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jbarnoud/HClust with ward on psi_md_traj_all.PB.fasta

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HClust with ward on psi_md_traj_all.PB.fasta
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"import PBlib as PB\n",
"import PBclust\n",
"import numpy as np\n",
"from sklearn.cluster import AgglomerativeClustering\n",
"import scipy.cluster.hierarchy as scipyh"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"R version 3.2.0 (2015-04-16) -- \"Full of Ingredients\"\r\n",
"Copyright (C) 2015 The R Foundation for Statistical Computing\r\n",
"Platform: x86_64-apple-darwin13.4.0 (64-bit)\r\n",
"\r\n",
"R is free software and comes with ABSOLUTELY NO WARRANTY.\r\n",
"You are welcome to redistribute it under the terms of the\r\n",
"GNU General Public License versions 2 or 3.\r\n",
"For more information about these matters see\r\n",
"http://www.gnu.org/licenses/.\r\n",
"\r\n"
]
}
],
"source": [
"!R --version"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"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"
]
},
{
"cell_type": "code",
"execution_count": 4,
"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": 5,
"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": 6,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"nclusters = 5\n",
"\n",
"#R way\n",
"clusters_R_D, medoid_R_D = PB.hclust(distance_mat, nclusters=nclusters, method='ward.D')\n",
"clusters_R_D2, medoid_R_D2 = PB.hclust(distance_mat, nclusters=nclusters, method='ward.D2')\n",
"\n",
"#Scikit-learn way\n",
"ward = AgglomerativeClustering(n_clusters=nclusters, linkage='ward').fit(distance_mat)\n",
"clusters_sklearn = list(ward.labels_)\n",
"medoid_sklearn = medoids(distance_mat, clusters_sklearn)\n",
"\n",
"# Scipy way\n",
"data_link = scipyh.ward(distance_mat)\n",
"clusters_scipy = scipyh.fcluster(data_link, nclusters, criterion='maxclust')\n",
"medoid_scipy = medoids(distance_mat, clusters_scipy)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"R clustering ward.D\n",
"cluster 1: 90 sequences (33%)\n",
"cluster 2: 55 sequences (20%)\n",
"cluster 5: 55 sequences (20%)\n",
"cluster 3: 35 sequences (13%)\n",
"cluster 4: 35 sequences (13%)\n",
"Index of medoids: [65, 123, 164, 180, 267]\n",
"R clustering ward.D2\n",
"cluster 1: 90 sequences (33%)\n",
"cluster 3: 71 sequences (26%)\n",
"cluster 5: 58 sequences (21%)\n",
"cluster 4: 32 sequences (12%)\n",
"cluster 2: 19 sequences ( 7%)\n",
"Index of medoids: [65, 94, 164, 180, 267]\n",
"scikit-learn clustering\n",
"cluster 0: 90 sequences (33%)\n",
"cluster 1: 62 sequences (23%)\n",
"cluster 3: 51 sequences (19%)\n",
"cluster 2: 39 sequences (14%)\n",
"cluster 4: 28 sequences (10%)\n",
"Index of medoids: [65, 207, 118, 164, 259]\n",
"scipy clustering\n",
"cluster 1: 90 sequences (33%)\n",
"cluster 3: 62 sequences (23%)\n",
"cluster 4: 51 sequences (19%)\n",
"cluster 5: 39 sequences (14%)\n",
"cluster 2: 28 sequences (10%)\n",
"Index of medoids: [65, 259, 207, 164, 118]\n"
]
}
],
"source": [
"#Sum up the results\n",
"\n",
"print(\"R clustering ward.D\")\n",
"PBclust.display_clust_report(clusters_R_D)\n",
"print(\"Index of medoids: {0}\".format(medoid_R_D))\n",
"print(\"R clustering ward.D2\")\n",
"PBclust.display_clust_report(clusters_R_D2)\n",
"print(\"Index of medoids: {0}\".format(medoid_R_D2))\n",
"print(\"scikit-learn clustering\")\n",
"PBclust.display_clust_report(clusters_sklearn)\n",
"print(\"Index of medoids: {0}\".format(medoid_sklearn))\n",
"print(\"scipy clustering\")\n",
"PBclust.display_clust_report(clusters_scipy)\n",
"print(\"Index of medoids: {0}\".format(medoid_scipy))"
]
},
{
"cell_type": "code",
"execution_count": 10,
"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",
"seq psi_md_traj_1.pdb | model 0: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 1: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 2: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 3: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 4: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 5: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 6: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 7: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 8: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 9: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 10: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 11: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 12: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 13: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 14: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 15: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 16: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 17: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 18: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 19: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 20: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 21: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 22: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 23: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 24: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 25: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 26: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 27: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 28: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 29: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 30: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 31: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 32: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 33: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 34: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 35: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 36: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 37: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 38: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 39: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 40: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 41: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 42: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 43: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 44: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 45: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 46: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 47: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 48: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 49: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 50: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 51: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 52: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 53: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 54: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 55: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 56: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 57: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 58: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 59: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 60: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 61: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 62: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 63: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 64: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 65: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 66: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 67: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 68: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 69: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 70: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 71: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 72: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 73: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 74: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 75: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 76: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 77: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 78: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 79: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 80: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 81: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 82: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 83: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 84: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 85: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 86: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 87: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 88: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_1.pdb | model 89: 1 (R.D), 1 (R.D2), 0 (sklearn), 1 (scipy)\n",
