Skip to content

Instantly share code, notes, and snippets.

@HubLot

HubLot/HClust with ward on psi_md_traj_all.PB.fasta

Last active August 29, 2015 14:20
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save HubLot/9e0f76bc987489aedabe to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save HubLot/9e0f76bc987489aedabe to your computer and use it in GitHub Desktop.
Download ZIP
Test scikit-learn VS R clustering for PBxplore
Raw
HClust with ward on psi_md_traj_all.PB.fasta
{
"cells": [
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"import PBlib as PB\n",
"import PBclust\n",
"import numpy as np\n",
"from sklearn.cluster import AgglomerativeClustering"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"read 270 sequences in demo2_tmp/psi_md_traj_all.PB.fasta\n"
]
}
],
"source": [
"#Get the data\n",
"header_lst, seq_lst = PB.read_several_fasta([\"demo2_tmp/psi_md_traj_all.PB.fasta\"])\n",
"substitution_mat = PB.load_substitution_matrix(PB.SUBSTITUTION_MATRIX_NAME)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Building distance matrix\n",
"100%\n"
]
}
],
"source": [
"#Distances\n",
"distance_mat = PB.distance_matrix(seq_lst, substitution_mat)"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def medoids(dist, clusters_sklearn):\n",
" medo = []\n",
" for cluster in np.unique(clusters_sklearn):\n",
" medo.append(np.argmin(np.sum(dist[clusters_sklearn == cluster],axis=0)))\n",
" return medo\n",
"\n",
"#R way\n",
"clusters_R, medoid_id = PB.hclust(distance_mat, nclusters=3)\n",
"\n",
"#Scikit-learn way\n",
"ward = AgglomerativeClustering(n_clusters=3, linkage='ward').fit(distance_mat)\n",
"clusters_sklearn = list(ward.labels_)\n",
"medoid_sklearn = medoids(distance_mat, clusters_sklearn)\n",
"\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"R clustering\n",
"cluster 1: 90 sequences (33%)\n",
"cluster 2: 90 sequences (33%)\n",
"cluster 3: 90 sequences (33%)\n",
"Index of medoids: [65, 137, 221]\n",
"scikit-learn clustering\n",
"cluster 0: 90 sequences (33%)\n",
"cluster 1: 90 sequences (33%)\n",
"cluster 2: 90 sequences (33%)\n",
"Index of medoids: [137, 65, 221]\n"
]
}
],
"source": [
"#Sum up the results\n",
"\n",
"print(\"R clustering\")\n",
"PBclust.display_clust_report(clusters_R)\n",
"print(\"Index of medoids: {0}\".format(medoid_id))\n",
"print(\"scikit-learn clustering\")\n",
"PBclust.display_clust_report(clusters_sklearn)\n",
"print(\"Index of medoids: {0}\".format(medoid_sklearn))"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Careful! R clusters are between 1 & 3 whereas scikit-learn is between 0 & 2\n",
"\n",
"seq psi_md_traj_1.pdb | model 0: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 1: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 2: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 3: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 4: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 5: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 6: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 7: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 8: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 9: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 10: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 11: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 12: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 13: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 14: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 15: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 16: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 17: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 18: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 19: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 20: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 21: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 22: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 23: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 24: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 25: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 26: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 27: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 28: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 29: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 30: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 31: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 32: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 33: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 34: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 35: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 36: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 37: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 38: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 39: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 40: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 41: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 42: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 43: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 44: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 45: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 46: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 47: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 48: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 49: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 50: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 51: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 52: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 53: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 54: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 55: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 56: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 57: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 58: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 59: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 60: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 61: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 62: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 63: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 64: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 65: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 66: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 67: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 68: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 69: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 70: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 71: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 72: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 73: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 74: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 75: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 76: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 77: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 78: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 79: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 80: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 81: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 82: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 83: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 84: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 85: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 86: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 87: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 88: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_1.pdb | model 89: 1 (R), 1 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 0: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 1: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 2: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 3: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 4: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 5: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 6: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 7: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 8: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 9: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 10: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 11: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 12: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 13: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 14: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 15: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 16: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 17: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 18: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 19: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 20: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 21: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 22: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 23: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 24: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 25: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 26: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 27: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 28: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 29: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 30: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 31: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 32: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 33: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 34: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 35: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 36: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 37: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 38: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 39: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 40: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 41: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 42: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 43: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 44: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 45: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 46: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 47: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 48: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 49: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 50: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 51: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 52: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 53: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 54: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 55: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 56: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 57: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 58: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 59: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 60: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 61: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 62: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 63: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 64: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 65: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 66: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 67: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 68: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 69: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 70: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 71: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 72: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 73: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 74: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 75: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 76: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 77: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 78: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 79: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 80: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 81: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 82: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 83: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 84: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 85: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 86: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 87: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 88: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_2.pdb | model 89: 2 (R), 0 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 0: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 1: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 2: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 3: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 4: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 5: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 6: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 7: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 8: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 9: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 10: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 11: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 12: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 13: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 14: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 15: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 16: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 17: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 18: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 19: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 20: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 21: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 22: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 23: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 24: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 25: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 26: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 27: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 28: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 29: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 30: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 31: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 32: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 33: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 34: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 35: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 36: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 37: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 38: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 39: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 40: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 41: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 42: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 43: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 44: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 45: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 46: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 47: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 48: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 49: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 50: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 51: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 52: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 53: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 54: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 55: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 56: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 57: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 58: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 59: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 60: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 61: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 62: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 63: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 64: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 65: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 66: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 67: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 68: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 69: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 70: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 71: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 72: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 73: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 74: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 75: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 76: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 77: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 78: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 79: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 80: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 81: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 82: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 83: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 84: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 85: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 86: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 87: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 88: 3 (R), 2 (sklearn)\n",
"seq psi_md_traj_3.pdb | model 89: 3 (R), 2 (sklearn)\n"
]
}
],
"source": [
"#all Results\n",
"\n",
"print(\"Careful! R clusters are between 1 & 3 whereas scikit-learn is between 0 & 2\")\n",
"print\n",
"\n",
"for i, name in enumerate(header_lst):\n",
" print(\"seq {0}: {1} (R), {2} (sklearn)\".format(name, clusters_R[i],clusters_sklearn[i]))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"\n"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment