def test_convert_placeholders(self):
inp_string = """
$$ $AAA$ $.AA$ $AA.$ $A.A $ $ A.A$
$2.CB$ $3.CA$ $LAST.ID$
"""
out_string = """
$$ $AAA$ $.AA$ $AA.$ $A.A $ $ A.A$
11 19 456
""".split()
qstruct = QStruct("data/all_amino_acids.mol2", "mol2")
assert qstruct.convert_placeholders(inp_string).split() == out_string
# FAIL
with pytest.raises(QStructError):
qstruct.convert_placeholders("$1.CB$")
def test_convert_placeholders(self):
inp_string = """
$$ $AAA$ $.AA$ $AA.$ $A.A $ $ A.A$
$2.CB$ $3.CA$ $LAST.ID$
"""
out_string = """
$$ $AAA$ $.AA$ $AA.$ $A.A $ $ A.A$
11 21 25
""".strip()
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
assert qstruct.convert_placeholders(inp_string).strip() == out_string
"--help",
action="help",
help="show this "
"help message and exit")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
for k, v in six.iteritems(vars(args)):
if k in ["inp", "pdb"] and not os.path.lexists(v):
print("FATAL! File '{}' doesn't exist.".format(v))
sys.exit(1)
inpstr = open(args.inp, "r").read()
try:
qstruct = QStruct(args.pdb, "pdb", ignore_errors=args.ignore_errors)
outstring = qstruct.convert_placeholders(inpstr)
except QStructError as e:
print("FATAL! Exception raised: {}".format(str(e)))
sys.exit(1)
backup = backup_file(args.out)
if backup:
print("Backed up '{}' to '{}'".format(args.out, backup))
open(args.out, "w").write(outstring)
print("Created file '{}'...".format(args.out))
def genrelax(relax_proc_file,
outdir,
restraint,
top_file=None,
fep_file=None,
runscript_file=None,
pdb_file=None,
cont_file=None,
ignore_errors=False):
"""Generates inputs for an MD simulation with Q (qdyn5).
Arguments:
relax_proc_file (string): genrelax procedure file pathname
outdir (string): output directory
restraint (string): restraint coordinate (a)
Optional arguments (b)
top_file (string): Q topology pathname
fep_file (string): fep file pathname
runscript_file (string): slurm/sge run script
pdb_file (string): pdb pathname (used to convert placeholders)
cont_file (string): pathname of previous qdyn5 input (continuation)
ignore_errors (boolean): passed to QStruct and QDynInp - write to
logger instead of raising exceptions on
non-critical things
(a) Restraint coordinate can be set to:
'top' - topology
'cont_inp' - whatever is defined in cont_file
'cont_final' - endpoint of previous simulation
(final restart of cont_file)
(b) top_file and cont_file are mutually exclusive, one of them has to
be provided
"""
# check if files exist
for k, v in locals().iteritems():
if k in [
"pdb_file", "cont_file", "relax_proc_file", "fep_file",
"top_file", "runscript_file", "relax_input"
]:
if v and not os.path.lexists(v):
raise QGenrelaxError("File '{}' doesn't exist.".format(v))
if restraint not in ["top", "cont_inp", "cont_final"]:
raise QGenrelaxError("Argument 'restraint' has to be either "
"'cont_inp', 'top' or 'cont_final'")
# constants
PREFIX = "relax_"
DIR = os.path.join(os.getcwd(), outdir)
if os.path.lexists(DIR):
raise QGenrelaxError("Directory '{}' exists. Please (re)move it "
"or set 'outdir'.".format(DIR))
TMPDIR = tempfile.mkdtemp()
header_comment = """\
# Generated with QTools, version {}
# Date: {}
# CWD: {}
# Cmdline: {}
""".format(__version__, time.ctime(), os.getcwd(), " ".join(sys.argv))
# find and replace placeholders. if not PDB was given to replace them, exit
relax_proc_str = open(relax_proc_file, 'r').read()
c = find_placeholders(relax_proc_str)
if c and not pdb_file:
raise QGenrelaxError("Found placeholders in proc.file, but no PDB "
"was given: {}".format(", ".join(c)))
elif c:
logger.info("These placeholders will be replaced with atom indices: {}"
"".format(", ".join(c)))
try:
qstruct = QStruct(pdb_file, "pdb", ignore_errors=ignore_errors)
relax_proc_str = qstruct.convert_placeholders(relax_proc_str)
except QStructError as err_msg:
raise QGenrelaxError("Failed to replace placeholders: "
"{}".format(err_msg))
# get topology and fep and others from previous input if given (--cont)
if cont_file:
if top_file:
raise QGenrelaxError("'top_file' and 'cont_file' don't like each "
"other. Difficult to continue with a "
"different topology...")
