options = sparser.Options([
# opt attribute type num default multi description
("--help", "help", bool, 0, False, False, "Print help and exit"),
("-v", "verbose", bool, 0, False, False, "Be verbose"),
("-tpr", "tpr", str, 1, None, False, "Run input file (TPR)"),
("-trr", "trajectory", str, 1, None, False, "Input trajectory (TRR)"),
("-parent", "parent", str, 1, None, False, "Parent trajectory (TRR)"),
("-lmb", "lmb", str, 1, None, False, "Input lambda file (DAT)"),
("-par", "parfile", str, 1, None, False, "Input TPS parameter file"),
("-ndx", "index", str, 1, None, True, "Input index file"),
("-out", "out", str, 1, "lambda.dat", False, "Lambda output file"),
("-pi", "pathinfiles", str, 1, None, True, "Path input file(s)"),
("-po", "pathoutfile", str, 1, None, False, "Path output file"),
("-log", "log", str, 1, "tipsi.log", False, "Output file"),
("-fw", "forward", str, 1, None, False, "Forward shooting point"),
("-bw", "backward", str, 1, None, False, "Backward shooting point"),
"Monitoring options:",
("-offset", "offset", int, 1, 0, False, "Trajectory file offset"),
("-pid", "pid", int, 1, None, False, "PID to monitor"),
("-sleep", "interval", float, 1, 600, False,
"Interval between checks for active processes"),
"Molecular/mathematical expressions evaluated in context of reference and frame:",
("-init", "init", str, 1, None, True,
"Expressions evaluated before loading trajectory: -I const=expression"),
("-E", "expressions", str, 1, None, True,
"Expressions not saved to output file: -E tmp=expression"),
("-P", "parameters", str, 1, None, True,
"Parameter expressions: -P param=expression"),
("-S", "states", str, 1, None, True,
"State expressions: -S state=expression"),
("-I", "interfaces", str, 1, None, True,
"Interface expressions: -I iface=expression"),
("-B", "bias", str, 1, None, True,
"Shooting point selection bias expressions: -B expression"),
("-Q", "stop", str, 1, None, False, "Stop condition: -Q expression"),
("-O", "print", str, 1, None, True, "Print to terminal: -P expression"),
("-W", "write", str, 2, None, True, "Write to file: -W file expression"),
("-X", "coords", str, 1, None, True,
"Coordinate sets (PDB/GRO/TPR/TRR): -X ref1=file.gro"),
"Path options",
("-R", "recrossing", str, 1, None, True, "Recrossing rules: -R A-I-A=A"),
("-2way", "twowayprob", str, 1, "0", False,
"Probability of two-way shooting"),
("-rand", "randomize", str, 1, "0", False, "Velocity randomization"),
("-minlen", "minpathlength", int, 1, 10, False, "Minimum path length"),
"Further TPS/MD control:",
("-maxf", "maxframes", int, 1, -1, False,
"Maximum number of frames per run"),
("-mdp", "mdparam", str, 1, None, True, "MD parameters: -mdp par=val"),
])
#!/usr/bin/env python2.7
import sys, sparser
options = sparser.Options([
# opt attribute type num default multi description
( "--help", "help", bool, 0, False, False, "Print help and exit"),
( "-s", "tpr", str, 1, None, False, "Run input file (TPR)"),
( "-f", "trr", str, 1, None, False, "Input trajectory (TRR|GRO|PDB)"),
( "-n", "index", str, 1, None, False, "Input index file"),
( "-e", "expression", str, 1, None, True, "Expression"),
( "-o", "output", str, 1, None, False, "Output file (stdout if not given)"),
( "-offset", "offset", int, 1, 0, False, "File offset for reading trajectory"),
])
def main(argv=None):
options.parse(argv or sys.argv[1:])
return 0
if __name__ == "__main__":
sys.exit(main())
"""
Command line editor for Gromacs' TPR files.
"""
__author__ = "Tsjerk A. Wassenaar"
__year__ = 2015
import sys
import gmx
import sparser
options = sparser.Options([
# opt attribute type num default multi description
("--help", "help", bool, 0, False, False, "Print help and exit"),
("-tpr", "tpr", str, 1, None, False, "Run input file (TPR)"),
("-o", "out", str, 1, None, False, "Output run input file (TPR)"),
("-p", "par", str, 1, None, True, "Read or set parameters: par=val"),
])
def main(argv=None):
if argv == None:
argv = sys.argv
options.parse(argv[1:])
tpr = gmx.tpr.TPR(options.tpr)
edited = False
for par in options.par:
"""
MOlecular DYnamics CAlculator.
(c)2014 Tsjerk A. Wassenaar
"""
import sys
import sparser # Simple parser
import calculator # General purpose extensible calculator
import gmx # Gromacs stuff
options = sparser.Options([
# opt attribute type num default multi description
( "--help", "help", bool, 0, False, False, "Print help and exit"),
( "-s", "ref", str, 1, None, False, "Reference file (TPR|GRO|PDB|TRR)"),
( "-f", "trj", str, 1, None, False, "Input trajectory (TRR|GRO|PDB)"),
( "-n", "index", str, 1, None, True, "Input index file"),
( "-e", "expression", str, 1, None, True, "Expression"),
])
def main(argv=None):
options.parse(argv or sys.argv[1:])
if not options.trj:
print "No input trajectory file (TRR|PDB|GRO) given."
return 1
trj = gmx.open(options.trj)
if options.ref:
options = sparser.Options([
# opt attribute type num default multi description
("--help", "help", bool, 0, False, False, "Print help and exit"),
("-tpr", "tpr", str, 1, None, False, "Run input file (TPR)"),
("-trr", "trj", str, 1, None, False, "Input trajectory (TRR)"),
("-f", "parfile", str, 1, None, False, "Input TPS parameter file"),
("-n", "index", str, 1, None, True, "Input index file"),
("-o", "out", str, 1, None, False, "Output file"),
("-fw", "forward", str, 1, None, False, "Forward shooting point"),
("-bw", "backward", str, 1, None, False, "Backward shooting point"),
("-log", "log", str, 1, None, False, "Log file"),
"Monitoring options:",
("-offset", "offset", int, 1, 0, False, "Trajectory file offset"),
("-pid", "pid", int, 1, None, False, "PID to monitor"),
"Molecular/mathematical expressions evaluated in context of reference and frame:",
("-init", "init", str, 1, None, True,
"Expressions evaluated before loading trajectory"),
("-E", "expressions", str, 1, None, True,
"Expressions not saved to output file"),
("-P", "parameters", str, 1, None, True, "Parameter expressions"),
("-S", "states", str, 1, None, True, "State expressions"),
("-I", "interfaces", str, 1, None, True, "Interface expressions"),
("-B", "bias", str, 1, None, True,
"Shooting point selection bias expressions"),
("-stop", "stop", str, 1, None, False, "Stop conditions (expression)"),
("-2way", "twowayprob", str, 1, "0", False,
"Probability of two-way shooting"),
("-rand", "randomize", str, 1, "0", False, "Velocity randomization"),
"Further TPS control:",
("-maxf", "maxframes", int, 1, -1, False,
"Maximum number of frames per run"),
])