Mercurial > repos > chemteam > mdanalysis_rdf
comparison pca_cosine.py @ 4:36babbdd7818 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:51:57 -0400 |
| parents | 49dac57d004a |
| children |
comparison
equal
deleted
inserted
replaced
| 3:49dac57d004a | 4:36babbdd7818 |
|---|---|
| 10 import numpy as np | 10 import numpy as np |
| 11 | 11 |
| 12 | 12 |
| 13 def parse_command_line(argv): | 13 def parse_command_line(argv): |
| 14 parser = argparse.ArgumentParser() | 14 parser = argparse.ArgumentParser() |
| 15 parser.add_argument('--idcd', help='input dcd') | 15 parser.add_argument('--itraj', help='input traj') |
| 16 parser.add_argument('--ipdb', help='input pdb') | 16 parser.add_argument('--istr', help='input str') |
| 17 parser.add_argument('--itrajext', help='input traj ext') | |
| 18 parser.add_argument('--istrext', help='input str ext') | |
| 17 parser.add_argument('--icomponents', help='number of principle components') | 19 parser.add_argument('--icomponents', help='number of principle components') |
| 18 parser.add_argument('--iindex', help='index of the PC') | 20 parser.add_argument('--iindex', help='index of the PC') |
| 19 parser.add_argument('--output', help='output') | 21 parser.add_argument('--output', help='output') |
| 20 parser.add_argument('--cosout', help='cosine output') | 22 parser.add_argument('--cosout', help='cosine output') |
| 21 return parser.parse_args() | 23 return parser.parse_args() |
| 22 | 24 |
| 23 | 25 |
| 24 args = parse_command_line(sys.argv) | 26 args = parse_command_line(sys.argv) |
| 25 | 27 |
| 26 u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") | 28 u = mda.Universe(args.istr, args.itraj, |
| 29 topology_format=args.istrext, format=args.itrajext) | |
| 27 | 30 |
| 28 components = int(args.icomponents) | 31 components = int(args.icomponents) |
| 29 pca_index = int(args.iindex) | 32 pca_index = int(args.iindex) |
| 30 | 33 |
| 31 PSF_pca = pca.PCA(u, select='backbone') | 34 PSF_pca = pca.PCA(u, select='backbone') |