def main(argv=None):
global VERBOSE
args = process_args(argv)
VERBOSE = args['verbose'] or 0
# Get sequence(s):
seqs = load_seq(args)
# What to export:
export_criteria_list = get_export_criteria_list(args)
if VERBOSE > 1:
print("export criteria list:")
print(yaml.dump(export_criteria_list))
for cadnano_file in args["cadnano_files"]:
# folder = os.path.realpath(os.path.dirname(cadnano_file))
# "141105_longer_catenane_BsoBI-frag_offset6nt.json"
design = os.path.splitext(os.path.basename(cadnano_file))[0]
staples_outputfn = args["output"].format(design=design,
cadnano_file=cadnano_file,
seqfile=args["seqfile"])
if not ok_to_write_to_file(staples_outputfn, args):
print("Aborting staple file write for file", cadnano_file)
continue
print("\nLoading design:", design)
doc = Document()
with open(cadnano_file) as fp:
nno_dict = json.load(fp)
decode(doc, nno_dict)
print(cadnano_file, "loaded!")
part = get_part(doc)
apply_sequences(part, seqs, offset=args.get("offset")) # global offset
export_oligo_seqs(part,
csvfilepath=staples_outputfn,
criteria_list=export_criteria_list)
def finishInit(self):
global decodeFile
global Document
global DocumentController
from cadnano.document import Document
from cadnano.fileio.decode import decodeFile
from cadnano.controllers.documentcontroller import DocumentController
from cadnano.views.pathview import pathstyles as styles
styles.setFontMetrics()
doc = Document()
self._document = self.createDocument(base_doc=doc)
if os.environ.get('CADNANO_DISCARD_UNSAVED', False) and not self.ignoreEnv():
self.dontAskAndJustDiscardUnsavedChanges = True
self.dontAskAndJustDiscardUnsavedChanges = True
util.loadAllPlugins()
if self.argns.interactive:
print("Welcome to cadnano's debug mode!")
print("Some handy locals:")
print("\ta\tcadnano.app() (the shared cadnano application object)")
print("\td()\tthe last created Document")
def d():
return self._document
print("\tw()\tshortcut for d().controller().window()")
def w():
return self._document.controller().window()
print("\tp()\tshortcut for d().selectedInstance().reference()")
def p():
return self._document.selectedInstance().reference()
print("\tpi()\tthe PartItem displaying p()")
def pi():
part_instance = self._document.selectedInstance()
return w().pathroot.partItemForPart(part_instance)
print("\tvh(i)\tshortcut for p().reference().getStrandSets(i)")
def strandsets(id_num):
return p().reference().getStrandSets(id_num)
print("\tvhi(i)\tvirtualHelixItem displaying vh(i)")
def vhi(id_num):
partitem = pi()
return partitem.vhItemForIdNum(id_num)
print("\tquit()\tquit (for when the menu fails)")
print("\tgraphicsItm.findChild() see help(pi().findChild)")
interact('', local={'a': self, 'd': d, 'w': w,
'p': p, 'pi': pi, 'vhi': vhi,
})
def decodeFile(filename, document=None):
with io.open(filename, 'r', encoding='utf-8') as fd:
nno_dict = json.load(fd)
if document is None:
document = Document()
decode(document, nno_dict)
return document
def main():
#Initialize cadnano
app = cadnano.app()
doc = app.document = Document()
FILENAME = 'PFD_2hb_loop'
INPUT_FILENAME = '../../cadnano-files/' + FILENAME + '.json'
OUTPUT_FILENAME_1 = '../../cadnano-files/carbs_output/' + FILENAME + '_RB.gsd'
OUTPUT_FILENAME_2 = '../../cadnano-files/carbs_output/' + FILENAME + '_CG.gsd'
PICKLE_FILE = 'data/origami_relaxed.pckl'
RELAX = False
doc.readFile(INPUT_FILENAME)
#Parse the structure for simulation
new_origami = origami.Origami()
new_origami.part = doc.activePart()
new_origami.list_oligos()
