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GitHub - prody/ProDy: A Python Package for Protein Dynamics Analysis
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flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item"> <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false"> Product <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1"> <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path> </svg> </button> <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 pt-2 pt-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 pb-2 pb-lg-4 d-lg-flex flex-wrap dropdown-menu-wide"> <div class="HeaderMenu-column px-lg-4 border-lg-right mb-4 mb-lg-0 pr-lg-7"> <div class="border-bottom pb-3 pb-lg-0 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.368-.014.733-.052 1.086.23.462.477 1.088.644 1.517 1.258.364 2.233 1.721 2.605 2.656a.832.832 0 0 1 .053.22v2.869a.641.641 0 0 1-.078.256ZM12.172 11h-.344a4.323 4.323 0 0 1-.355.508C10.703 12.455 9.555 13 7.965 13c-1.725 0-2.989-.359-3.782-1.259a2.005 2.005 0 0 1-.085-.104L4 11.741v6.585c1.435.779 4.514 2.179 8 2.179 3.486 0 6.565-1.4 8-2.179v-6.585l-.098-.104s-.033.045-.085.104c-.793.9-2.057 1.259-3.782 1.259-1.59 0-2.738-.545-3.508-1.492a4.323 4.323 0 0 1-.355-.508h-.016.016Zm.641-2.935c.136 1.057.403 1.913.878 2.497.442.544 1.134.938 2.344.938 1.573 0 2.292-.337 2.657-.751.384-.435.558-1.15.558-2.361 0-1.14-.243-1.847-.705-2.319-.477-.488-1.319-.862-2.824-1.025-1.487-.161-2.192.138-2.533.529-.269.307-.437.808-.438 1.578v.021c0 .265.021.562.063.893Zm-1.626 0c.042-.331.063-.628.063-.894v-.02c-.001-.77-.169-1.271-.438-1.578-.341-.391-1.046-.69-2.533-.529-1.505.163-2.347.537-2.824 1.025-.462.472-.705 1.179-.705 2.319 0 1.211.175 1.926.558 2.361.365.414 1.084.751 2.657.751 1.21 0 1.902-.394 2.344-.938.475-.584.742-1.44.878-2.497Z"></path><path d="M14.5 14.25a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Zm-5 0a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Z"></path> </svg> <div> <div class="color-fg-default h4">GitHub Copilot</div> Write better code with AI </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"security","context":"product","tag":"link","label":"security_link_product_navbar"}" href="https://github.com/features/security"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-shield-check color-fg-subtle mr-3"> <path d="M16.53 9.78a.75.75 0 0 0-1.06-1.06L11 13.19l-1.97-1.97a.75.75 0 0 0-1.06 1.06l2.5 2.5a.75.75 0 0 0 1.06 0l5-5Z"></path><path d="m12.54.637 8.25 2.675A1.75 1.75 0 0 1 22 4.976V10c0 6.19-3.771 10.704-9.401 12.83a1.704 1.704 0 0 1-1.198 0C5.77 20.705 2 16.19 2 10V4.976c0-.758.489-1.43 1.21-1.664L11.46.637a1.748 1.748 0 0 1 1.08 0Zm-.617 1.426-8.25 2.676a.249.249 0 0 0-.173.237V10c0 5.46 3.28 9.483 8.43 11.426a.199.199 0 0 0 .14 0C17.22 19.483 20.5 15.461 20.5 10V4.976a.25.25 0 0 0-.173-.237l-8.25-2.676a.253.253 0 0 0-.154 0Z"></path> </svg> <div> <div class="color-fg-default h4">Security</div> Find and fix vulnerabilities </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"actions","context":"product","tag":"link","label":"actions_link_product_navbar"}" href="https://github.com/features/actions"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-workflow color-fg-subtle mr-3"> <path d="M1 3a2 2 0 0 1 2-2h6.5a2 2 0 0 1 2 2v6.5a2 2 0 0 1-2 2H7v4.063C7 16.355 7.644 17 8.438 17H12.5v-2.5a2 2 0 0 1 2-2H21a2 2 0 0 1 2 2V21a2 2 0 0 1-2 2h-6.5a2 2 0 0 1-2-2v-2.5H8.437A2.939 2.939 0 0 1 5.5 15.562V11.5H3a2 2 0 0 1-2-2Zm2-.5a.5.5 0 0 0-.5.5v6.5a.5.5 0 0 0 .5.5h6.5a.5.5 0 0 0 .5-.5V3a.5.5 0 0 0-.5-.5ZM14.5 14a.5.5 0 0 0-.5.5V21a.5.5 0 0 0 .5.5H21a.5.5 0 0 0 .5-.5v-6.5a.5.5 0 0 0-.5-.5Z"></path> </svg> <div> <div class="color-fg-default h4">Actions</div> Automate any workflow </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"codespaces","context":"product","tag":"link","label":"codespaces_link_product_navbar"}" href="https://github.com/features/codespaces"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-codespaces color-fg-subtle mr-3"> <path d="M3.5 3.75C3.5 2.784 4.284 2 5.25 2h13.5c.966 0 1.75.784 1.75 1.75v7.5A1.75 1.75 0 0 1 18.75 13H5.25a1.75 1.75 0 0 1-1.75-1.75Zm-2 12c0-.966.784-1.75 1.75-1.75h17.5c.966 0 1.75.784 1.75 1.75v4a1.75 1.75 0 0 1-1.75 1.75H3.25a1.75 1.75 0 0 1-1.75-1.75ZM5.25 3.