def create_directories(self, remove_existing = True):
self.notify("MSG","Creating workspace...")
for path in self.data:
if os.path.exists(self.data[path]) and remove_existing:
self.notify("Removing Directory",self.data[path])
shutil.rmtree(self.data[path])
scripts_common.create_directory(self.data[path])
def save_params_handler(self, data):
data = convert_to_utf8(json.loads(data))
create_directory("wizard/scripts")
my_hash = hashlib.sha1()
my_hash.update(str(time.time()))
path = os.path.join("wizard","scripts",my_hash.hexdigest()[:10]+".ppc")
script_handler = open(path,"w")
script_handler.write(json.dumps(data, sort_keys=False, indent=4, separators=(',', ': ')))
script_handler.close()
self.wfile.write('{"file_url":"'+path+'"}')
def create_directories(self):
"""
Recreates the workspace structure. Removes the old location if necessary.
"""
self.notify("MSG", "Creating workspace...")
if self.parameters.get_value("overwrite", default_value=True):
self.clear_directories(self.data.keys())
for folder_key in self.data:
scripts_common.create_directory(self.data[folder_key])
def create_directories(self):
"""
Recreates the workspace structure. Removes the old location if necessary.
"""
self.notify("MSG","Creating workspace...")
if self.parameters.get_value("overwrite", default_value = True) :
self.clear_directories(self.data.keys())
for folder_key in self.data:
scripts_common.create_directory(self.data[folder_key])
def show_results_handler(self, data):
try:
data = convert_to_utf8(json.loads(data))
print "show_results_handler", data
create_directory("results/tmp")
results = data["results"] if "results" in data else "results"
results_path = os.path.join(data["base"],results,"results.json")
shutil.copyfile(results_path,os.path.join("results","tmp","data.json"))
webbrowser.open("http://"+IP+":"+str(PORT)+"/results.html", new = 0, autoraise=True)
self.wfile.write("OK")
except IOError:
self.wfile.write("KO")
def create_directory(self,data):
data = convert_to_utf8(json.loads(data))
print data
try:
success = create_directory(data['location'], ensure_writability = True)
self.wfile.write(json.dumps({"done":success}))
except:
self.wfile.write(json.dumps({"done":False}))
def preprocess_pdb(args):
pdb_file = args[1]
output = "./" + args[2]+"/"+args[2]
create_directory("./" + args[2])
cluster_frames = get_frame_numbers(args)
pdb = prody.parsePDB(pdb_file)
# Get a copy of the pdb coords
input_coordsets = numpy.array(pdb.getCoordsets()[cluster_frames])
# Empty pdb
pdb.delCoordset(range(pdb.numCoordsets()))
# Build another pdb to store it
input_pdb = prody.parsePDB(pdb_file)
input_pdb.delCoordset(range(input_pdb.numCoordsets()))
# And add the chosen coordsets
for i in range(len(cluster_frames)):
input_pdb.addCoordset(input_coordsets[i])
prody.writePDB(output+"_ini.pdb", input_pdb)
print_matrix(input_pdb.select("name CA").getCoordsets(), output)
return pdb, input_coordsets, cluster_frames, output
def preprocess_pdb(args):
pdb_file = args[1]
output = "./" + args[2] + "/" + args[2]
create_directory("./" + args[2])
cluster_frames = get_frame_numbers(args)
pdb = prody.parsePDB(pdb_file)
# Get a copy of the pdb coords
input_coordsets = numpy.array(pdb.getCoordsets()[cluster_frames])
# Empty pdb
pdb.delCoordset(range(pdb.numCoordsets()))
# Build another pdb to store it
input_pdb = prody.parsePDB(pdb_file)
input_pdb.delCoordset(range(input_pdb.numCoordsets()))
# And add the chosen coordsets
for i in range(len(cluster_frames)):
input_pdb.addCoordset(input_coordsets[i])
prody.writePDB(output + "_ini.pdb", input_pdb)
print_matrix(input_pdb.select("name CA").getCoordsets(), output)
return pdb, input_coordsets, cluster_frames, output
def test_create_directory(self):
create_directory("tmp_test/test")
self.assertTrue(os.path.exists("tmp_test/test"))
os.system("rm -rf tmp_test")
self.assertFalse(create_directory("/folder_at_root", True))
"""
Created on 05/06/2014
@author: victor
"""
import sys
import os.path
import pyproct.tools.scriptTools as tools
level = sys.argv[1]
execution_range = int(sys.argv[2]), int(sys.argv[3]) + 1 #second is included
