蛋白质-配体相互作用指纹图谱
prolif的Python项目详细描述
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蛋白质-配体相互作用指纹
：警告：此项目正在积极开发中，可能会发生重大更改。自担风险使用：警告：
说明
prolift是一个工具，用于生成相互作用指纹（ifp）和计算蛋白质-配体相互作用的相似性分数，给出一个参考配体和一系列结合位点残基。
安装
prolift是用python 3编写的，它使用以下非标准库：
- 努比
- rdkit
在继续下一步之前，请确保已安装RDKit:
conda install -c rdkit rdkit
完成后，您可以使用pip:
pip install prolif
用法
INPUT arguments:
-r fileName, --reference fileName
Path to your reference ligand.
-l fileName [fileName ...], --ligand fileName [fileName ...]
Path to your ligand(s).
-p fileName, --protein fileName
Path to your protein.
--residues RESIDUES [RESIDUES ...]
Residues chosen for the interactions. Default: automatically detect residues within --cutoff of the reference ligand
--cutoff float Cutoff for automatic residue detection: distance between centroids. Default: 12.0 Å
--json fileName Path to a custom parameters file. Default: /home/cedric/Dropbox/work/prolif/prolif/parameters.json
OUTPUT arguments:
-o filename, --output filename
Path to the output CSV file
--log level Set the level of the logger. Default: ERROR
-v, --version Show version and exit
Other arguments:
--interactions bit [bit ...]
List of interactions used to build the fingerprint.
│ Class Ligand Residue
│―――――――――――――――――――――――――――――――――――――――――――――
HBdonor │ Hydrogen bond donor acceptor
HBacceptor │ Hydrogen bond acceptor donor
XBdonor │ Halogen bond donor acceptor
XBacceptor │ Halogen bond acceptor donor
cation │ Ionic cation anion
anion │ Ionic anion cation
hydrophobic │ Hydrophobic hydrophobic hydrophobic
FaceToFace │ Pi-stacking aromatic aromatic
FaceToEdge │ Pi-stacking aromatic aromatic
pi-cation │ Pi-cation aromatic cation
cation-pi │ Pi-cation cation aromatic
MBdonor │ Metal metal ligand
MBacceptor │ Metal ligand metal
Default: HBdonor HBacceptor cation anion FaceToFace FaceToEdge hydrophobic
--score {tanimoto,dice,tversky}
Similarity score between molecule A and B :
Let 'a' and 'b' be the number of bits activated in molecules A and B, and 'c' the number of activated bits in common.
-) tanimoto : c/(a+b-c). Used by default
-) dice : 2c/(a+b)
-) tversky : c/(alpha*(a-c)+beta*(b-c)+c)
--alpha int Alpha parameter for Tversky. Default: 0.7
--beta int Beta parameter for Tversky. Default: 0.3
Mandatory arguments: --reference --ligand --protein
MOL2 files only.
许可证
除非另有说明，否则此目录和所有子目录中的所有文件都是在2.0版apache许可下分发的：
Copyright 2017-2018 Cédric BOUYSSET
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
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