def test_generate_json_tet_p5LD3():
name = "test"
entire_sequence = "MMMSPEDEIQSLEEKNSQLKQEISQLEEKNQQLKYGELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKGKGDGELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKGKGDGSPEDKISQLKEENQQLEQKIQQLKEENSQLEYGGDGKGLEHHHHH"
segments_str = """
SPED EIQSLEE KNSQLKQ EISQLEE KNQQLKY G P7mS
GKGDG
ELKQLEE ELQAIEE QLAQLQW KAQARKE KLAQLK APHshort
GKGDG
ELKQLEE ELQAIEE QLAQLQW KAQARKE KLAQLK APHshort
GKGDG
SPED KISQLKE ENQQLEQ KIQQLKE ENSQLEY G P8mS
GDGKG
"""
pairs = [{
"pair": ["APHshort", "APHshort"],
"type": "A",
"chains": ["A", "B"],
"template": "APH.pdb"
}, {
"pair": ["P7mS", "P8mS"],
"type": "P",
"chains": ["A", "B"],
"template": "p7_p8.pdb"
}]
out_name = tempfile.NamedTemporaryFile().name
mj.generate_json(name,
entire_sequence,
segments_str,
pairs,
out_name=out_name)
d = u.load_json_data(out_name)
assert d.name == name
assert d.entire_sequence == entire_sequence
assert len(d.segments) == 4
assert d.segments[0].id == 1
assert d.segments[0].start == 4
assert d.segments[0].end == 4 + 33 - 1
assert d.segments[0].pair_id == 4
assert d.segments[0].pair_type == "P"
assert d.segments[0].pdb_template == "p7_p8.pdb"
assert d.segments[0].pdb_chain == "A"
assert d.segments[2].id == 3
assert d.segments[2].start == 76
assert d.segments[2].end == 109
assert d.segments[2].pair_id == 2
assert d.segments[2].pair_type == "A"
assert d.segments[2].pdb_template == "APH.pdb"
assert d.segments[2].pdb_chain == "B"
os.remove(out_name)
type=str)
parser.add_argument(
'-r',
'--rand-seed',
help=
'Random seed. For modeler it mist be between -2 and -50000. If none, a random number will be chosen',
default=None,
type=int)
args = parser.parse_args()
if args.rand_seed is None:
import random
args.rand_seed = random.randint(-50000, -2)
d = u.load_json_data(args.json)
env = environ(rand_seed=args.rand_seed)
log.verbose() # request verbose output
if args.out_dir is None:
args.out_dir = d.name + u.id_generator()
if not os.path.exists(args.out_dir):
os.makedirs(args.out_dir)
#convert to absolute path before chdir
args.alnfile = os.path.abspath(args.alnfile)
os.chdir(args.out_dir)
def test_find_pair():
json = u.relative_to(__file__, 'data/data.json')
d = u.load_json_data(json)
p1, p2, pdb = u.find_pair('APHshE', d.segments)
assert p1 == d.segments[4]['id'] - 1
def chimera_color(json_file,
out_file,
model_number="",
verbose=True,
color_map=None,
default_color="#d2d2b4b48c8c",
add_surface=True,
thick_vdw_size=2.5,
default_vdw_size=1.7,
print_thick_vdw=False):
"""Print scipt for coloring in chimera"""
d = u.load_json_data(json_file)
with open(out_file + '.chimera', 'w') as f:
def print_segment(s, vdw_size=None):
template = """color {color} #{model}:{start}-{end}"""
s['model'] = model_number
s['vdw_size'] = vdw_size
#override the color of segments if map is present
if not color_map is None:
s['color'] = color_map.get(s.name,
s.get('color', default_color))
else:
s['color'] = s.get('color', default_color)
line = template.format(**s)
print_and_write("#" + s.name, f, verbose)
print_and_write(line, f, verbose)
if vdw_size:
#define the VDW scale
line = """vdwdefine {vdw_size} #{model}:{start}-{end}""".format(
**s)
print_and_write(line, f, verbose)
#color the model with the default color (the color for the linkers)
print_and_write("#Default model color and vdw size", f, verbose)
line = "color {color} #{model}".format(color=default_color,
model=model_number)
print_and_write(line, f, verbose)