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h13.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Zm-2 12a.25.25 0 0 0-.25.25v4c0 .138.112.25.25.25h17.5a.25.25 0 0 0 .25-.25v-4a.25.25 0 0 0-.25-.25Z"></path><path d="M10 17.75a.75.75 0 0 1 .75-.75h6.5a.75.75 0 0 1 0 1.5h-6.5a.75.75 0 0 1-.75-.75Zm-4 0a.75.75 0 0 1 .75-.75h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1-.75-.75Z"></path> </svg> <div> <div class="color-fg-default h4">Codespaces</div> Instant dev environments </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"issues","context":"product","tag":"link","label":"issues_link_product_navbar"}" href="https://github.com/features/issues"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-issue-opened color-fg-subtle mr-3"> <path d="M12 1c6.075 0 11 4.925 11 11s-4.925 11-11 11S1 18.075 1 12 5.925 1 12 1ZM2.5 12a9.5 9.5 0 0 0 9.5 9.5 9.5 9.5 0 0 0 9.5-9.5A9.5 9.5 0 0 0 12 2.5 9.5 9.5 0 0 0 2.5 12Zm9.5 2a2 2 0 1 1-.001-3.999A2 2 0 0 1 12 14Z"></path> </svg> <div> <div class="color-fg-default h4">Issues</div> Plan and track work </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"code_review","context":"product","tag":"link","label":"code_review_link_product_navbar"}" href="https://github.com/features/code-review"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-code-review color-fg-subtle mr-3"> <path d="M10.3 6.74a.75.75 0 0 1-.04 1.06l-2.908 2.7 2.908 2.7a.75.75 0 1 1-1.02 1.1l-3.5-3.25a.75.75 0 0 1 0-1.1l3.5-3.25a.75.75 0 0 1 1.06.04Zm3.44 1.06a.75.75 0 1 1 1.02-1.1l3.5 3.25a.75.75 0 0 1 0 1.1l-3.5 3.25a.75.75 0 1 1-1.02-1.1l2.908-2.7-2.908-2.7Z"></path><path d="M1.5 4.25c0-.966.784-1.75 1.75-1.75h17.5c.966 0 1.75.784 1.75 1.75v12.5a1.75 1.75 0 0 1-1.75 1.75h-9.69l-3.573 3.573A1.458 1.458 0 0 1 5 21.043V18.5H3.25a1.75 1.75 0 0 1-1.75-1.75ZM3.25 4a.25.25 0 0 0-.25.25v12.5c0 .138.112.25.25.25h2.5a.75.75 0 0 1 .75.75v3.19l3.72-3.72a.749.749 0 0 1 .53-.22h10a.25.25 0 0 0 .25-.25V4.25a.25.25 0 0 0-.25-.25Z"></path> </svg> <div> <div class="color-fg-default h4">Code Review</div> Manage code changes </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block 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20H10.75A1.75 1.75 0 0 1 9 18.25v-1.465a.75.75 0 0 1 1.5 0v1.465c0 .138.112.25.25.25h5.5a.75.75 0 0 1 .53.22l2.72 2.72v-2.19a.75.75 0 0 1 .75-.75h2a.25.25 0 0 0 .25-.25v-9.5Z"></path> </svg> <div> <div class="color-fg-default h4">Discussions</div> Collaborate outside of code </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description" data-analytics-event="{"location":"navbar","action":"code_search","context":"product","tag":"link","label":"code_search_link_product_navbar"}" href="https://github.com/features/code-search"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-code-square color-fg-subtle mr-3"> <path d="M10.3 8.24a.75.75 0 0 1-.04 1.06L7.352 12l2.908 2.7a.75.75 0 1 1-1.02 1.1l-3.5-3.25a.75.75 0 0 1 0-1.1l3.5-3.25a.75.75 0 0 1 1.06.04Zm3.44 1.06a.75.75 0 1 1 1.02-1.1l3.5 3.25a.75.75 0 0 1 0 1.1l-3.5 3.25a.75.75 0 1 1-1.02-1.1l2.908-2.7-2.908-2.7Z"></path><path d="M2 3.75C2 2.784 2.784 2 3.75 2h16.5c.966 0 1.75.784 1.75 1.75v16.5A1.75 1.75 0 0 1 20.25 22H3.75A1.75 1.75 0 0 1 2 20.25Zm1.75-.25a.25.25 0 0 0-.25.25v16.5c0 .138.112.25.25.25h16.5a.25.25 0 0 0 .25-.25V3.75a.25.25 0 0 0-.25-.25Z"></path> </svg> <div> <div class="color-fg-default h4">Code Search</div> Find more, search less </div> </a></li> </ul> </div> </div> <div class="HeaderMenu-column px-lg-4"> <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0 border-bottom-0"> <span class="d-block h4 color-fg-default my-1" id="product-explore-heading">Explore</span> <ul class="list-style-none