try:
c = QDynInput(open(cont_file, 'r').read(),
ignore_errors=ignore_errors)
except QDynInputError as err_msg:
raise QGenrelaxError("There is something wrong with the given "
"input file ({}): {}".format(
cont_file, err_msg))
cont_files = c.parameters["files"]
di = os.path.dirname(cont_file)
top_fn = cont_files["topology"]
cont_re_fn = cont_files["final"]
re_fn = "cont_{}".format(cont_re_fn)
shutil.copy2(os.path.join(di, top_fn), TMPDIR)
shutil.copy2(os.path.join(di, cont_re_fn), os.path.join(TMPDIR, re_fn))
if restraint == "cont_inp" and "restraint" in cont_files:
cont_rest_fn = cont_files["restraint"]
rest_fn = "cont_{}".format(cont_rest_fn)
elif restraint == "cont_final":
cont_rest_fn = cont_re_fn
rest_fn = "cont_{}.rest".format(cont_rest_fn)
else:
rest_fn = None
if rest_fn:
shutil.copy2(os.path.join(di, cont_rest_fn),
os.path.join(TMPDIR, rest_fn))
if fep_file:
logger.warning("Using the fep file '{}', instead of the one "
"found in the input".format(fep_file))
fep_fn = os.path.basename(fep_file)
shutil.copy2(fep_file, TMPDIR)
else:
try:
fep_fn = cont_files["fep"]
shutil.copy2(os.path.join(di, fep_fn), TMPDIR)
except KeyError:
logger.info("No FEP file found in the input")
# or take the arguments
else:
if not top_file:
raise QGenrelaxError("Please specify the topology file or "
"a previous input for a continuation run.")
cont_files = None
top_fn = os.path.basename(top_file)
shutil.copy2(top_file, TMPDIR)
try:
fep_fn = os.path.basename(fep_file)
shutil.copy2(fep_file, TMPDIR)
except AttributeError:
logger.info("NOTE: No FEP file!")
if restraint in ["cont_inp", "cont_final"]:
raise QGenrelaxError("Can't restrain to '{}'. Specify 'cont_file'."
"".format(restraint))
else:
rest_fn = None
logger.info("Restraining to: '{}'".format(rest_fn or 'topology'))
try:
shutil.copy2(runscript_file, TMPDIR)
except AttributeError:
logger.info("No submission script was given.")
general_inp = []
steps_inps = [
[],
]
script_vars = {}
section = ""
for line in relax_proc_str.split("\n"):
# remove comments and strip whitespaces.
line = re.split("#|\!", line)[0].strip()
# empty lines are useless
if line == "":
continue
# found a section
if line[0] == "{":
section = line.strip("{}").lower()
continue
if not section:
raise QGenrelaxError("Failed to parse '{}'... this line - '{}' "
"is not inside any section:"
"".format(relax_proc_file, line))
if section == "script_vars":
c = line.split()
var = c[0]
value = " ".join(c[1:])
script_vars[var] = value
elif section == "general":
general_inp.append(line)
elif section == "steps":
if "__________" in line:
steps_inps.append([])
else:
steps_inps[-1].append(line)
if "fep_fn" in locals():
# find and replace atom placeholders in FEP file
# if no PDB was given to replace them, exit
fep_tmp = os.path.join(TMPDIR, fep_fn)
fep_file_str = open(fep_tmp, 'r').read()
c = find_placeholders(fep_file_str)
if c and not pdb_file:
raise QGenfepsError("Found placeholders in FEP file, but no "
"PDB was given: {}".format(", ".join(c)))
elif c:
logger.info("Replacing FEP file placeholders...")