line = "vdwdefine {vdw_size} #{model}".format(
vdw_size=default_vdw_size, model=model_number)
print_and_write(line, f, verbose)
#group the commands by pairs of segments
printed_segments_ids = []
for s in d.segments:
if not s.id in printed_segments_ids:
print_segment(s)
print_segment(d.segments[s.pair_id - 1])
printed_segments_ids.extend([s.id, s.pair_id])
if add_surface:
print_and_write("", f, verbose)
line = "surface probeRadius 3 vertexDensity 2 allComponents false protein"
print_and_write(line, f, verbose)
line = "surface probeRadius 3 vertexDensity 2 allComponents false protein"
line = "transparency 80,s #{model}:".format(model=model_number)
print_and_write(line, f, verbose)
if print_thick_vdw:
print_and_write("", f, verbose)
print_and_write("#Thicker segments", f, verbose)
printed_segments_ids = []
for s in d.segments:
if not s.id in printed_segments_ids:
print_segment(s, thick_vdw_size)
print_segment(d.segments[s.pair_id - 1], thick_vdw_size)
printed_segments_ids.extend([s.id, s.pair_id])
)
parser.add_argument("-v",
"--verbose",
default=True,
help='print scripts to screen')
parser.add_argument(
"-m",
"--color-map",
default=None,
help=
'colormap to override colors given in the json. Works even if no colors are present in the Json'
)
parser.add_argument(
"-t",
"--thick_vdw",
default=True,
help='Print specification for thicker segments (for movie creation).')
a = parser.parse_args()
if a.out_file is None:
a.out_file = a.json.replace('.json', '')
if not a.color_map is None:
a.color_map = u.load_json_data(a.color_map)
chimera_color(a.json,
a.out_file,
verbose=a.verbose,
color_map=a.color_map,
print_thick_vdw=a.thick_vdw)
from modeller import *
if __name__ == "__main__":
parser = argparse.ArgumentParser(__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-j', '--json', help="json file name", default='data.json')
parser.add_argument('-aln', '--alignment', help="alignment file name", default='alignment-file.ali')
parser.add_argument('-p', '--path', help="path to template pdb files", default=None)
args = parser.parse_args()
if args.path is None:
#the default path should be raltive to the scripts directroy
args.path = u.relative_to(__file__,'../building_blocks')
d = u.load_json_data(args.json) #read json file
aln_str = d.entire_sequence
with open(args.alignment, 'w') as f1:
for pair in d.pairs: #go through all CC pairs
pair_1_id, pair_2_id, pdbname = u.find_pair(pair['pair'][0], d.segments)
pair_name = d.segments[pair_1_id].name + "_" + d.segments[pair_2_id].name
md_obj = md.load(os.path.join(args.path, pdbname))
topology = md_obj.topology #read topology
position = md_obj.xyz #and position from pdb file
pair_1_seq = u.mdtraj_to_fasta(topology,0)
pair_2_seq = u.mdtraj_to_fasta(topology,1) #convert topology to fasta sequence
parser.add_argument('-j',
'--json',
help='Json file from which to load aminoacid sequnce.',
type=str)
parser.add_argument('-e',
'--auto-exit',
help='Exit at the end of script',
type=bool,
default=True)
a = parser.parse_args()
if not a.json is None:
d = u.load_json_data(a.json)
a.seq = d.entire_sequence
chimera_path = 'chimera'
script_dir = os.path.dirname(os.path.realpath(__file__))
chimera_flags = "" #"--nogui"
if a.debug:
chimera_flags += " --debug"
cmd = "bash -c \"{path} {flags} --script '{script_dir}/make_helix_chimera.py --out-file={out_file} --seq={seq} --auto-exit={ae} '\"".format(
path=chimera_path,
flags=chimera_flags,
script_dir=script_dir,
out_file=a.out_file,
seq=a.seq,