f5" aria-labelledby="product-explore-heading"> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{"location":"navbar","action":"all_features","context":"product","tag":"link","label":"all_features_link_product_navbar"}" href="https://github.com/features"> 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alt=\"https://img.shields.io/github/actions/workflow/status/prody/prody/main.yml\" src=\"https://camo.githubusercontent.com/8beca19ca068805e24366b845105571742f50c69e656482dc084e69a67d20356/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f616374696f6e732f776f726b666c6f772f7374617475732f70726f64792f70726f64792f6d61696e2e796d6c\" data-canonical-src=\"https://img.shields.io/github/actions/workflow/status/prody/prody/main.yml\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003ca href=\"https://pypi.org/project/ProDy/\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/074e97c9c1118d09bfea3499495ba257f1b6e89642a089913144873bcbc521c0/68747470733a2f2f696d672e736869656c64732e696f2f707970692f762f50726f44792e737667\" data-canonical-src=\"https://img.shields.io/pypi/v/ProDy.svg\" style=\"max-width: 100%;\"\u003e\n\u003c/a\u003e\n\u003ca href=\"https://github.com/prody/ProDy/commits/master\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/96014a2a41bb9f2e0b9b72d0f5e1783263cc34a24f8a032aa73694f527348896/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f636f6d6d69742d61637469766974792f6d2f70726f64792f50726f44792e737667\" data-canonical-src=\"https://img.shields.io/github/commit-activity/m/prody/ProDy.svg\" style=\"max-width: 100%;\"\u003e\n\u003c/a\u003e\n\u003ca href=\"http://www.bahargroup.org/prody/downloads/\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/b7d72ef39c7900ddcd2ccc429018c7cdfe1bff0193f7afcb2fab8f27f82cd502/68747470733a2f2f696d672e736869656c64732e696f2f707970692f646d2f50726f44792e737667\" data-canonical-src=\"https://img.shields.io/pypi/dm/ProDy.svg\" style=\"max-width: 100%;\"\u003e\n\u003c/a\u003e\n\u003ca name=\"user-content-synopsis\"\u003e\u003c/a\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eSYNOPSIS\u003c/h2\u003e\u003ca id=\"user-content-synopsis\" class=\"anchor\" aria-label=\"Permalink: SYNOPSIS\" href=\"#synopsis\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eProDy is a free and open-source Python package for protein structure, dynamics,\nand sequence analysis. It allows for comparative analysis and modeling of\nprotein structural dynamics and sequence co-evolution. Fast and flexible ProDy\nAPI is for interactive usage as well as application development. ProDy also\ncomes with several analysis applications and a graphical user interface for\nvisual analysis.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eFurther details are described in the ProDy papers:\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cdiv dir=\"auto\"\u003e\n\u003cdiv dir=\"auto\"\u003eBakan A, Meireles LM, Bahar I.\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\u003cem\u003eProDy\u003c/em\u003e: Protein Dynamics Inferred from Theory and Experiments.\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\u003cem\u003eBioinformatics\u003c/em\u003e \u003cstrong\u003e2011\u003c/strong\u003e 27(11):1575-1577.\u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\n\u003cdiv dir=\"auto\"\u003eBakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I.\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\u003cem\u003eEvol\u003c/em\u003e and \u003cem\u003eProDy\u003c/em\u003e for Bridging Protein Sequence Evolution and Structural Dynamics.\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\u003cem\u003eBioinformatics\u003c/em\u003e \u003cstrong\u003e2014\u003c/strong\u003e 30(18):2681-2683.\u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\n\u003cdiv dir=\"auto\"\u003eZhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I.\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\u003cem\u003eProDy\u003c/em\u003e 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python.\u003c/div\u003e\n\u003cdiv dir=\"auto\"\u003e\u003cem\u003eBioinformatics\u003c/em\u003e \u003cstrong\u003e2021\u003c/strong\u003e 37(20):3657-3659.