shinji iida physicshinzui

## colabfoldのインストール手順とsingularityを使った使用方法.md

      
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                physicshinzui
                / colabfoldのインストール手順とsingularityを使った使用方法.md
            
            
              Created
              April 6, 2024 00:10
            
              
                colabfoldのインストール手順とsingularityを使った使用方法.md
              
          
    #colabfold
#alphafold
#singularity
Update: 2024-04-05
Reference


https://github.com/sokrypton/ColabFold/wiki/Running-ColabFold-in-Docker

１. ディレクトリを作成し移動

mkdir colabfold


## pepflow_err_cuda.md

      
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                physicshinzui
                / pepflow_err_cuda.md
            
            
              Created
              March 19, 2024 00:58
            
              
                pepflow_err_cuda.md
              
          
    ../aten/src/ATen/native/cuda/Indexing.cu:1141: indexSelectLargeIndex: block: [17,0,0], thread: [64,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1141: indexSelectLargeIndex: block: [17,0,0], thread: [65,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1141: indexSelectLargeIndex: block: [17,0,0], thread: [66,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1141: indexSelectLargeIndex: block: [17,0,0], thread: [67,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1141: indexSelectLargeIndex: block: [17,0,0], thread: [68,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1141: indexSelectLargeIndex: block: [17,0,0], thread: [69,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1141: indexSelectLargeIndex: block: [17,0,0], thread: [70,0,0] Asse


## ２次元heatmapのpython関数.md

      
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                physicshinzui
                / ２次元heatmapのpython関数.md
            
            
              Last active
              March 7, 2024 11:52
            
              
                ２次元heatmapのpython関数.md
              
          
    #heatmap
#matplotlib
#ramachandran
#dihedral
def draw_2DFEL(x, y, bins=40, levels=[0,8]):
    H, xedges, yedges = np.histogram2d(x, y, bins=bins)

 # Plot the contour lines

  
## metad_alphabeta.dat
# Activate MOLINFO functionalities
MOLINFO STRUCTURE=ref.pdb

# -0.994838 = -57.0 deg (phi)
ALPHABETA ...
ATOMS1=@phi-2 REFERENCE=-0.994838
ATOMS2=@phi-3
ATOMS3=@phi-4
ATOMS4=@phi-5
ATOMS5=@phi-6

## perturb_bimodal_distrib_using_noise.ipynb

      
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                physicshinzui
                / perturb_bimodal_distrib_using_noise.ipynb
            
            
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              October 31, 2023 02:14
            
          
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## je.jl
using Plots
using Statistics

function read_xvg(filename)
    file = open(filename, "r")
    xs, ys = [], []
    for line in eachline(file)
        if !startswith(line, "#") && !startswith(line, "@")
            x, y = split(line)
            push!(xs, x)

## perturb_bimodal_distrib_using_noise.ipynb

      
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                physicshinzui
                / perturb_bimodal_distrib_using_noise.ipynb
            
            
              Created
              May 17, 2023 00:23
            
              
                perturb_bimodal_distrib_using_noise.ipynb
              
          
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## get_interacting_residues by PyMOL.md

      
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                physicshinzui
                / get_interacting_residues by PyMOL.md
            
            
              Created
              February 7, 2023 02:32
            
              
                get_interacting_residues by PyMOL.md
              
          
    #pymol-script
#pymol
from pymol import cmd

import sys

 
## generate_data_lammps.ipynb

      
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                physicshinzui
                / generate_data_lammps.ipynb
            
            
              Created
              November 8, 2022 07:55
            
              
                generate_data_lammps.ipynb
              
          
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## input_03.lammps
# 1) Initialization
units lj
dimension 2
atom_style atomic
pair_style lj/cut 2.5
boundary p p p

# 2) System definition
read_data minimized_coordinate.data
	# Activate MOLINFO functionalities
	MOLINFO STRUCTURE=ref.pdb

	# -0.994838 = -57.0 deg (phi)
	ALPHABETA ...
	ATOMS1=@phi-2 REFERENCE=-0.994838
	ATOMS2=@phi-3
	ATOMS3=@phi-4
	ATOMS4=@phi-5
	ATOMS5=@phi-6
	using Plots
	using Statistics

	function read_xvg(filename)
	file = open(filename, "r")
	xs, ys = [], []
	for line in eachline(file)
	if !startswith(line, "#") && !startswith(line, "@")
	x, y = split(line)
	push!(xs, x)
	# 1) Initialization
	units lj
	dimension 2
	atom_style atomic
	pair_style lj/cut 2.5
	boundary p p p

	# 2) System definition
	read_data minimized_coordinate.data