Spaces:
Runtime error
Runtime error
File size: 5,379 Bytes
0605e17 ce9089f 0605e17 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 |
from pymol import cmd
import requests
# from gradio_client import Client
def color_plddt(selection="all"):
"""
AUTHOR
Jinyuan Sun
https://github.com/JinyuanSun/PymolFold/tree/main
MIT License
DESCRIPTION
Colors Predicted Structures by pLDDT
USAGE
color_plddt sele
PARAMETERS
sele (string)
The name of the selection/object to color by pLDDT. Default: all
"""
# Alphafold color scheme for plddt
cmd.set_color("high_lddt_c", [0, 0.325490196078431, 0.843137254901961])
cmd.set_color(
"normal_lddt_c", [0.341176470588235, 0.792156862745098, 0.976470588235294]
)
cmd.set_color("medium_lddt_c", [1, 0.858823529411765, 0.070588235294118])
cmd.set_color("low_lddt_c", [1, 0.494117647058824, 0.270588235294118])
# test the scale of predicted_lddt (0~1 or 0~100 ) as b-factors
cmd.select("test_b_scale", f"b>1 and ({selection})")
b_scale = cmd.count_atoms("test_b_scale")
if b_scale > 0:
cmd.select("high_lddt", f"({selection}) and (b >90 or b =90)")
cmd.select("normal_lddt", f"({selection}) and ((b <90 and b >70) or (b =70))")
cmd.select("medium_lddt", f"({selection}) and ((b <70 and b >50) or (b=50))")
cmd.select("low_lddt", f"({selection}) and ((b <50 and b >0 ) or (b=0))")
else:
cmd.select("high_lddt", f"({selection}) and (b >.90 or b =.90)")
cmd.select(
"normal_lddt", f"({selection}) and ((b <.90 and b >.70) or (b =.70))"
)
cmd.select("medium_lddt", f"({selection}) and ((b <.70 and b >.50) or (b=.50))")
cmd.select("low_lddt", f"({selection}) and ((b <.50 and b >0 ) or (b=0))")
cmd.delete("test_b_scale")
# set color based on plddt values
cmd.color("high_lddt_c", "high_lddt")
cmd.color("normal_lddt_c", "normal_lddt")
cmd.color("medium_lddt_c", "medium_lddt")
cmd.color("low_lddt_c", "low_lddt")
# set background color
cmd.bg_color("white")
def query_rosettafold2(
sequence: str,
jobname: str,
sym: str = "X",
order: int = 1,
msa_concat_mode: str = "diag",
msa_method: str = "single_sequence",
pair_mode: str = "unpaired_paired",
collapse_identical: bool = True,
num_recycles: int = 0,
use_mlm: bool = True,
use_dropout: bool = True,
max_msa: int = 16,
random_seed: int = 0,
num_models: int = 0,
):
"""
AUTHOR
Simon Duerr
https://twitter.com/simonduerr
DESCRIPTION
Predict a structure using rosettafold2
USAGE
rosettafold2 sequence, jobname, [sym, order, msa_concat_mode, msa_method, pair_mode, collapse_identical, num_recycles, use_mlm, use_dropout, max_msa, random_seed, num_models]
PARAMETERS
sequence: (string)
one letter amino acid codes that you want to predict
jobname: string
name of the pdbfile that will be outputted
sym: string
symmetry Default: X
order:
Default 1,
msa_concat_mode:
MSA concatenation mode Default:"diag" Options: "diag", "repeat", "default"
msa_method:
MSA method Default:"single_sequence" Options: "mmseqs2", "single_sequence"
pair_mode:
Pair mode Default:"unpaired_paired" Options: "unpaired_paired", "paired", "unpaired"
collapse_identical:
Collapse identical sequences Default:True
num_recycles:
Number of recycles Default:0 Options: 0, 1, 3, 6, 12, 24
use_mlm:
Use MLM Default:True
use_dropout:
Use dropout Default:True
max_msa:
Max MSA Default:16
random_seed:
Random seed Default:0
num_models:
Number of models Default:0
"""
response = requests.post(
"https://simonduerr-rosettafold2.hf.space/run/rosettafold2/",
json={
"data": [
sequence, # str in 'sequence' Textbox component
jobname, # str in 'jobname' Textbox component
sym, # str in 'sym' Textbox component
order, # int | float (numeric value between 1 and 12) in 'order' Slider component
"diag", # str (Option from: ['diag', 'repeat', 'default']) in 'msa_concat_mode' Dropdown component
"single_sequence", # str (Option from: ['mmseqs2', 'single_sequence', 'custom_a3m']) in 'msa_method' Dropdown component
"unpaired_paired", # str (Option from: ['unpaired_paired', 'paired', 'unpaired']) in 'pair_mode' Dropdown component
True, # bool in 'collapse_identical' Checkbox component
0, # int (Option from: ['0', '1', '3', '6', '12', '24']) in 'num_recycles' Dropdown component
True, # bool in 'use_mlm' Checkbox component
True, # bool in 'use_dropout' Checkbox component
16, # int (Option from: ['16', '32', '64', '128', '256', '512']) in 'max_msa' Dropdown component
0, # int in 'random_seed' Textbox component
1, # int (Option from: ['1', '2', '4', '8', '16', '32']) in 'num_models' Dropdown component
]
},
).json()
try:
data = response["data"]
except KeyError:
print(response["error"])
return None
with open(f"{jobname}.pdb", "w") as out:
out.writelines(data)
cmd.load(f"{jobname}.pdb")
cmd.extend("rosettafold2", query_rosettafold2)
cmd.extend("color_plddt", color_plddt)
|