try:
qstruct = QStruct(pdb_file, "pdb", ignore_errors=ignore_errors)
fep_file_str = qstruct.convert_placeholders(fep_file_str)
except QStructError as err_msg:
raise QGenfepsError("Failed to replace placeholders: {}"
"".format(err_msg))
else:
open(fep_tmp, 'w').write(fep_file_str)
# check for steps with no parameters
# (too many _________ lines)and remove them
for i in range(len(steps_inps) - 1, -1, -1):
if not steps_inps[i]:
steps_inps.pop(i)
# join lists of lines to strings and replace the placeholders
gen_inp_s = "\n".join(general_inp)
for placeholder, value in script_vars.iteritems():
gen_inp_s = gen_inp_s.replace(placeholder, value)
step_inps_s = []
for i, step_inp in enumerate(steps_inps):
s = "\n".join(step_inp)
for placeholder, value in script_vars.iteritems():
s = s.replace(placeholder, value)
step_inps_s.append(s)
# make and save the inputs
steps = []
overridden_prms_all = []
step_n = 1
inp_fns = [] # to store the filenames and use the return value
for step_inp_s in step_inps_s:
# create the files section
final = "{}{:03d}.re".format(PREFIX, step_n)
dcd = "{}{:03d}.dcd".format(PREFIX, step_n)
files = {"final": final, "trajectory": dcd, "topology": top_fn}
try:
files["fep"] = fep_fn
except NameError:
pass
if step_n != 1:
prev_step = step_n - 1
files["restart"] = "{}{:03d}.re".format(PREFIX, prev_step)
elif cont_files:
files["restart"] = re_fn
if rest_fn != None:
files["restraint"] = rest_fn
try:
# parse the general input
inp = QDynInput(gen_inp_s, ignore_errors=ignore_errors)
# update the general parameters with step input, printout the
# overriden parms, update the files section
overridden_prms = inp.update(step_inp_s)
if overridden_prms:
overridden_prms_all.append((step_n, ", ".join(
["{}:{}->{}".format(key, value_old, value_new) \
for key, (value_old, value_new) in \
overridden_prms.iteritems()])))
if "energy" in inp.parameters["intervals"]:
files["energy"] = "{}{:03d}.en".format(PREFIX, step_n)
inp.update(parameters={"files": files})
except QDynInputError as err_msg:
raise QGenrelaxError("Problem with step no. {}: {}"
"".format(step_n, err_msg))
# set the random seed
mdp = inp.parameters["md"]
if "random_seed" in mdp and int(mdp["random_seed"]) < 1:
rs = random.randint(1, 1000000)
inp.update(parameters={"md": {"random_seed": rs}})
logger.info("Generated random seed in step {}: {}"
"".format(step_n, rs))
# get the input string
try:
inpstr = inp.get_string()
except QDynInputError as err_msg:
raise QGenrelaxError("Error in step {}: {}"
"".format(step_n, err_msg))
inpfn = "{}{:03d}.inp".format(PREFIX, step_n)
inp_fns.append(os.path.join(DIR, inpfn))
s = header_comment + inpstr
open(os.path.join(TMPDIR, inpfn), 'w').write(s)
steps.append(inp)
step_n += 1
try:
shutil.copytree(TMPDIR, DIR)
except OSError:
raise QGenrelaxError("Cannot create directory '{}'.".format(DIR))
# remove temporary directory
shutil.rmtree(TMPDIR)
logger.info("Created inputs {}{:03d}.inp - {}{:03d}.inp"
"".format(PREFIX, 1, PREFIX, len(steps)))
# print some useful information
if overridden_prms_all:
logger.info("Overridden parameters:")
for step_n, op in overridden_prms_all:
logger.info("{}: {}".format(step_n, op))
summary = """
Quick summary
{0:<10} {1:>5} {2:>10} {3:>10} {4:^10} {5:^10} {6:^10} {7:^30} {8:^10} {9:>10}
""".format("Step", "T", "Stepsize", "Steps", "Seq.rest", "Dist.rest",
"Ang.rest", "Shake", "Rand.Seed", "Data (MB)")
locale.setlocale(locale.LC_ALL, '')
restraints = []
total_time = 0
# print out how much data this run will produce
# for this we need the atom count from the topology
for line in open(os.path.join(DIR, top_fn), 'r').readlines(1024):
if "no. of atoms, no. of solute atoms" in line:
num_atoms_all = int(line.strip().split()[0])
break
REST_B_PER_ATOM = 48.0
TRJ_B_PER_ATOM = 12.0
# very rough estimate, depends on Q version
# it can double if group_contributions are calculated
EN_B_PER_STEP = 370.0
CONV_MB = 2**20
# very rough estimate
OUT_B_PER_STEP = 2000
TEMP_B_PER_STEP = 160
NB_B_PER_STEP = 80
# intervals mapping: q_parameter_key, q_default_value, approx_bytes_per_frame
qintervals = {
"trj": ["trajectory", 100, num_atoms_all * TRJ_B_PER_ATOM],
"log": ["output", 10, OUT_B_PER_STEP],
"temp": ["temperature", 10, TEMP_B_PER_STEP],
"en": ["energy", 10, EN_B_PER_STEP],
"nb": ["non_bond", 10, NB_B_PER_STEP]
}
total_data = {"trj": 0, "log": 0, "en": 0, "rest": 0}
for i, step in enumerate(steps):
nstep = i + 1
try:
# get md parameters
mdparms = step.parameters["md"]
total_time += float(mdparms["stepsize"]) * int(mdparms["steps"])
random_seed = mdparms.get("random_seed", "")
