From fdc216005a05ed4bb56db021a432c2bf93046ca6 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 28 Aug 2018 12:59:34 -0500
Subject: [PATCH] Added dnarbd binary to repository for command line invocation
---
bin/dnarbd | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
setup.py | 1 +
2 files changed, 68 insertions(+)
create mode 100644 bin/dnarbd
diff --git a/bin/dnarbd b/bin/dnarbd
new file mode 100644
index 0000000..703c3d8
--- /dev/null
+++ b/bin/dnarbd
@@ -0,0 +1,67 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import re
+from dnarbd.simulate import multiresolution_simulation as simulate
+
+parser = argparse.ArgumentParser(prog="dnarbd",
+ description="""Easy multiresolution simulations of DNA nanotechnology objects using ARBD""")
+
+parser.add_argument('-o','--output-prefix', type=str, default=None,
+ help="Name for your job's output")
+parser.add_argument('-d','--directory', type=str, default=None,
+ help='Directory for simulation; does not need to exist yet')
+parser.add_argument('-g','--gpu', type=int, default=0,
+ help='GPU for simulation; check nvidia-smi for availability')
+parser.add_argument('--coarse-steps', type=int, default=1e7,
+ help='Simulation steps for coarse model (200 fs/step)')
+parser.add_argument('--fine-steps', type=int, default=1e7,
+ help='Simulation steps for fine model (50 fs/step)')
+parser.add_argument('--backbone-scale', type=float, default=1.0,
+ help='Factor to scale DNA backbone in atomic model; try 0.25 to avoid clashes for atomistic simulations')
+
+parser.add_argument('input_file', type=str,
+ help="""Any of the following:
+ (1) a cadnano JSON file;
+ (2) a vHelix Maya (.ma) file;
+ (3) an atomic PDB file""")
+
+args = parser.parse_args()
+
+if __name__ == '__main__':
+
+ infile = args.input_file
+ try:
+ re_result = re.match("(.*)\.([^.]+)",infile)
+ prefix = re_result.group(1)
+ extension = re_result.group(2).lower()
+ except:
+ raise Exception("Unrecognized input file '{}'".format(infile))
+
+ if extension == 'json':
+ from dnarbd.readers import read_cadnano as read_model
+ elif extension == 'ma':
+ from dnarbd.readers import read_vhelix as read_model
+ elif extension == 'pdb':
+ from dnarbd.readers import read_atomic_pdb as read_model
+ else:
+ raise Exception("Unrecognized input file '{}'".format(infile))
+
+ model = read_model( infile )
+
+ run_args = dict(
+ model = model,
+ output_name = args.output_prefix,
+ job_id = "job-"+args.output_prefix,
+ directory = args.directory,
+ gpu = args.gpu,
+ coarse_steps = args.coarse_steps,
+ fine_steps = args.fine_steps,
+ backbone_scale = args.backbone_scale
+ )
+
+ if args.output_prefix == None:
+ run_args['output_name'] = prefix
+
+ simulate( **run_args )
diff --git a/setup.py b/setup.py
index af491de..9cf1532 100644
--- a/setup.py
+++ b/setup.py
@@ -19,6 +19,7 @@ setuptools.setup(
url="https://gitlab.engr.illinois.edu/tbgl/tools/dnarbd",
packages=setuptools.find_packages(),
include_package_data=True,
+ scripts=['bin/dnarbd'],
install_requires=(
'numpy>=1.14',
'scipy>=1.1',
--
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