new_origami.initialize_nucleotide_matrix()
new_origami.find_skips()
new_origami.create_oligos_list()
new_origami.get_connections()
new_origami.assign_nucleotide_types()
new_origami.incorporate_skips()
new_origami.assign_nucleotide_connections()
new_origami.cluster_into_bodies()
new_origami.parse_skip_connections()
new_origami.calculate_quaternions_from_positions()
#Start relaxation simulation
if RELAX == True:
relax_simulation = RBSimulation.RigidBodySimulation()
relax_simulation.origami = new_origami
relax_simulation.initialize_relax_md()
relax_simulation.initialize_particles()
relax_simulation.create_rigid_bodies()
relax_simulation.create_bonds()
relax_simulation.set_initial_harmonic_bonds()
relax_simulation.set_lj_potentials()
relax_simulation.dump_settings(OUTPUT_FILENAME_1, 1)
relax_simulation.run(1)
relax_simulation.update_positions_and_quaternions()
relax_simulation.save_to_pickle(PICKLE_FILE)
#Start coarse-grained simulation
elif RELAX == False:
cg_simulation = CGSimulation.CGSimulation()
cg_simulation.parse_origami_from_pickle(PICKLE_FILE)
cg_simulation.initialize_cg_md()
cg_simulation.initialize_particles()
cg_simulation.initialize_system()
cg_simulation.create_adjacent_bonds()
cg_simulation.set_harmonic_bonds()
cg_simulation.set_dihedral_bonds()
cg_simulation.set_lj_potentials()
cg_simulation.dump_settings(OUTPUT_FILENAME_2, 1)
cg_simulation.run(2)
def finishInit(self):
global decode
global Document
global DocumentController
from cadnano.document import Document
from cadnano.fileio.nnodecode import decode
from cadnano.gui.controllers.documentcontroller import DocumentController
from cadnano.gui.views import styles
doc = Document()
self.d = self.newDocument(base_doc=doc)
styles.setFontMetrics()
os.environ['CADNANO_DISCARD_UNSAVED'] = 'True' ## added by Nick
if os.environ.get('CADNANO_DISCARD_UNSAVED', False) and not self.ignoreEnv():
self.dontAskAndJustDiscardUnsavedChanges = True
if os.environ.get('CADNANO_DEFAULT_DOCUMENT', False) and not self.ignoreEnv():
self.shouldPerformBoilerplateStartupScript = True
util.loadAllPlugins()
if "-i" in self.argv:
print("Welcome to cadnano's debug mode!")
print("Some handy locals:")
print("\ta\tcadnano.app() (the shared cadnano application object)")
print("\td()\tthe last created Document")
def d():
return self.d
print("\tw()\tshortcut for d().controller().window()")
def w():
return self.d.controller().window()
print("\tp()\tshortcut for d().selectedPart()")
def p():
return self.d.selectedPart()
print("\tpi()\tthe PartItem displaying p()")
def pi():
return w().pathroot.partItemForPart(p())
print( "\tvh(i)\tshortcut for p().virtualHelix(i)")
def vh(vhref):
return p().virtualHelix(vhref)
print( "\tvhi(i)\tvirtualHelixItem displaying vh(i)")
def vhi(vhref):
partitem = pi()
vHelix = vh(vhref)
return partitem.vhItemForVH(vHelix)
print("\tquit()\tquit (for when the menu fails)")
print("\tgraphicsItm.findChild() see help(pi().findChild)")
interact('', local={'a':self, 'd':d, 'w':w,\
'p':p, 'pi':pi, 'vh':vh, 'vhi':vhi,\
})
def test_create_adjacent_bonds_with_skip(self):
PICKLE_FILE = '/Users/damasceno/Documents/1_work/2_codes/carbs/carbs/tests/data/skip_2hb.test.pckl'
app = cadnano.app()
doc = app.document = Document()
cg_simulation = CGSimulation.CGSimulation()
cg_simulation.parse_origami_from_pickle(PICKLE_FILE)
cg_simulation.initialize_cg_md()
cg_simulation.initialize_particles()
cg_simulation.initialize_system()
cg_simulation.create_adjacent_bonds()
assert len(cg_simulation.system.bonds) == 110
