def main(): dataset_name = sys.argv[1] homedir = shell('echo $HOME') if homedir == '/home/sry': print('---On server ibm') maximumlst = [11, 12, 13, 14, 15] elif homedir == '/public/home/sry': print('---On server hp') maximumlst = [5, 6, 7, 8, 9, 10] else: print('[ERROR] Failed to select server!') exit(1) class_numlst = [2, 8] centerlst = ['CA', 'geometric'] minimum = 0.1 # maximumlst = [5,6,7,8,9,10,11,12,13,14,15] steplst = [0.5, 1, 1.5, 2] # class_numlst = [2,8]# @@++ # centerlst = ['CA','geometric']# @@++ # minimum = 0.5# @@++ # maximumlst = [5]# @@++ # steplst = [1.5]# @@++ QR = QsubRunner(homedir, dataset_name, class_numlst, centerlst, minimum, maximumlst, steplst) QR.mCSM_runner()
def main(): dataset_name = sys.argv[1] HOMEdir = shell('echo $HOME') Calculator = CalculateMSA(dataset_name, HOMEdir) Calculator.pdb2seq() Calculator.run_psiblast() Calculator.blast2msa()
def main(): dataset_name = 'TR' homedir = shell('echo $HOME') appdir = '%s/bin/stride' % homedir pdb_wild_dir = '%s/mCNN/dataset/%s/pdb_chain' % (homedir, dataset_name ) #wild_pdb_dir pdb_TR_dir = '%s/mCNN/dataset/%s/output' % (homedir, dataset_name) outdir_wild = '%s/mCNN/dataset/%s/feature/stride/wild' % (homedir, dataset_name) outdir_TR = '%s/mCNN/dataset/%s/feature/stride/TR' % (homedir, dataset_name) calSA(appdir, outdir_wild, outdir_TR, pdb_wild_dir, pdb_TR_dir)
def main(): homedir = shell('echo $HOME') featurelst = ' '.join([ 'depth', 'rsa', 'thermo', 'onehot', 'pharm', 'hp', 'mass', 'deltar', 'pharm_deltar', 'hp_deltar', 'msa', 'energy', 'ddg' ]) # ------------------------------------------------------------------------------------------------------------------ ## parse argument parser = argparse.ArgumentParser() parser.add_argument('dataset_name', type=str, help='dataset name') parser.add_argument( '--flag', type=str, choices=['first', 'all'], default='all', help= '"first" calc df_feature only, "all" calc df_neighbor and df_feature, default is "all".' ) parser.add_argument('-k', '--k_neighbor', type=int, required=True, nargs='+', help='The k_neighbor list.') parser.add_argument('-C', '--center', type=str, required=True, nargs='+', choices=['CA', 'geometric'], help='The MT site center type.') parser.add_argument('-T', '--pca', type=str, default='False', choices=['False', 'True'], help='If consider pca transform, the default is False') args = parser.parse_args() dataset_name = args.dataset_name flag = args.flag k_neighborlst = args.k_neighbor centerlst = args.center pca = str2bool(args.pca) QR = CoordRunner(homedir, dataset_name, flag, k_neighborlst, centerlst, featurelst) QR.coord_runner() if flag == 'first': ## first means only calc df_feature (ALL the ATOMS), do not run the latter part in this main function exit(0)
def main(): dataset_name = sys.argv[1] homedir = shell('echo $HOME') appdir = '%s/mCNN/src/Stride/stride' % homedir pdb_ref_path = '%s/mCNN/dataset/%s/feature/rosetta/ref_output' % ( homedir, dataset_name) pdb_mut_path = '%s/mCNN/dataset/%s/feature/rosetta/mut_output' % ( homedir, dataset_name) outdir_mutant = '%s/mCNN/dataset/%s/feature/stride/mutant' % (homedir, dataset_name) outdir_wild = '%s/mCNN/dataset/%s/feature/stride/wild' % (homedir, dataset_name) calSA(appdir, outdir_mutant, outdir_wild, pdb_ref_path, pdb_mut_path)
def main(): dataset_name, flag = sys.argv[1:] HOMEdir = shell('echo $HOME') ROS = RosettaEnergy(dataset_name, HOMEdir) if flag == 'first': ROS.get_mdl0( ) # mdl0 are needed by others, split two steps for this parallel computing. elif flag == 'second': ROS.run_ref() ROS.mapping_pos() ROS.rewrite_mtcsv() ROS.run_mut() ROS.check_result() ROS.get_energy()
#!/usr/bin/env python # -*- coding: utf-8 -*- import sys, os from mCNN.processing import shell dataset_name = sys.argv[1] homedir = shell('echo $HOME') def check_mCNN(homedir,dataset_name): wild_qsublog_dir = '%s/mCNN/dataset/%s/feature/mCNN/wild/qsublog'%(homedir,dataset_name) mutant_qsublog_dir = '%s/mCNN/dataset/%s/feature/mCNN/mutant/qsublog'%(homedir,dataset_name) wild_qsubtag_dir_lst = [wild_qsublog_dir+'/'+x for x in os.listdir(wild_qsublog_dir)] mutant_qsubtag_dir_lst = [mutant_qsublog_dir+'/'+x for x in os.listdir(mutant_qsublog_dir)] for wild_qsubtag_dir in wild_qsubtag_dir_lst: errdirlst = [wild_qsubtag_dir+'/'+x+'/err' for x in os.listdir(wild_qsubtag_dir)] for errdir in errdirlst: if not os.path.exists(errdir): print('DO Not Exist',errdir) continue if int(os.path.getsize(errdir)) > 0: # print(os.path.getsize(errdir)) # print(type(os.path.getsize(errdir))) print(errdir) for mutant_qsubtag_dir in mutant_qsubtag_dir_lst: errdirlst = [mutant_qsubtag_dir+'/'+x+'/err' for x in os.listdir(mutant_qsubtag_dir)] for errdir in errdirlst: if not os.path.exists(errdir): print('DO Not Exist',errdir)