exec_path = os.getcwd()
base_folder = {"level2": "scripts", "level1": "scripts", "level0": ""}
base = os.path.join(base_folder[level], level, "run")
tools.create_directory(base)
for script_number in range(*execution_range):
pyproct_script = os.path.join(base_folder[level], level,
"script_%s_%d.json" % (level, script_number))
os.system("python -m pyproct.main %s" % pyproct_script)
# load colors per cluster
#colors = [(1.,0.,0.), (0.,1.,0.), (0.,0.,1.)]*10
import seaborn as sns
colors = sns.hls_palette(15, l=.3, s=.8)
# VMD execution template
template = open("/home/victor/git/PhD-GPCR/PhD-GPCR-2/data/load_script_representatives.tcl").read()
for line in open(options.input):
protein, drug, folder = line.strip().split()
# sorted clusters and same color generation always make the same cluster_id, color pair
representatives_file = os.path.join(folder, "representatives.pdb")
output_folder = os.path.join(options.output_folder, drug, protein)
create_directory(output_folder)
pdb = parsePDB(representatives_file)
writePDB(os.path.join(output_folder,"protein.pdb"), pdb.select("protein"), csets = [0])
writePDB(os.path.join(output_folder,"ligands.pdb"), pdb.select("resname %s"%drug))
num_clusters = pdb.numCoordsets()
clusters_file = open(os.path.join(output_folder,"cluster_colors"), "w")
for i in range(num_clusters):
clusters_file.write("%.2f %.2f %.2f%s"%( colors[i][0],
colors[i][1],
colors[i][2],
("\n" if i <(num_clusters-1) else "")))
clusters_file.close()
camera_settings = ""; camera_settings_zoomed = ""; option_camera = "#"; pre_render_file = ""; rendered_file = ""; option_zoom = "#"
"""
import json
import os.path
import validation.bidimensional.datasets as data
import validation.bidimensional.validationTools as vtools
from pyproct.tools.scriptTools import create_directory
from pyproct.driver.parameters import ProtocolParameters
from pyproct.driver.observer.observer import Observer
from pyproct.driver.driver import Driver
from pyproct.tools.commonTools import convert_to_utf8
from pyproct.clustering.clustering import Clustering
from pyproct.data.matrix.matrixHandler import MatrixHandler
if __name__ == '__main__':
create_directory("./clustering_images")
create_directory("./matrices")
create_directory("./tmp")
condensed_matrices, all_observations = vtools.create_matrices(data)
# Saving matrices
for dataset_name in data.all_datasets:
handler = MatrixHandler(condensed_matrices[dataset_name],
{"method": "load"})
handler.save_matrix("./matrices/%s" % dataset_name)
# Run pyProCT for each of them
base_script = "".join(open("base_script.json", "r").readlines())
for dataset_name in ['concentric_circles'
]: #data.all_datasets: #["spaeth_06"]:#
print dataset_name
"""
import json
import os.path
import validation.bidimensional.datasets as data
import validation.bidimensional.validationTools as vtools
from pyproct.tools.scriptTools import create_directory
from pyproct.driver.parameters import ProtocolParameters
from pyproct.driver.observer.observer import Observer
from pyproct.driver.driver import Driver
from pyproct.tools.commonTools import convert_to_utf8
from pyproct.clustering.clustering import Clustering
from pyproct.data.matrix.matrixHandler import MatrixHandler
if __name__ == '__main__':
create_directory("./clustering_images")
create_directory("./matrices")
create_directory("./tmp")
condensed_matrices, all_observations = vtools.create_matrices(data)
# Saving matrices
for dataset_name in data.all_datasets:
handler = MatrixHandler(condensed_matrices[dataset_name], {"method":"load"})
handler.save_matrix("./matrices/%s"%dataset_name)
# Run pyProCT for each of them
base_script = "".join(open("base_script.json","r").readlines())
for dataset_name in ['concentric_circles']: #data.all_datasets: #["spaeth_06"]:#
print dataset_name
# Change placeholders
script_str = base_script%(os.path.abspath("./tmp/%s"%dataset_name),"./matrices/%s"%dataset_name)
options, args = parser.parse_args()
input_file = args[0]
control_info = json.loads(open(input_file, "r").read())
print "Selected action = %s" % options.action
