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fmaschietto / mdigest

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paths should be corrected #11

Open SnehaBheemireddy1 opened 1 month ago

SnehaBheemireddy1 commented 1 month ago

open Pymol locally

from pymol import cmd, util import seaborn as sns import warnings from draw_network_pymol import * warnings.filterwarnings('ignore') cmd.delete('all') cmd.bg_color('black')

place yourself in the visualize_network folder

cd visualize_network

execute pymol locally calling pymol from inside the directory.

provide path to pdb and data_frame data_frame: change accordingly

path = 'mdigest-RESULTS/plots/'

cmd.load(path + '1u2p.pdb', '1u2p') cmd.color('grey80', '1u2p') cmd.remove('!(polymer)') cmd.run('draw_network_pymol.py') cmd.hide('lines', '')

cmd.set_view((\ 0.264859468, -0.952457845, -0.150496021,\ -0.843045175, -0.304483652, 0.443325162,\ -0.468080193, 0.009453356, -0.883612871,\ 0.000000000, 0.000000000, -133.785675049,\ 8.123708725, 6.384021759, 22.244569778,\ 105.477645874, 162.093704224, -20.000000000))

draw_network_from_df(path +'network_Ptpa_Q75L_filter_d_0_5.pkl', which='gcc_Q75L', color_by='gcc_Q75L', sns_palette=sns.color_palette("tab20"), label='gcc_Q75L', edge_norm=1) draw_network_from_df(path + 'network_Ptpa_WT_filter_d_0_5.pkl', which='gcc_WT', color_by='gcc_WT', sns_palette=sns.color_palette("tab20"), label='gcc_WT', edge_norm=1) draw_network_from_df(path +'network_Ptpa_Q75L_filter_d_0_5.pkl', which='dgcc_Q75L', color_by='dgcc_Q75L', sns_palette=sns.color_palette("tab20"), label='dgcc_Q75L', edge_norm=1) draw_network_from_df(path + 'network_Ptpa_WT_filter_d_0_5.pkl', which='dgcc_WT', color_by='dgcc_WT', sns_palette=sns.color_palette("tab20"), label='dgcc_WT', edge_norm=1) draw_network_from_df(path +'network_Ptpa_Q75L_filter_d_0_5.pkl', which='ks_gcc_Q75L', color_by='ks_gcc_Q75L', sns_palette=sns.color_palette("tab20"), label='ks_gcc_Q75L', edge_norm=1) draw_network_from_df(path + 'network_Ptpa_WT_filter_d_0_5.pkl', which='ks_gcc_WT', color_by='ks_gcc_WT', sns_palette=sns.color_palette("tab20"), label='ks_gcc_WT', edge_norm=1)

SnehaBheemireddy1 commented 1 month ago

Also, key error 156.

KeyError Traceback (most recent call last) Cell In[1], line 32 22 cmd.hide('lines', '*') 24 cmd.set_view((\ 25 0.264859468, -0.952457845, -0.150496021,\ 26 -0.843045175, -0.304483652, 0.443325162,\ (...) 29 8.123708725, 6.384021759, 22.244569778,\ 30 105.477645874, 162.093704224, -20.000000000)) ---> 32 draw_network_from_df(path +'network_Ptpa_Q75L_filter_d_0_5.pkl', which='gcc_Q75L', color_by='gcc_Q75L', sns_palette=sns.color_palette("tab20"), label='gcc_Q75L', edge_norm=1) 33 draw_network_from_df(path + 'network_Ptpa_WT_filter_d_0_5.pkl', which='gcc_WT', color_by='gcc_WT', sns_palette=sns.color_palette("tab20"), label='gcc_WT', edge_norm=1) 34 draw_network_from_df(path +'network_Ptpa_Q75L_filter_d_0_5.pkl', which='dgcc_Q75L', color_by='dgcc_Q75L', sns_palette=sns.color_palette("tab20"), label='dgcc_Q75L', edge_norm=1)

File ~/work/mdigest/draw_network_pymol.py:30, in draw_network_from_df(path_to_df, reset_view, hide_nodes, kwargs) 28 view = cmd.get_view() 29 df = load_df(path_to_df) ---> 30 draw_network(df, kwargs) 31 if reset_view: 32 cmd.set_view(view)

File ~/work/mdigest/draw_network_pymol.py:353, in draw_network(df, key, selection, which, w1, w2, reset_view, default_color, check_nodeIDs, center, label, color_sign, color_by, sns_palette, edge_norm, flattenweight, group_by, r) 350 print("we are at 342", color_sign) 351 #print(len(df.columns),df.columns) 352 #print(df) --> 353 _draw_df(df, label=label, flattenweight=flattenweight)

File ~/work/mdigest/draw_network_pymol.py:254, in draw_network.._draw_df(df, label, default_color, flattenweight) 250 else: 251 color2 = color 252 print("line", CYLINDER, 253 node2CA[row[key[0]]], --> 254 node2CA[row[key[1]]], 255 radius, 256 color, 257 color2) 259 objs += [CYLINDER, 260 node2CA[row[key[0]]], 261 node2CA[row[key[1]]], 262 radius, 263 color, 264 color2] 266 cmd.load_cgo(objs, '{}edges'.format(label))

KeyError: 156

vas2201 commented 3 days ago

Are you able to resolve this error (KeyError : 156 ) ?

vas2201 commented 1 day ago

This issue is resolved by using pdb file from given example, don't use pdb from PDB database. the residue index is not same in both cases. causing this error.

fmaschietto commented 1 day ago

I see,
thanks I’, goint to fix this asap. Federica

On Nov 25, 2024, at 12:10 PM, vas penu @.***> wrote:

This issue is resolved by using pdb file from given example, don't use pdb from PDB database ?. the residue index is not same in both cases. causing this error.

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