def decodeFile(filename, document=None, emit_signals=False):
with io.open(filename, 'r', encoding='utf-8') as fd:
nno_dict = json.load(fd)
if document is None:
from cadnano.document import Document
document = Document()
if 'format' not in nno_dict:
if os.path.splitext(filename)[1] == '.c25':
c25decode.decode(document, nno_dict, emit_signals=emit_signals)
else:
v2decode.decode(document, nno_dict, emit_signals=emit_signals)
else:
v3decode.decode(document, nno_dict, emit_signals=emit_signals)
return document
def finishInit(self):
global decodeFile
global Document
global DocumentController
from cadnano.document import Document
from cadnano.fileio.decode import decodeFile
from cadnano.controllers.documentcontroller import DocumentController
from cadnano.views.pathview import pathstyles as styles
styles.setFontMetrics()
doc = Document()
self._document = self.createDocument(base_doc=doc)
if os.environ.get('CADNANO_DISCARD_UNSAVED', False) and not self.ignoreEnv():
self.dontAskAndJustDiscardUnsavedChanges = True
self.dontAskAndJustDiscardUnsavedChanges = True
def __init__(self, cnjsonpath: str, sequence:str) -> None:
super(CadnanoDocument, self).__init__()
self.cnjsonpath = cnjsonpath
app = cadnano.app()
doc = app.document = Document()
with redirect_stdout(sys.stderr):
doc.readFile(cnjsonpath)
self.part = part = doc.activePart()
self.part_props = part_props = part.getModelProperties().copy()
self.vh_order = part_props['virtual_helix_order']
self.vh_props, self.vh_origins = part.helixPropertiesAndOrigins()
self.vh_radius = part.radius()
self.max_vhelix_length = max(self.vh_props['length'])
self.insertions, self.skips = self.getInsertionsAndSkips()
self.sequence_applied = False
self.max_oligo_length = 0
self.applySequenceToSameLengthOligos(sequence)
def test_pickle_creation(self):
#Initialize cadnano
app = cadnano.app()
doc = app.document = Document()
INPUT_FILENAME = 'data/skip_2hb.test.json'
PICKLE_FILE = 'data/skip_2hb.test.pckl'
assert os.path.exists(INPUT_FILENAME) == True
if os.path.exists(PICKLE_FILE):
os.remove(PICKLE_FILE)
doc.readFile(INPUT_FILENAME)
#Parse the structure for simulation
new_origami = origami.Origami()
new_origami.part = doc.activePart()
new_origami.list_oligos()
new_origami.initialize_nucleotide_matrix()
new_origami.find_skips()
new_origami.create_oligos_list()
new_origami.get_connections()
new_origami.assign_nucleotide_types()
new_origami.incorporate_skips()
new_origami.assign_nucleotide_connections()
new_origami.cluster_into_bodies()
new_origami.parse_skip_connections()
relax_simulation = RBSimulation.RigidBodySimulation()
relax_simulation.origami = new_origami
relax_simulation.initialize_relax_md()
relax_simulation.initialize_particles()
relax_simulation.create_rigid_bodies()
relax_simulation.create_bonds()
relax_simulation.set_initial_harmonic_bonds()
relax_simulation.set_lj_potentials()
relax_simulation.run(1e1)
relax_simulation.update_positions()
relax_simulation.save_to_pickle(PICKLE_FILE)
assert os.path.exists(PICKLE_FILE) == True
def __init__(self, cnjsonpath: str) -> None:
super(CadnanoDocument, self).__init__()
self.cnjsonpath = cnjsonpath
app = cadnano.app()
doc = app.document = Document()
doc.readFile(cnjsonpath)
self.part = part = doc.activePart()
self.part_props = part_props = part.getModelProperties().copy()
self.vh_order = part_props['virtual_helix_order']
self.vh_props, self.vh_origins = part.helixPropertiesAndOrigins()
self.vh_radius = part.radius()
self.max_vhelix_length = max(self.vh_props['length'])
