrices(sb_mat_out,
sb_table_dict,
pdb)
li.save_output_dict(sb_mat_dict, sb_graph)
########################### HYDROGEN BONDS ############################
if do_hb:
# Atom selection for main chain hydrogen bonds
mc_sel = "backbone or name H or name H1 or name H2 " \
"or name H3 or name O1 or name O2 or name OXT"
# Atom selection for side chain hydrogen bonds
sc_sel = f"protein and (not {mc_sel})"
# Custom atom selection
if (hb_group1 and hb_group2) and hb_class != "custom":
warnstr = \
"Hydrogen bond custom groups have been specified; " \
"they will be used. Please use --hb-class=custom to " \
"get rid of this warning!"
log.warning(warnstr)
hb_class = "custom"
if hb_class == "custom":
if not hb_group1 or not hb_group2:
errstr = \
"Hydrogen bond class 'custom' requires the " \
"definition of two interation groups. (see " \
"options --hb-custom-group1 and --hb-custom-group2)"
log.error(errstr)
exit(1)
# All hydrogen bonds
elif hb_class == "all":
hb_group1 = "protein"
hb_group2 = "protein"
# Main chain - main chain hydrogen bonds
elif hb_class == "mc-mc":
hb_group1 = mc_sel
hb_group2 = mc_sel
# Side chain - side chain hydrogen bonds
elif hb_class == "sc-sc":
hb_group1 = sc_sel
hb_group2 = sc_sel
# Main chain - side chain hydrogen bonds
elif hb_class == "mc-sc":
hb_group1 = mc_sel
hb_group2 = sc_sel
# Check if selection 1 is valid
try:
uni.select_atoms(hb_group1)
except:
log.error("Selection 1 is invalid", exc_info=True)
exit(1)
# Check if selection 2 is valid
try:
uni.select_atoms(hb_group2)
except:
log.error("Selection 2 is invalid", exc_info=True)
exit(1)
# Check the donors-acceptors file
try:
hbs = li.parse_hbs_file(hbs_file)
except IOError:
logstr = f"Problems reading {hbs_file}."
log.error(logstr, exc_info=True)
exit(1)
except:
logstr = f"Could not parse {hbs_file}."
log.error(logstr, exc_info=True)
exit(1)
# Whether to compute the full matrix
do_fullmatrix = True if hb_graph else False
# Whtether to group the hydrogen bonds per residue
perresidue = False
# Compute the table and the matrix
hb_table_out, hb_mat_out = \
li.do_hbonds(sel1 = hb_group1,
sel2 = hb_group2,
pdb = pdb,
uni = uni,
distance = hb_co,
angle = hb_angle,
perco = hb_perco,
do_fullmatrix = do_fullmatrix,
other_hbs = hbs,
perresidue = perresidue)
# Save .csv
hb_table_dict = li.create_dict_tables(hb_table_out)
li.save_output_dict(hb_table_dict, hb_csv)
# Save .dat (if available)
if hb_mat_out is not None and hb_graph is not None:
hb_mat_dict = \
li.create_dict_matrices(hb_mat_out,
hb_table_dict,
pdb)
li.save_output_dict(hb_mat_dict, hb_graph)
######################## STATISTICAL POTENTIAL ########################
if do_kbp:
# Residue list for potential calculation - all canonical but GLY
kbp_reslist = \
["ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "HIS",
"ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR",
"TRP", "TYR", "VAL"]
# Parse the atom list
kbp_atomlist = li.parse_atomlist(kbp_atomlist)
# Whether to compute the full matrix
do_fullmatrix = True if kbp_graph else False
# Compute the output table and the matrix
kbp_table_out, kbp_mat_out = \
li.do_potential(kbp_atomlist = kbp_atomlist,
residues_list = kbp_reslist,
potential_file = kbp_ff,
uni = uni,
pdb = pdb,
do_fullmatrix = do_fullmatrix,
kbT = kbp_kbt,
seq_dist_co = 0)
# Save .csv
kbp_table_dict = li.create_dict_tables(kbp_table_out)
li.save_output_dict(kbp_table_dict, kbp_csv)
# Save .mat (if available)
if kbp_mat_out is not None and kbp_graph is not None:
np.savetxt(kbp_graph, kbp_mat_out, fmt="%.3f")
def test_parse_cg_file(sb_cg_file):
# Test the parsing of the charged groups file
li.parse_cgs_file(sb_cg_file)
def sb_charged_groups(sb_cg_file):
# Charged groups to calculate the electrostatic interactions
return li.parse_cgs_file(sb_cg_file)