\u003c/div\u003e\n\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003ca name=\"user-content-installing-prody\"\u003e\u003c/a\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eINSTALLING PRODY\u003c/h3\u003e\u003ca id=\"user-content-installing-prody\" class=\"anchor\" aria-label=\"Permalink: INSTALLING PRODY\" href=\"#installing-prody\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eProDy is under active development, so we recommend installing it from source from GitHub to ensure everything works properly.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eWe recommend downloading and installing the Anaconda package manager to handle dependencies in controlled environments.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThen you should download the ProDy code either as a zipped folder to extract or using git as directed at the big green button says code. For example, if you have git installed then you can do the following.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003egit clone \u003ca href=\"https://github.com/prody/ProDy.git\"\u003ehttps://github.com/prody/ProDy.git\u003c/a\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThen change directory into the ProDy directory tree and install it by running the following commands.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003ecd ProDy\u003c/p\u003e\n\u003cp dir=\"auto\"\u003epython setup.py build_ext --inplace --force\u003c/p\u003e\n\u003cp dir=\"auto\"\u003epip install -Ue .\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eMore instructions can be found at \u003ca href=\"http://bahargroup.org/prody/downloads/\" rel=\"nofollow\"\u003ehttp://bahargroup.org/prody/downloads/\u003c/a\u003e and \u003ca href=\"http://bahargroup.org/prody/manual/devel/develop.html\" rel=\"nofollow\"\u003ehttp://bahargroup.org/prody/manual/devel/develop.html\u003c/a\u003e\u003c/p\u003e\n\u003ca name=\"user-content-modules\"\u003e\u003c/a\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eMODULES\u003c/h2\u003e\u003ca id=\"user-content-modules\" class=\"anchor\" aria-label=\"Permalink: MODULES\" href=\"#modules\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eProDy has a modular structure with modules inside various subpackages.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThe main ones are:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#id1\"\u003e\u003cspan id=\"user-content-id2\"\u003e:mod:`~prody.atomic`\u003c/span\u003e\u003c/a\u003e handles all \u003ca href=\"#id3\"\u003e\u003cspan id=\"user-content-id4\"\u003e:class:`~prody.atomic.Atomic`\u003c/span\u003e\u003c/a\u003e objects including \u003ca href=\"#id5\"\u003e\u003cspan id=\"user-content-id6\"\u003e:class:`~prody.atomic.AtomGroup`\u003c/span\u003e\u003c/a\u003e and \u003ca href=\"#id7\"\u003e\u003cspan id=\"user-content-id8\"\u003e:class:`.Selection`\u003c/span\u003e\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#id9\"\u003e\u003cspan id=\"user-content-id10\"\u003e:mod:`~prody.database`\u003c/span\u003e\u003c/a\u003e interfaces with databases such as CATH, DALI, UniProt and Pfam\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#id11\"\u003e\u003cspan id=\"user-content-id12\"\u003e:mod:`~prody.dynamics`\u003c/span\u003e\u003c/a\u003e provides all the modules for normal mode analysis with various elastic network models,\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eas well as PCA, SignDy (\u003ca href=\"#id13\"\u003e\u003cspan id=\"user-content-id14\"\u003e:mod:`~prody.dynamics.signature`\u003c/span\u003e\u003c/a\u003e), hybrid methods such as \u003ca href=\"#id15\"\u003e\u003cspan id=\"user-content-id16\"\u003e:mod:`~prody.dynamics.clustenm`\u003c/span\u003e\u003c/a\u003e,\nallosteric signal propagation methods \u003ca href=\"#id17\"\u003e\u003cspan id=\"user-content-id18\"\u003e:mod:`~prody.dynamics.perturb`\u003c/span\u003e\u003c/a\u003e (PRS) and \u003ca href=\"#id19\"\u003e\u003cspan id=\"user-content-id20\"\u003e:func:`~prody.dynamics.analysis.calcHitTime`\u003c/span\u003e\u003c/a\u003e (Markovian hitting time),\nand various analysis and plotting functions.