# get restraints
step_rests = {
"sequence_restraints": [],
"distance_restraints": [],
"angle_restraints": []
}
for rest_type in step_rests.keys():
for seqrest in step.parameters.get(rest_type, []):
if seqrest in restraints:
rest_num = restraints.index(seqrest) + 1
step_rests[rest_type].append(str(rest_num))
else:
restraints.append(seqrest)
step_rests[rest_type].append(str(len(restraints)))
seq = ",".join(step_rests["sequence_restraints"])
dist = ",".join(step_rests["distance_restraints"])
angle = ",".join(step_rests["angle_restraints"])
# get shake parameters
shake = []
# this is a Q default, hopefully it will not change
if mdparms.get("shake_solvent", "on") == "on":
shake.append("solvent")
if mdparms.get("shake_hydrogens", "off") == "on":
shake.append("hydrogens")
if mdparms.get("shake_solute", "off") == "on":
shake.append("solute")
shake = ",".join(shake)
# calculate approx amount of data
data = {}
mdsteps = int(mdparms["steps"])
for k, v in qintervals.iteritems():
interval_key = v[0]
default_interval = v[1]
bytes_per_step = v[2]
try:
interval = int(step.parameters["intervals"][interval_key])
data[k] = mdsteps / interval * bytes_per_step
except KeyError:
# default
data[k] = mdsteps / default_interval * bytes_per_step
except ZeroDivisionError:
data[k] = 0 # no printout
finally:
# if energy or trajectory, check that files for output are
# defined, otherwise set the printout to 0
if interval_key in ("energy", "trajectory") and not \
interval_key in step.parameters["files"].keys():
data[k] = 0
trj_data = data["trj"]
en_data = data["en"]
log_data = (data["log"] + data["temp"] + data["nb"])
rest_data = num_atoms_all * REST_B_PER_ATOM
total_data["trj"] += trj_data
total_data["log"] += log_data
total_data["en"] += en_data
total_data["rest"] += rest_data
data = (trj_data + log_data + rest_data + en_data) / CONV_MB
summary += "{:<10} {:>5} {:>10} {:>10} {:^10} {:^10} {:^10} "\
"{:^30} {:^10} {:>10.2f}\n" \
"".format(nstep, mdparms["temperature"],
mdparms["stepsize"],
locale.format('%d', mdsteps, 1),
seq, dist, angle, shake, random_seed, data)
except KeyError as err_msg:
raise QGenrelaxError("You are missing either 'steps', "
"'temperature' or 'stepsize' in one of your "
"relaxation steps. These parameters are "
"quite important you know...")
summary += "Restraints:\n"
for i, rest in enumerate(restraints):
summary += "{}: {}\n".format(i + 1, rest)
summary += """
Total time: {} ps
Total wasted storage (wild approximation): \
{:.2f} MB (trj: {:.1f}, log: {:.1f}, en: {:.1f}, rest: {:.1f})
""".format(total_time / 1000.0,
sum(total_data.values()) / CONV_MB, total_data["trj"] / CONV_MB,
total_data["log"] / CONV_MB, total_data["en"] / CONV_MB,
total_data["rest"] / CONV_MB)
for l in summary.split("\n"):
logger.info(l)
return inp_fns
def genfeps(fep_proc_file,
relax_input_file,
restraint,
energy_list_fn,
frames,
repeats,
fromlambda,
prefix,
first_frame_eq,
pdb_file=None,
fep_file=None,
runscript_file=None,
ignore_errors=False):
"""Generates inputs for a FEP/MD simulation with Q (qdyn5).
Arguments:
fep_proc_file (string): genfeps procedure file pathname
relax_input_file (string): pathname of last relaxation step input
restraint (string): restraint coordinate (a)
energy_list_fn (string): name of file that will contain the en.f.list
frames (int): number of FEP frames
repeats (int): number of repeats/replicas
fromlambda (float): starting lambda (0.0 - 1.0)
prefix (string): prefix for repeat directories
first_frame_eq (boolean): use equil instead of first frame (cadee)
Optional arguments:
pdb_file (string): pdb pathname (used to convert placeholders)
fep_file (string): alternate fep file pathname (ignoring input's fep)
runscript_file (string): slurm/sge run script
ignore_errors (boolean): passed to QStruct and QDynInp - write to
logger instead of raising exceptions on
non-critical things
Returns:
rep_dirs (list): list of created replica folders
(a) Restraint coordinate can be set to:
'inp' - whatever is defined in relax_input_file
'top' - topology
'relax' - endpoint of relaxation
"""
frames = int(frames)
repeats = int(repeats)
if fromlambda != None:
fromlambda = float(fromlambda)
# constants
PREFIX_EQ = "equil_"
PREFIX_FEP = "fep_"
# check if files exist
for k, v in locals().iteritems():
if k in [
"pdb_file", "fep_proc_file", "fep_file", "runscript_file",
"relax_input_file"
]:
if v and not os.path.lexists(v):
raise QGenfepsError("File '{}' doesn't exist.".format(v))
if restraint not in ["top", "relax", "inp"]:
raise QGenfepsError("Argument 'restraint' has to be either "
"'inp', 'top' or 'relax'")