"seq psi_md_traj_2.pdb | model 0: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 1: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 2: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 3: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 4: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 5: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 6: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 7: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 8: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 9: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 10: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 11: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 12: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 13: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 14: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 15: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 16: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 17: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 18: 2 (R.D), 2 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 19: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 20: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 21: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 22: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 23: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 24: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 25: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 26: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 27: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 28: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 29: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 30: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 31: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 32: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 33: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 34: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 35: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 36: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 37: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 38: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 39: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 40: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 41: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 42: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 43: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 44: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 45: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 46: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 47: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 48: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 49: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 50: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 51: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 52: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 53: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 54: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 55: 2 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 56: 2 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 57: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 58: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 59: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 60: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 61: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 62: 3 (R.D), 3 (R.D2), 2 (sklearn), 5 (scipy)\n",
"seq psi_md_traj_2.pdb | model 63: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 64: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 65: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 66: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 67: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 68: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 69: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 70: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 71: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 72: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 73: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 74: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 75: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 76: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 77: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 78: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 79: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 80: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 81: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 82: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 83: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 84: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 85: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 86: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 87: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 88: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_2.pdb | model 89: 3 (R.D), 3 (R.D2), 3 (sklearn), 4 (scipy)\n",
"seq psi_md_traj_3.pdb | model 0: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 1: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 2: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 3: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 4: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 5: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 6: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 7: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 8: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 9: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 10: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 11: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 12: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 13: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 14: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 15: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 16: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 17: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 18: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 19: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 20: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 21: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 22: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 23: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 24: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 25: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 26: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 27: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 28: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 29: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 30: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 31: 4 (R.D), 4 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 32: 4 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 33: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 34: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 35: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 36: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 37: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 38: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 39: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 40: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 41: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 42: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 43: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 44: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 45: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 46: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 47: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 48: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 49: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 50: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 51: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 52: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 53: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 54: 4 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 55: 4 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 56: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 57: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 58: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 59: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 60: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 61: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 62: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 63: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 64: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 65: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 66: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 67: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 68: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 69: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 70: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 71: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 72: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 73: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 74: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 75: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 76: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 77: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 78: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 79: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 80: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 81: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 82: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 83: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 84: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 85: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 86: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 87: 5 (R.D), 5 (R.D2), 1 (sklearn), 3 (scipy)\n",
"seq psi_md_traj_3.pdb | model 88: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\n",
"seq psi_md_traj_3.pdb | model 89: 5 (R.D), 5 (R.D2), 4 (sklearn), 2 (scipy)\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 {}: {} (R.D), {} (R.D2), {} (sklearn), {} (scipy)\".format(\n",
" name, clusters_R_D[i], clusters_R_D2[i], clusters_sklearn[i], clusters_scipy[i]))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.4.1"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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