# Generate regression tests
if options.action == "GENERATE":
print "Generating Expected Results"
for test_info in control_info:
print "Generating: %s" % test_info["name"]
stdout_file, stderr_file = execute_pyproct(test_info["script"])
script = json.loads(tools.remove_comments(open(test_info["script"], "r").read()))
workspace = script["global"]["workspace"]
s_tools.create_directory(test_info["expected_results_dir"])
# Move the generated files
os.system("mv %s %s %s"%(stdout_file, stderr_file,test_info["expected_results_dir"]))
for subpath in test_info["files_to_check"]:
for file in test_info["files_to_check"][subpath]:
os.system("mv %s %s"%(os.path.join(workspace["base"],subpath,file),
test_info["expected_results_dir"]))
# clean(workspace)
# Execute regression tests
elif options.action == "TEST":
print "Testing results against Expected Results dir"
log_handler = open(options.log_file,"w")
"""
Created on 05/06/2014
@author: victor
"""
import sys
import os.path
import pyproct.tools.scriptTools as tools
level = sys.argv[1]
execution_range = int(sys.argv[2]) , int(sys.argv[3])+1 #second is included
exec_path = os.getcwd()
base_folder = {
"level2":"scripts",
"level1":"scripts",
"level0":""
}
base = os.path.join(base_folder[level], level, "run")
tools.create_directory(base)
for script_number in range(*execution_range):
pyproct_script = os.path.join(base_folder[level], level, "script_%s_%d.json"%(level,script_number))
os.system("python -m pyproct.main %s"%pyproct_script)
"""
Created on 05/06/2014
@author: victor
"""
import pyproct.tools.scriptTools as tools
import os.path
import sys
LEVEL = sys.argv[1]
tools.create_directory("scripts/level2")
tools.create_directory("scripts/level1")
tools.create_directory("scripts/level0")
all_initial_files = open(sys.argv[2])
print "Working with filelist: %s"%sys.argv[2]
BASE_TRAJ_FOLDER = "/gpfs/scratch/bsc72/bsc72476/Victor/2JOF"
BASE_SCRIPT_FOLDER = "scripts"
BASE_CLUSTERING_FOLDER = "compressions"
script_index = 0
all_scripts = []
LEVEL_TEMPLATE = "".join(open(os.path.join(BASE_SCRIPT_FOLDER, "%s_base.json"%LEVEL)).readlines())
for file_path in all_initial_files.readlines():
traj_path = os.path.join(BASE_TRAJ_FOLDER, file_path.strip())
def test_create_directory(self):
create_directory("tmp_test/test")
self.assertTrue(os.path.exists("tmp_test/test"))
os.system("rm -rf tmp_test")
self.assertFalse(create_directory("/folder_at_root", True))
options, args = parser.parse_args()
input_file = args[0]
control_info = json.loads(open(input_file, "r").read())
print "Selected action = %s" % options.action
# Generate regression tests
if options.action == "GENERATE":
print "Generating Expected Results"
for test_info in control_info:
print "Generating: %s" % test_info["name"]
stdout_file, stderr_file = execute_pyproct(test_info["script"])
script = json.loads(
tools.remove_comments(open(test_info["script"], "r").read()))
workspace = script["global"]["workspace"]
s_tools.create_directory(test_info["expected_results_dir"])
# Move the generated files
os.system(
"mv %s %s %s" %
(stdout_file, stderr_file, test_info["expected_results_dir"]))
for subpath in test_info["files_to_check"]:
for file in test_info["files_to_check"][subpath]:
os.system("mv %s %s" %
(os.path.join(workspace["base"], subpath, file),
test_info["expected_results_dir"]))
# clean(workspace)
# Execute regression tests
elif options.action == "TEST":
"""
Created on 05/06/2014
@author: victor
"""
import pyproct.tools.scriptTools as tools
import os.path
import sys
LEVEL = sys.argv[1]
tools.create_directory("scripts/level2")
tools.create_directory("scripts/level1")
tools.create_directory("scripts/level0")
all_initial_files = open(sys.argv[2])
print "Working with filelist: %s" % sys.argv[2]
BASE_TRAJ_FOLDER = "/gpfs/scratch/bsc72/bsc72476/Victor/2JOF"
BASE_SCRIPT_FOLDER = "scripts"
BASE_CLUSTERING_FOLDER = "compressions"
script_index = 0
all_scripts = []
LEVEL_TEMPLATE = "".join(
open(os.path.join(BASE_SCRIPT_FOLDER, "%s_base.json" % LEVEL)).readlines())
for file_path in all_initial_files.readlines():
traj_path = os.path.join(BASE_TRAJ_FOLDER, file_path.strip())