# find and replace atom placeholders.
# if no PDB was given to replace them, exit
fep_proc_str = open(fep_proc_file, 'r').read()
c = find_placeholders(fep_proc_str)
if c and not pdb_file:
raise QGenfepsError("Found placeholders in proc. file, but no PDB "
"was given: {}".format(", ".join(c)))
elif c:
logger.info("These placeholders will be replaced with atom indices: " +
", ".join(c))
try:
qstruct = QStruct(pdb_file, "pdb", ignore_errors=ignore_errors)
fep_proc_str = qstruct.convert_placeholders(fep_proc_str)
except QStructError as err_msg:
raise QGenfepsError("Failed to replace placeholders: {}"
"".format(err_msg))
# make a nice header comment in each input file with the
header_comment = """\
# Generated with QTools, version {}
# Date: {}
# CWD: {}
# Cmdline: {}
""".format(__version__, time.ctime(), os.getcwd(), " ".join(sys.argv))
# get topology and fep and others from the last relaxation input
top_file_abs, fep_file_abs, re_file_abs, rest_file = None, None, None, None
lambda_initial = None
try:
c = QDynInput(open(relax_input_file, 'r').read(),
ignore_errors=ignore_errors)
except QDynInputError as err_msg:
raise QGenfepsError("There is something wrong with the given input "
"file ({}): {}".format(relax_input_file, err_msg))
di = os.path.dirname(relax_input_file)
try:
files = c.parameters["files"]
lambda_initial = float(c.parameters["lambdas"].split()[0])
top_file_abs = os.path.join(di, files["topology"])
re_file_abs = os.path.join(di, files["final"])
fep_file_abs = os.path.join(di, files["fep"])
if "restraint" in files:
rest_file = os.path.join(di, files["restraint"])
except KeyError as err_msg:
raise QGenfepsError("Parsing the relaxation input file failed, "
"keyword missing... {}".format(err_msg))
# check if the files actually exist
for fn, descr in [(top_file_abs, "topology"), (fep_file_abs, "fep"),
(re_file_abs, "final"), (rest_file, "restraint")]:
if fn and not os.path.lexists(fn):
raise QGenfepsError("When parsing the input, found this filename "
"'{}' next to the '{}' command. Unfortunately,"
" the file doesnt exist...".format(fn, descr))
# change the FEP (when debugging your system, you might want to
# use an old relax and not waste 100M core hours when changing
# a soft core value in the fep)
if fep_file:
fep_file_abs = os.path.abspath(fep_file)
# find and replace atom placeholders in FEP file
# if no PDB was given to replace them, exit
fep_file_str = open(fep_file_abs, 'r').read()
c = find_placeholders(fep_file_str)
if c and not pdb_file:
raise QGenfepsError("Found placeholders in FEP file, but no PDB was "
"given: {}".format(", ".join(c)))
elif c:
logger.info("Replacing FEP file placeholders...")
try:
qstruct = QStruct(pdb_file, "pdb", ignore_errors=ignore_errors)
fep_file_str = qstruct.convert_placeholders(fep_file_str)
except QStructError as err_msg:
raise QGenfepsError("Failed to replace placeholders: {}"
"".format(err_msg))
# change the inital lambda (this is not recommended, the system should
# be properly relaxed at a particual lambda before doing FEP)
if fromlambda != None:
lambda_initial = float(fromlambda)
if lambda_initial > 1.0 or lambda_initial < 0.0:
raise QGenfepsError("Lambda value is bogus, are you on drugs?")
# create lambda values, find the closest to the starting one and
# rearrange accordingly: [0.0, 0.02, 0.04, ... 0.98, 1.0] for frames==51
lambdas = [float(num) / (frames - 1) for num in xrange(0, frames)]
# [2,] for lambda_initial == 0.04 (or close to 0.04) and frames==51
l_i = [i for i in xrange(0, frames) if \
abs(lambdas[i] - lambda_initial) <= (1.0 / frames)]
# there should be only one
l_i = l_i[0]
lambda_initial = lambdas[l_i]
# [0.02, 0.0,] for the case of lambda_initial == 0.04 and frames == 51
forward_lambdas = list(reversed(lambdas[0:l_i]))
# [0.06, 0.08, ..., 1.0] for the case of lambda_initial == 0.04, fr. == 51
backward_lambdas = lambdas[l_i + 1:]
lambdas = [
lambda_initial,
] + forward_lambdas + backward_lambdas
# print out some useful information
logger.info("Using restart file: {}"
"".format(os.path.relpath(re_file_abs)))
logger.info("Using topology file: {}"
"".format(os.path.relpath(top_file_abs)))
logger.info("Using FEP file: {}" "".format(os.path.relpath(fep_file_abs)))
logger.info("Starting from lambda value (state 1): {}"
"".format(lambda_initial))
logger.info("Number of FEP frames: {} ".format(frames))
# create a temporary directory to store the files that are identical
# in all replicas - top, fep, runscript, relax restart, restraint file
# (if any) and copy the common files
TMPDIR = tempfile.mkdtemp()
top_fn = os.path.basename(top_file_abs)
fep_fn = os.path.basename(fep_file_abs)
relax_re_fn = "cont_" + os.path.basename(re_file_abs)
shutil.copy2(top_file_abs, TMPDIR)
shutil.copy2(re_file_abs, os.path.join(TMPDIR, relax_re_fn))
open(os.path.join(TMPDIR, fep_fn), "w").write(fep_file_str)
if runscript_file:
shutil.copy2(runscript_file, TMPDIR)
else:
logger.info("No Q runscript given.")