# Determine part coordinate boundaries
xLL, yLL, xUR, yUR = part.getVirtualHelixOriginLimits()
# print(xLL, yLL, xUR, yUR)
self.slice_width = xUR - xLL + self.vh_radius * 8
self.slice_height = yUR - yLL + self.vh_radius * 6
self.x_offset = self.slice_width / 2
self.y_offset = self.slice_height / 2
#!/usr/bin/env python3
# bare_bones_example.py
# Shawn M Douglas, April 2017
# BSD-3 open-source license
import cadnano
from cadnano.document import Document
app = cadnano.app()
doc = app.document = Document()
doc.readFile('myfile.json')
part = doc.activePart()
oligos = part.oligos()
for oligo in oligos:
print("{0}\t{1}\t\'{2}\'\t{3}".format(oligo,
oligo.length(),
oligo.getColor(),
oligo.sequence()))
vhs = list(part.getIdNums()) # convert set to list
for vh_id in vhs[:3]: # display first 3 vhs
fwd_ss, rev_ss = part.getStrandSets(vh_id)
print('VH{0}'.format(vh_id))
print('\t', fwd_ss, '\t', [s.idxs() for s in fwd_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in fwd_ss.strands()])
print('\t', rev_ss, '\t', [s.idxs() for s in rev_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in rev_ss.strands()])
def __init__(self):
# Document import must be here so as to allow for GUI tests to be run
from cadnano.document import Document
self.document = Document()
def main():
# Parse command-line arguments
parser = argparse.ArgumentParser(
description=
'Convert cadnano2.5 file into legacy json format, if possible.')
parser.add_argument("-i",
"--input",
help="source cadnano file",
metavar='FILENAME',
required=True)
parser.add_argument("-o",
"--output",
help="destination json file",
metavar='FILENAME')
args = parser.parse_args()
# Check input file exists
src_file = args.input
if not path.exists(src_file):
sys.exit("Input file {0} not found".format(src_file))
# Determine output filename
if args.output:
dest_file = args.output
else:
# Use a timestamped derivative of input filename
timestamp = "{:%y%m%d.%H%M%S}".format(datetime.now())
src_ext = path.splitext(src_file)
dest_file = '.'.join([src_ext[0], timestamp, 'json'])
if (src_file == dest_file):
sys.exit(
"Please choose an output that doesn't match the input filename")
print("Reading {0}, will export to {1}".format(
colored(src_file, 'yellow'), colored(dest_file, 'yellow')))
# Basic init
app = cadnano.app()
doc = app.document = Document()
# Read input design
doc.readFile(src_file)
part = doc.activePart()
oligos = part.oligos()
# We want to perform some operations on the scaffold and staples.
# First, we need references to the corresponding oligos within the data model.
# We can just hard-code a location we know is in the scaffold
start_vh = 0
start_strandset = 0 # 0 is forward (drawn 5->3 on top), 1 is reverse (3'<-5' on bottom)
start_idx = 22
scaf_start = (start_vh, start_strandset, start_idx)
scaf_oligo = part.getOligoAt(*scaf_start) # unpack the tuple with *
# For fun we might guess that the scaffold is simply the longest oligo
oligos_sorted_by_length = sorted(oligos,
key=lambda x: x.length(),
reverse=True)
longest_oligo = oligos_sorted_by_length[0]
staple_oligos = oligos_sorted_by_length[1:]
print("> Does the longest oligo contain %s?" % str(scaf_start), 'green',
colorBool(longest_oligo == scaf_oligo))
printInfo("Splitting circular oligos...")
circular_oligos = part.getCircularOligos()
if circular_oligos:
printInfo("Breaking circular oligos...")
for circ_oligo in circular_oligos:
strand5p = circ_oligo.strand5p()
strand3p = strand5p.connection3p()
part.removeXover(strand5p, strand3p)
printInfo("Splitting long oligos...")
