{"action":"opened","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/965","repository_url":"https://api.github.com/repos/markovmodel/PyEMMA","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/965/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/965/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/965/events","html_url":"https://github.com/markovmodel/PyEMMA/issues/965","id":183207840,"number":965,"title":"Is there deviation between tica_ojb.get_output() and pca_obj.get_output() calculation?","user":{"login":"funnybomb","id":3928507,"avatar_url":"https://avatars.githubusercontent.com/u/3928507?v=3","gravatar_id":"","url":"https://api.github.com/users/funnybomb","html_url":"https://github.com/funnybomb","followers_url":"https://api.github.com/users/funnybomb/followers","following_url":"https://api.github.com/users/funnybomb/following{/other_user}","gists_url":"https://api.github.com/users/funnybomb/gists{/gist_id}","starred_url":"https://api.github.com/users/funnybomb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/funnybomb/subscriptions","organizations_url":"https://api.github.com/users/funnybomb/orgs","repos_url":"https://api.github.com/users/funnybomb/repos","events_url":"https://api.github.com/users/funnybomb/events{/privacy}","received_events_url":"https://api.github.com/users/funnybomb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-10-15T12:44:56Z","updated_at":"2016-10-15T12:44:56Z","closed_at":null,"body":"I have a start pdb file named \"a.pdb\", and a corresponding simulation file named \"a.xtc\", I want to mark the point of the pdb structure on the first two PCs. So when I test the projection, I got different results by manually calculated projection via np.dot(dev,eigenvectors)[:2] when using TICA, but same result when using PCA\r\n```python\r\ntraj='a.xtc'\r\nfeat = coor.featurize('a.pdb')\r\nfeat.add_backbone_torsions(cossin=True）\r\ninp = coor.load(traj, feat)\r\ninp.shape\r\n(50000,872)\r\ntica_obj = coor.tica(inp)\r\ntica_Y = tica_obj.get_output()[0]\r\npca_ojb = coor.pca(inp)\r\npca_Y = pca_obj.get_output()[0]\r\nmanual_tica_f0 = np.dot( (inp[0,:] - tica_obj.mean), tica_obj.eigenvectors )\r\nmanual_pca_f0 = np.dot( (inp[0,:] - pca_obj.mean), pca_obj.eigenvectors )\r\nmanual_tica_f0[:2] - tica_Y[0,:2]\r\nOut[47]: array([-0.00618514,  0.00866887])\r\nmanual_pca_f0[:2] - pca_Y[0,:2]\r\nOut[48]: array([ -2.79164256e-08,   1.37719329e-08])\r\n```"}}
{"actor":{"display_login":"funnybomb"}}