# handle the whole restraint coordinates crap...
# rest_file is the file from the relaxation input (if any)
# rest_fn is the basename of the restraints file (either from input
# or relaxed.re.rest), or None if rest. to topology
if restraint == "relax":
logger.info("Restraining to: relaxation")
rest_fn = "cont_" + os.path.basename(re_file_abs) + ".rest"
shutil.copy2(re_file_abs, os.path.join(TMPDIR, rest_fn))
elif restraint == "top":
logger.info("Restraining to: topology")
rest_fn = None
else: # default, from input
if rest_file:
logger.info("Restraining to: {} (from input)"
"".format(os.path.relpath(rest_file)))
rest_fn = "cont_" + os.path.basename(rest_file)
shutil.copy2(rest_file, os.path.join(TMPDIR, rest_fn))
else:
logger.info("Restraining to: topology (from input)")
rest_fn = None
# parse the proc file
general_inp = []
eq_steps_inps = [
[],
]
fep_inp = []
script_vars = {}
section = ""
for line in fep_proc_str.split("\n"):
# remove comments and strip whitespaces.
line = re.split("#|\!", line)[0].strip()
# empty lines are useless
if line == "":
continue
# found a section
if line[0] == "{":
section = line.strip("{}").lower()
continue
if not section:
raise QGenfepsError("Parsing the procedure file failed... This "
"line: '{}' is not inside any section:"
"".format(line))
if section == "script_vars":
c = line.split()
var, value = c[0], " ".join(c[1:])
script_vars[var] = value
elif section == "general":
general_inp.append(line)
elif section == "steps_equil":
if "__________" in line:
eq_steps_inps.append([])
else:
eq_steps_inps[-1].append(line)
elif section == "fep":
fep_inp.append(line)
else:
raise QGenfepsError("Parsing the procedure file failed: "
"Unsupported section: '{}'".format(section))
# check for steps with no parameters (too many _________ lines)
# and remove them
for i in range(len(eq_steps_inps) - 1, -1, -1):
if not eq_steps_inps[i]:
eq_steps_inps.pop(i)
# check for missing sections
for l, n in ((general_inp, "GENERAL"), (eq_steps_inps, "STEPS_EQUIL"),
(fep_inp, "FEP")):
if not l:
raise QGenfepsError("Parsing the procedure file failed: "
"Section '{}' is missing".format(n))
# join lists of lines to strings and replace the placeholders
script_variables = sorted(script_vars.items(), reverse=True)
gen_inp_s = "\n".join(general_inp)
fep_inp_s = "\n".join(fep_inp)
eq_steps_inps_s = ["\n".join(eq_s_inp) for eq_s_inp in eq_steps_inps]
for placeholder, value in script_variables:
gen_inp_s = gen_inp_s.replace(placeholder, value)
fep_inp_s = fep_inp_s.replace(placeholder, value)
for step_i, eq_step_inp_s in enumerate(eq_steps_inps_s):
eq_steps_inps_s[step_i] = eq_step_inp_s.replace(placeholder, value)
####################
# make equil. inputs
eq_steps = []
for step_n, eq_step_inp_s in enumerate(eq_steps_inps_s):
# create the files section
final = "{}{:03d}_{:4.3f}.re".format(PREFIX_EQ, step_n, lambda_initial)
dcd = "{}{:03d}_{:4.3f}.dcd".format(PREFIX_EQ, step_n, lambda_initial)
files = {
"final": final,
"trajectory": dcd,
"topology": top_fn,
"fep": fep_fn
}
if first_frame_eq:
files["energy"] = "{}{:03d}_{:4.3f}.en".format(
PREFIX_EQ, step_n, lambda_initial)
if rest_fn:
files["restraint"] = rest_fn
if step_n != 0:
files["restart"] = "{}{:03d}_{:4.3f}.re".format(
PREFIX_EQ, step_n - 1, lambda_initial)
else:
files["restart"] = relax_re_fn
# parse the general input and update with step input and files section
try:
inp = QDynInput(gen_inp_s, ignore_errors=ignore_errors)
inp.update(eq_step_inp_s)
if "energy" in inp.parameters["intervals"]:
files["energy"] = "{}{:03d}_{:4.3f}.en".format(
PREFIX_EQ, step_n, lambda_initial)
elif first_frame_eq:
raise QGenfepsError("Argument 'first_frame_eq' requires the "
"energy printout defined in the intervals "
"section of the equilibration "
"(e.g. 'energy 10')")
inp.update(parameters={"files": files})
inp.update(
parameters={
"lambdas":
"{:9.7f} {:9.7f}"
"".format(lambda_initial, 1 - lambda_initial)
})
except QDynInputError as err_msg:
raise QGenfepsError("Problem with equil. step no. {}: {}"
"".format(step_n, err_msg))
# test the input string
try:
_ = inp.get_string()
except QDynInputError as err_msg:
raise QGenfepsError("Error in equil. step {}: {}"
"".format(step_n, err_msg))
# check if random seed is not defined or is fixed in the first step
if step_n == 0:
if repeats > 1:
if ("random_seed" not in inp.parameters["md"]) or \
(int(inp.parameters["md"]["random_seed"]) > 0):
raise QGenfepsError("Fixed random seed (or restart "
"velocities) works only with one "
"repeat (others will be identical).\n"
"Please use 'random_seed -1' in "
"your first equilibration step to "
"generate random random seeds.")
