From edd1867550cb8ced74bc319055135c8d76474333 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Javier=20Gonz=C3=A1lez-Delgado?= <jgonzalezd@laas.fr>
Date: Mon, 6 Nov 2023 10:05:44 +0000
Subject: [PATCH] Add error messages for missing atoms.
---
wario/get_coordinates.ipynb | 22 +++++++++++++++++++++-
1 file changed, 21 insertions(+), 1 deletion(-)
diff --git a/wario/get_coordinates.ipynb b/wario/get_coordinates.ipynb
index 4c935ad..09c3727 100644
--- a/wario/get_coordinates.ipynb
+++ b/wario/get_coordinates.ipynb
@@ -14,6 +14,7 @@
"import itertools\n",
"import pandas as pd \n",
"from Bio import PDB \n",
+ "import sys\n",
"import warnings #Optional\n",
"warnings.filterwarnings(\"ignore\") #Optional"
]
@@ -120,9 +121,20 @@
" # 1. Definition of the reference frame on every sequence position\n",
"\n",
" CA_coor = df.loc[ (df.Atom == 'CA') , ['coor_x','coor_y','coor_z']].to_numpy() # CA coordinates \n",
+ " \n",
+ " if np.shape(CA_coor)[0] != L:\n",
+ " sys.exit('The number of CA atoms does not match the number of residues.')\n",
+ " \n",
" N_coor = df.loc[ (df.Atom == 'N') , ['coor_x','coor_y','coor_z']].to_numpy() # N coordinates \n",
+ " \n",
+ " if np.shape(N_coor)[0] != L:\n",
+ " sys.exit('The number of N atoms does not match the number of residues.')\n",
+ " \n",
" C_coor = df.loc[ (df.Atom == 'C') , ['coor_x','coor_y','coor_z']].to_numpy() # C coordinates \n",
" \n",
+ " if np.shape(C_coor)[0] != L:\n",
+ " sys.exit('The number of C atoms does not match the number of residues.')\n",
+ " \n",
" N_CA_coor = N_coor - CA_coor; N_CA_coor = N_CA_coor / np.linalg.norm(N_CA_coor, axis = 1)[:, None]\n",
" C_CA_coor = C_coor - CA_coor; C_CA_coor = C_CA_coor / np.linalg.norm(C_CA_coor, axis = 1)[:, None]\n",
" CxN_coor = np.cross(C_CA_coor, N_CA_coor); CxN_coor = CxN_coor / np.linalg.norm(CxN_coor, axis = 1)[:, None]\n",
@@ -166,6 +178,14 @@
" \n",
" return positions_and_frames"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "58692e89-a456-40c1-8b76-254696b702d4",
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {
@@ -184,7 +204,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.16"
+ "version": "3.10.9"
}
},
"nbformat": 4,
--
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