From 9e8f156cafaa01b09fa05721c115ba14a78f3d52 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Javier=20Gonz=C3=A1lez-Delgado?= <jgonzalezd@laas.fr>
Date: Wed, 8 Nov 2023 14:08:15 +0000
Subject: [PATCH] Add option to only analyze an arbitrary sequence subset
---
wario/get_contacts.ipynb | 23 +++++++++++++++++++----
1 file changed, 19 insertions(+), 4 deletions(-)
diff --git a/wario/get_contacts.ipynb b/wario/get_contacts.ipynb
index acd883a..36ffdfe 100644
--- a/wario/get_contacts.ipynb
+++ b/wario/get_contacts.ipynb
@@ -18,7 +18,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 3,
"id": "57a23fbe",
"metadata": {},
"outputs": [],
@@ -26,7 +26,6 @@
"def get_contacts(coor_conf, threshold_file, assort = False):\n",
"\n",
" L = int(0.5*(1 + np.sqrt(1 + 8*np.shape(coor_conf)[0])))\n",
- " pos_pairs = np.array(list(itertools.combinations(range(L), 2)))\n",
"\n",
" contact_thresholds = pd.read_csv(threshold_file, sep=\" \", header=0)\n",
" contact_thresholds['th11'] = np.deg2rad(contact_thresholds['th11'])\n",
@@ -51,7 +50,7 @@
" contact_thresholds.delta_min = mins\n",
" contact_thresholds.delta_max = maxs\n",
"\n",
- " coor_conf = pd.DataFrame(np.concatenate([coor_conf, pos_pairs], axis = 1),\n",
+ " coor_conf = pd.DataFrame(coor_conf,\n",
" columns = ['coor_x','coor_y','coor_z','or1_x','or1_y','or1_z','or2_x','or2_y','or2_z','AA1','AA2','pos1','pos2'])\n",
" coor_conf.range = np.abs(coor_conf['pos1'] - coor_conf['pos2'])\n",
" coor_conf.range = (coor_conf.range*(coor_conf.range<5) + 5*(coor_conf.range>=5)).astype('int') \n",
@@ -104,6 +103,22 @@
" else:\n",
" return coor_conf.w_dis_se3"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "4672ddec-7dec-4036-984c-aaaa7246ce1f",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "715a891c-5221-42bb-ab86-36a6e825ed97",
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {
@@ -122,7 +137,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.16"
+ "version": "3.10.9"
}
},
"nbformat": 4,
--
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