elif "random_seed" not in inp.parameters["md"]:
logger.info("No random seed in first step of equilibration,"
"using restart velocities.")
if (not rest_file and rest_fn) or (not rest_fn and rest_file) \
or (rest_file and (os.path.basename(rest_file) != rest_fn)):
logger.warning("This will not be a true continuation run! "
"The relaxation restraint does not match "
"yours. Use 'inp' instead of 'top' or "
"'relax' for the restraint.")
# append the input
eq_steps.append(inp)
#################
# make FEP inputs
en_filenames = []
feps = []
for step_n, lam in enumerate(lambdas):
# create the files section
final = "{}{:03d}_{:4.3f}.re".format(PREFIX_FEP, step_n, lam)
dcd = "{}{:03d}_{:4.3f}.dcd".format(PREFIX_FEP, step_n, lam)
en = "{}{:03d}_{:4.3f}.en".format(PREFIX_FEP, step_n, lam)
files = {
"final": final,
"trajectory": dcd,
"topology": top_fn,
"energy": en,
"fep": fep_fn
}
# if this step is in new direction (backwards) then
# set the previous lambda and step to initial
if backward_lambdas and lam == backward_lambdas[0]:
prev_fep = feps[0]
elif step_n == 0:
prev_fep = eq_steps[-1]
else:
prev_fep = feps[-1]
# if this flag is set, all steps that point to the first step
# should point to the last eq step
if first_frame_eq:
if step_n == 1 or (backward_lambdas
and lam == backward_lambdas[0]):
prev_fep = eq_steps[-1]
if rest_fn:
files["restraint"] = rest_fn
files["restart"] = prev_fep.parameters["files"]["final"]
# update the parameters and check the input
try:
inp = QDynInput(gen_inp_s, ignore_errors=ignore_errors)
inp.update(fep_inp_s)
if "energy" not in inp.parameters["intervals"]:
raise QGenfepsError("FEP stage requires the energy printout "
"defined in the intervals section "
"(e.g. 'energy 10')")
inp.update(parameters={"files": files})
inp.update(parameters={
"lambdas": "{:9.7f} {:9.7f}"
"".format(lam, 1 - lam)
})
inp.check()
except QDynInputError as err_msg:
raise QGenfepsError("Error in FEP step {}: {}"
"".format(step_n, err_msg))
# append the input
feps.append(inp)
# add the energy filename to the list
en_filenames.append(inp.parameters["files"]["energy"])
# if first_frame_eq is set add the energy file and remove the
# first fep frame
if first_frame_eq:
logger.info("Replacing the first FEP frame with the last "
"equilibration step")
en_filenames[0] = eq_steps[-1].parameters["files"]["energy"]
feps.pop(0)
# check random seed in fep
if "random_seed" in feps[0].parameters["md"] and \
int(feps[0].parameters["md"]["random_seed"]) < 1:
logger.warning("Generating random seeds in FEP inputs. "
"Are you sure this is ok?")
# write a file that contains the names of all energy files in proper order
# this file is used later by q_mapper.py
# sort the enfiles according to lambda (1.0 -> 0.0) so that the mapping
# will always go from reactants to products
enfiles_lambdas = sorted([(enf.split("_")[-1], i) for i, enf in \
enumerate(en_filenames)], reverse=True)
en_filenames_sorted = [en_filenames[i] for l, i in enfiles_lambdas]
enf = os.path.join(TMPDIR, energy_list_fn)
open(enf, 'w').write("\n".join(en_filenames_sorted))