\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#id21\"\u003e\u003cspan id=\"user-content-id22\"\u003e:mod:`~prody.ensemble`\u003c/span\u003e\u003c/a\u003e enables construction of heterogeneous structural ensembles for exploring dynamics from experiments and simulations\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#id23\"\u003e\u003cspan id=\"user-content-id24\"\u003e:mod:`~prody.proteins`\u003c/span\u003e\u003c/a\u003e provides various modules for parsing different kinds of protein structure files including PDB, mmCIF, MMTF and maps,\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eas well as tools to align and compare structures, and analysis of \u003ca href=\"#id25\"\u003e\u003cspan id=\"user-content-id26\"\u003e:mod:`~prody.proteins.interactions`\u003c/span\u003e\u003c/a\u003e within and between proteins (InSty) and\nfind \u003ca href=\"#id27\"\u003e\u003cspan id=\"user-content-id28\"\u003e:mod:`~prody.proteins.waterbridges`\u003c/span\u003e\u003c/a\u003e (WatFinder).\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#id29\"\u003e\u003cspan id=\"user-content-id30\"\u003e:mod:`~prody.sequence`\u003c/span\u003e\u003c/a\u003e has all the sequence alignment and evolutionary analysis tools of Evol\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eSmaller ones include:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#id31\"\u003e\u003cspan id=\"user-content-id32\"\u003e:mod:`~prody.chromatin`\u003c/span\u003e\u003c/a\u003e specific to chromatin dynamics (ChromDy) including \u003ca href=\"#id33\"\u003e\u003cspan id=\"user-content-id34\"\u003e:mod:`~prody.chromatin.hic`\u003c/span\u003e\u003c/a\u003e and \u003ca href=\"#id35\"\u003e\u003cspan id=\"user-content-id36\"\u003e:mod:`~prody.chromatin.cluster`\u003c/span\u003e\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#id37\"\u003e\u003cspan id=\"user-content-id38\"\u003e:mod:`~prody.compounds`\u003c/span\u003e\u003c/a\u003e for parsing small molecule compounds/ligands from the PDB and related databases\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#id39\"\u003e\u003cspan id=\"user-content-id40\"\u003e:mod:`~prody.domain_decomposition`\u003c/span\u003e\u003c/a\u003e for Spectrus dynamical domain decomposition\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#id41\"\u003e\u003cspan id=\"user-content-id42\"\u003e:mod:`~prody.trajectory`\u003c/span\u003e\u003c/a\u003e for trajectories in DCD format\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#id43\"\u003e\u003cspan id=\"user-content-id44\"\u003e:mod:`~prody.utilities`\u003c/span\u003e\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003ca name=\"user-content-getting-prody\"\u003e\u003c/a\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eGETTING PRODY\u003c/h2\u003e\u003ca id=\"user-content-getting-prody\" class=\"anchor\" aria-label=\"Permalink: GETTING PRODY\" href=\"#getting-prody\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can run ProDy on all major platforms. For download and installation\ninstructions see:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"http://www.bahargroup.org/prody/downloads/\" rel=\"nofollow\"\u003ehttp://www.bahargroup.org/prody/downloads/\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003ca name=\"user-content-documentation\"\u003e\u003c/a\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDOCUMENTATION\u003c/h2\u003e\u003ca id=\"user-content-documentation\" class=\"anchor\" aria-label=\"Permalink: DOCUMENTATION\" href=\"#documentation\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eHomepage: \u003ca href=\"http://www.bahargroup.org/prody/\" rel=\"nofollow\"\u003ehttp://www.bahargroup.org/prody/\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003eTutorials: \u003ca href=\"http://www.bahargroup.org/prody/tutorials\" rel=\"nofollow\"\u003ehttp://www.bahargroup.org/prody/tutorials\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003eReference: \u003ca