# Naively break staples at xovers using greedy algorithm
min_split_len = 35 # break oligos longer than this
for staple in staple_oligos:
unbroken_length = staple.length()
strand_lengths = staple.getStrandLengths()
split_idxs = []
next_strand_len = 0
num_bases_used = 0
for nbases in strand_lengths:
next_strand_len += nbases
num_bases_used += nbases
if min_split_len < next_strand_len and num_bases_used < unbroken_length:
split_idxs.append(num_bases_used)
next_strand_len = 0
if split_idxs:
staple.splitAtAbsoluteLengths(split_idxs)
# print(scaffold, scaffold.length(), scaffold.sequence())
p7560 = sequences['p7560']
scaf_oligo.applySequence(p7560)
# seqs = part.getSequences()
# print(seqs)
# oligos = part.oligos()
# oligos_sorted_by_color = sorted(oligos, key=lambda x: x.getColor())
# for oligo in oligos_sorted_by_color:
# if oligo == scaf_oligo:
# print("Scaffold {0} has length {1}".format(oligo, oligo.length()))
# else:
# # oligo_props = oligo.dump()
# printOligo(oligo)
print("Saving modified document as",
colored("{0}".format(dest_file), 'yellow'))
# printInfo("{0}".format(dest_file))
doc.writeToFile(dest_file)
def nnodecode(self,dict):
doc = Document()
doc.mainWindow = self.mainWindow
doc.dc = DocumentController(doc)
document = nnodecode.decode(doc,dict)
return document
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input", type=str, help="Cadnano json file")
parser.add_argument("-o",
"--output",
type=str,
help="Output directory",
default='.')
args = parser.parse_args()
#Assign the parameters
input_filename = args.input
output_directory = args.output
#Check if input file exists
if not os.path.isfile(input_filename):
sys.exit('Input file does not exist!')
#Check if output directory exists
if not os.path.isdir(output_directory):
sys.exit('Output directory does not exist!')
#Define output filename
head, tail = os.path.split(input_filename)
root, ext = os.path.splitext(tail)
output_filename = output_directory + '/' + root + '.gsd'
#Initialize cadnano
app = cadnano.app()
doc = app.document = Document()
#Read cadnano input file
doc.readFile(input_filename)
#Parse the structure for simulation
new_origami = Origami()
new_origami.part = doc.activePart()
new_origami.list_oligos()
new_origami.initialize_nucleotide_matrix()
new_origami.find_skips()
new_origami.create_oligos_list()
new_origami.get_connections()
new_origami.assign_nucleotide_types()
new_origami.incorporate_skips()
new_origami.assign_nucleotide_connections()
new_origami.cluster_into_bodies()
new_origami.parse_soft_connections()
new_origami.determine_coordinate_limits()
#Prepare the simulation
new_simulation = RigidBodySimulation()
new_simulation.origami = new_origami
new_simulation.determine_box_dimensions()
new_simulation.initialize_relax_md()
new_simulation.initialize_particles()
new_simulation.create_rigid_bodies()
new_simulation.create_bonds()
new_simulation.set_harmonic_bonds()
new_simulation.set_lj_potentials()
new_simulation.set_simulation_settings()
new_simulation.dump_settings(output_filename)
new_simulation.take_snapshot()
new_simulation.get_distances()
new_simulation.set_simulation_step()
new_simulation.folding_protocol()