# create directories for repeats/replicas (rep_000,rep_001,rep_002...)
# copy everything from TMPDIR (topology, fep file, relax restart and
# restraint file (if any)); create the eq and fep inputs
#
# first check for existing directories
for num in xrange(0, repeats):
rep = "{}{:03d}".format(prefix, num)
if os.path.lexists(rep):
raise QGenfepsError("Directory '{}' exists. Please (re)move it or "
"change the prefix with --prefix.".format(rep))
lsdir = os.listdir(TMPDIR)
rep_dirs = []
for num in xrange(0, repeats):
rep = "{}{:03d}".format(prefix, num)
os.mkdir(rep)
# copy stuff from TMPDIR
for f in lsdir:
shutil.copy2(os.path.join(TMPDIR, f), rep)
# create eq inputs
for step_n, eq_step in enumerate(eq_steps):
# check if random seed is a fixed value or not (generate random or fail)
eqs = copy.deepcopy(eq_step) # a copy
if "random_seed" in eqs.parameters["md"] and \
int(eqs.parameters["md"]["random_seed"]) < 1:
rs = random.randint(1, 1e6)
eqs.update(parameters={"md": {"random_seed": rs}})
try:
s = eqs.get_string()
except QDynInputError as err_msg:
raise QGenfepsError("Error in step {}: {}"
"".format(step_n, err_msg))
fn = os.path.join(
rep, "{}{:03d}_{:4.3f}.inp"
"".format(PREFIX_EQ, step_n, lambda_initial))
s = header_comment + s
open(fn, 'w').write(s)
last_eq_fn = fn
# create FEP inputs
for step_n, fep in enumerate(feps):
if first_frame_eq:
step_n += 1
fs = copy.deepcopy(fep) # a copy
if "random_seed" in fs.parameters["md"] and \
int(fs.parameters["md"]["random_seed"]) < 1:
rs = random.randint(1, 1e6)
fs.update(parameters={"md": {"random_seed": rs}})
try:
s = fs.get_string()
except QDynInputError as err_msg:
raise QGenfepsError("Error in step {}: {}"
"".format(step_n, err_msg))
lam = lambdas[step_n] # feps was created in lambdas iteration
fn = os.path.join(
rep, "{}{:03d}_{:4.3f}.inp"
"".format(PREFIX_FEP, step_n, lam))
s = header_comment + s
open(fn, 'w').write(s)
logger.info("Created inputs for repeat/replica '{}'.".format(rep))
rep_dirs.append(rep)
# get the amount of storage that will be wasted
# for this we need the atom count from the topology
for line in open(os.path.join(TMPDIR, top_fn), 'r').readlines(1024):
if "no. of atoms, no. of solute atoms" in line:
num_atoms_all = int(line.split()[0])
break
REST_B_PER_ATOM = 48.0
TRJ_B_PER_ATOM = 12.0
# very rough estimate, depends on Q version
# it can double if group_contributions are calculated
EN_B_PER_STEP = 370.0
CONV_MB = 2**20
# very rough estimate
OUT_B_PER_STEP = 2000
TEMP_B_PER_STEP = 160
NB_B_PER_STEP = 80
# intervals maps: q_parameter_key, q_default_value, approx_bytes_per_frame
qintervals = {
"trj": ["trajectory", 100, num_atoms_all * TRJ_B_PER_ATOM],
"log": ["output", 10, OUT_B_PER_STEP],
"temp": ["temperature", 10, TEMP_B_PER_STEP],
"en": ["energy", 10, EN_B_PER_STEP],
"nb": ["non_bond", 10, NB_B_PER_STEP]
}
total_data = {"trj": 0, "log": 0, "en": 0, "rest": 0}
# calculate approx amount of data
for i, step in enumerate(eq_steps + feps):
data = {}
mdsteps = int(step.parameters["md"]["steps"])
for k, v in qintervals.iteritems():
interval_key = v[0]
default_interval = v[1]
bytes_per_step = v[2]
try:
interval = int(step.parameters["intervals"][interval_key])
data[k] = mdsteps / interval * bytes_per_step
except KeyError:
# default
data[k] = mdsteps / default_interval * bytes_per_step
except ZeroDivisionError:
data[k] = 0 # no printout
finally:
# if energy or trajectory, check that files for output are
# defined, otherwise set the printout to 0
if interval_key in ("energy", "trajectory") and not \
interval_key in step.parameters["files"].keys():
data[k] = 0
trj_data = data["trj"]
en_data = data["en"]
log_data = (data["log"] + data["temp"] + data["nb"])
rest_data = num_atoms_all * REST_B_PER_ATOM
total_data["trj"] += trj_data
total_data["log"] += log_data
total_data["en"] += en_data
total_data["rest"] += rest_data
data = (trj_data + log_data + rest_data + en_data) / CONV_MB
logger.info("Your runs will waste approx. {:.2f} MB of storage. "
"Per replica: {:.2f} MB (trj: {:.1f}, log: {:.1f}, "
"en: {:.1f}, rest: {:.1f})".format(
sum(total_data.values()) / CONV_MB * repeats,
sum(total_data.values()) / CONV_MB,
total_data["trj"] / CONV_MB, total_data["log"] / CONV_MB,
total_data["en"] / CONV_MB, total_data["rest"] / CONV_MB))
# remove temporary directory
shutil.rmtree(TMPDIR)
return rep_dirs
def test_convert_placeholders_fail(self):
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
with pytest.raises(QStructError):
qstruct.convert_placeholders("$1.CB$")