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We found Websites Listing below when search with mdtraj.org on Search Engine
MDTraj Examples — MDTraj 1.6.1 documentation
MDTraj Examples¶. This page provides a series of examples, tutorials and recipes to help you get started with mdtraj.. Each subsection is a notebook. To open these notebooks in a “live” IPython session and execute the documentation interactively, you need to download the repository and start the IPython notebook.
Mdtraj.orgMDTraj Examples — MDTraj 1.1.0 documentation
MDTraj Examples¶. This page provides a series of examples, tutorials and recipes to help you get started with mdtraj.. Each subsection is a notebook. To open these notebooks in a “live” IPython session and execute the documentation interactively, you need to download the repository and start the IPython notebook.
Mdtraj.orgmdtraj.Trajectory — MDTraj 1.9.8.dev0 documentation
Mdtraj.Trajectory. A Trajectory represents a collection of one or more molecular structures, generally (but not necessarily) from a molecular dynamics trajectory. The Trajectory stores a number of fields describing the system through time, including the cartesian coordinates of each atoms ( xyz ), the topology of the molecular system ( topology ...
Mdtraj.orgQuestion about writing a PDB file · Issue #767 · mdtraj ...
2015-03-14 · Hi, I had a question about writing PDB files after clustering using KMeans algorithm. I just started using mdtraj - so my questions may be somewhat naive, but when I …
Github.com使用mdconvert转换分子动力学模拟轨迹 | Hope
2017-10-31 · 常见的分子动力学模拟软件包括Amber，Gromacs，Namd，openMM等，不同软件运行之后产生的轨迹文件格式不尽相同，而某些分析模块则只能处理特定格式的轨迹文件，因而需要一款足够稳健的工具来转换不同的文件格式，比如mdconvert。现将其使用方法记录于下，以作 …
Blog.chembiosim.comIssues with join · Issue #1697 · mdtraj/mdtraj · GitHub
2021-11-15 · I think it is failing because you are trying to set an array element ( rmsd_channel [channel]) with a sequence; mdtraj.rmsd gives back an array in the shape ( target.n_frames) with the rmsd for each frame in traj compared to traj [0]. This is not allowed in numpy.
Github.comInstalling mdtraj on cluster · Issue #1147 · mdtraj/mdtraj ...
2016-07-18 · SBolo commented on Jul 18, 2016. Hi everyone, from the installation procedure I found that mdtraj can only be installed via anaconda or pip. However I would like to install it on a cluster (because I need to perform some heavy calculations) and I need to know if …
Github.comMDTraj原子选择语句 | Hope
2020-05-12 · 内容主要来自于MDtraj官网。 Hope. 永远相信美好的事情终将发生. 首页; 归档; 分类; 标签; 关于; 搜索 MDTraj原子选择语句 发表于 2020-05-12 分类于 cc MDTraj是一款重要的MD轨迹分析工具，本文将介绍MDTraj中的原子选择语句。内容主要来自于MDtraj官网。 MDTraj基于分子的topology进行原子选择，选择语句的返回值 ...
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Mdteam.comBug#1009079: mdtraj: autopkgtest timeout on arm64 ...
2022-05-01 · The autopkgtest tets for mdtraj attempts to download a pdb file and then use that in calculations. This is failing (either all the time or intermittently) with a timeout: I looked at the results of the autopkgtest of you package because it was showing up as a regression for the upload of gcc-12. Because the unstable-to-testing migration software now blocks on …
Mail-archive.compython - setting an array element with a sequence using np ...
2022-03-30 · I have two lists which are something like the below: How can I put two of these lists in a list in the shape below: final : [[],[]] I did something like the …
Stackoverflow.comconverting Gromacs *.xtc trajectory file to dcd file using ...
2016-01-06 · Just to add to Tyler's email: In MDAnalysis you would do (inside the python interpreter): import MDAnalysis as mda u = mda.Universe(TPR, XTC) # …
Groups.google.comPython rmsd示例，mdtraj.rmsd Python示例 - HotExamples
Python rmsd - 已找到30个示例。这些是从开源项目中提取的最受好评的mdtraj.rmsd现实Python示例。您可以评价示例，以帮助我们提高示例质量。
Python.hotexamples.compython - what this means: shape=(num_pairs, 2) - Stack ...
2022-03-25 · mdtraj.compute_distances (traj, atom_pairs, periodic=True, opt=True) My problem is how can I define "atom_pairs", its definition is something like below (based on the mdtraj website) but still I don't know how can I define it? atom_pairsnp.ndarray, shape= (num_pairs, 2), dtype=int. Each row gives the indices of two atoms involved in the ...
Stackoverflow.comHow can I plot the output of mdtraj.compute_dssp?
Read 2 answers by scientists to the question asked by Marwa Abd El Kader Zaater on Dec 22, 2021
Researchgate.netProcessed: nbconvert is mistuned - mail-archive.com
2021-12-22 · Processing commands for [email protected]: > reassign 1002375 python3-nbconvert nbconvert/6.1.0-1 Bug #1002375 [src:mdtraj] mdtraj: FTBFS: AttributeError: module 'mistune' has no attribute 'BlockGrammar' Bug reassigned from package 'src:mdtraj' to 'python3-nbconvert'. No longer marked as found in versions mdtraj/1.9.6-3. Ignoring request to alter …
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