From 661ac4181f54dfd5a6019beb26a229775b232db0 Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Tue, 5 Jul 2016 16:02:36 +0100
Subject: [PATCH] Added logging to main module
---
pycgtool.py | 22 ++++++++++++++++++++--
pycgtool/interface.py | 1 +
2 files changed, 21 insertions(+), 2 deletions(-)
diff --git a/pycgtool.py b/pycgtool.py
index a33e6b0..c30d715 100755
--- a/pycgtool.py
+++ b/pycgtool.py
@@ -2,6 +2,7 @@
import argparse
import sys
+import logging
from pycgtool.frame import Frame
from pycgtool.mapping import Mapping
@@ -9,6 +10,8 @@ from pycgtool.bondset import BondSet
from pycgtool.forcefield import ForceField
from pycgtool.interface import Progress, Options
+logger = logging.getLogger(__name__)
+
def main(args, config):
"""
@@ -23,11 +26,17 @@ def main(args, config):
if args.bnd:
bonds = BondSet(args.bnd, config)
+ logger.info("Bond measurements will be made")
+ else:
+ logger.info("Bond measurements will not be made")
if args.map:
mapping = Mapping(args.map, config, itp=args.itp)
cgframe = mapping.apply(frame, exclude={"SOL"})
cgframe.output(config.output_name + ".gro", format=config.output)
+ logger.info("Mapping will be performed")
+ else:
+ logger.info("Mapping will not be performed")
# Main loop - perform mapping and measurement on every frame in XTC
def main_loop():
@@ -43,18 +52,23 @@ def main(args, config):
bonds.apply(cgframe)
numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin
+ logger.info("Beginning analysis of {0} frames".format(numframes))
Progress(numframes, postwhile=main_loop).run()
if args.bnd:
if args.map:
+ logger.info("Beginning Boltzmann inversion")
bonds.boltzmann_invert()
if config.output_forcefield:
+ logger.info("Creating GROMACS forcefield directory")
ff = ForceField("ff" + config.output_name + ".ff")
ff.write_rtp(config.output_name + ".rtp", mapping, bonds)
+ logger.info("GROMACS forcefield directory created")
else:
bonds.write_itp(config.output_name + ".itp", mapping=mapping)
if config.dump_measurements:
+ logger.info("Dumping bond measurements to file")
bonds.dump_values(config.dump_n_values)
@@ -71,8 +85,6 @@ def map_only(args, config):
cgframe.output(config.output_name + ".gro", format=config.output)
if args.xtc and (config.output_xtc or args.outputxtc):
- numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin
-
# Main loop - perform mapping and measurement on every frame in XTC
def main_loop():
nonlocal cgframe
@@ -80,6 +92,8 @@ def map_only(args, config):
cgframe = mapping.apply(frame, cgframe=cgframe, exclude={"SOL"})
cgframe.write_xtc(config.output_name + ".xtc")
+ numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin
+ logger.info("Beginning analysis of {0} frames".format(numframes))
Progress(numframes, postwhile=main_loop).run()
@@ -126,6 +140,10 @@ if __name__ == "__main__":
print("Using XTC: {0}".format(args.xtc))
if config.map_only:
+ logger.info("Starting: mapping only")
map_only(args, config)
else:
+ logger.info("Starting: parameter measurement")
main(args, config)
+
+ logger.info("Analysis complete")
diff --git a/pycgtool/interface.py b/pycgtool/interface.py
index 02c80a6..d22d3ed 100644
--- a/pycgtool/interface.py
+++ b/pycgtool/interface.py
@@ -264,6 +264,7 @@ class Progress:
Iterate through self until stopped by maximum iterations or False condition.
"""
collections.deque(self, maxlen=0)
+ return self._its
@property
def _bar(self):
--
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