href=\"http://www.bahargroup.org/prody/manual\" rel=\"nofollow\"\u003ehttp://www.bahargroup.org/prody/manual\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003eApplications: \u003ca href=\"http://www.bahargroup.org/prody/manual/apps\" rel=\"nofollow\"\u003ehttp://www.bahargroup.org/prody/manual/apps\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003eNMWiz GUI: \u003ca href=\"http://www.bahargroup.org/prody/nmwiz\" rel=\"nofollow\"\u003ehttp://www.bahargroup.org/prody/nmwiz\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003eChanges: \u003ca href=\"http://www.bahargroup.org/prody/manual/release\" rel=\"nofollow\"\u003ehttp://www.bahargroup.org/prody/manual/release\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eSee also \u003ca href=\"https://github.com/prody/ProDy-website\"\u003ehttps://github.com/prody/ProDy-website\u003c/a\u003e for latest versions.\u003c/p\u003e\n\u003ca name=\"user-content-source-code\"\u003e\u003c/a\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eSOURCE CODE\u003c/h2\u003e\u003ca id=\"user-content-source-code\" class=\"anchor\" aria-label=\"Permalink: SOURCE CODE\" href=\"#source-code\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eSource code: \u003ca href=\"https://github.com/prody/ProDy\"\u003ehttps://github.com/prody/ProDy\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003eIssue tracker: \u003ca href=\"https://github.com/prody/ProDy/issues\"\u003ehttps://github.com/prody/ProDy/issues\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003ca name=\"user-content-license\"\u003e\u003c/a\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eLICENSE\u003c/h2\u003e\u003ca id=\"user-content-license\" class=\"anchor\" aria-label=\"Permalink: LICENSE\" href=\"#license\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eProDy is available under MIT License. See LICENSE.txt for more details.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eBiopython (\u003ca href=\"http://biopython.org/\" rel=\"nofollow\"\u003ehttp://biopython.org/\u003c/a\u003e) KDTree and TreeConstruction modules are distributed\nwith ProDy. Biopython is developed by The Biopython Consortium and is available\nunder the Biopython license (\u003ca href=\"http://www.biopython.org/DIST/LICENSE\" rel=\"nofollow\"\u003ehttp://www.biopython.org/DIST/LICENSE\u003c/a\u003e).\u003c/p\u003e\n\u003cp dir=\"auto\"\u003ePyparsing (\u003ca href=\"https://github.com/pyparsing/pyparsing\"\u003ehttps://github.com/pyparsing/pyparsing\u003c/a\u003e) module is distributed with ProDy.\nPyparsing is developed by Paul T. McGuire and is available under the MIT\nlicense (\u003ca href=\"http://www.opensource.org/licenses/mit-license.php\" rel=\"nofollow\"\u003ehttp://www.opensource.org/licenses/mit-license.php\u003c/a\u003e).\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eCEalign module (\u003ca href=\"https://pymolwiki.org/index.php/Cealign_plugin\" rel=\"nofollow\"\u003ehttps://pymolwiki.org/index.php/Cealign_plugin\u003c/a\u003e) is distributed\nwith ProDy. The original CE method was developed by Ilya Shindyalov and Philip\nBourne. The Python version which is used by ProDy is developed by Jason Vertrees\nand available under the New BSD license.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eHbp module: The calculation of hydrophobic interactions, solvent accessible surface\narea (SASA) and volume for each residue is using geometric methods based on the\ninformation of the atoms in the molecule. The methods have been programmed in C++\nand can be compiled as a python module “hpb.so” which is then used by ProDy.\nFiles for compilation are stored at prody/proteins/hpbmodule folder and\nrequired C++ and Fortran compiler. After compilation hpb.so file can be\nstored in prody/proteins folder in ProDy or in the local directory which\nis used to perform calulations. The precompiled versions for Python 2.7,\n3.8, 3.9, and 3.10 are availabe in prody/proteins/hpbmodule. The user can\nchoose the correct version of hpb.so and copy to the prody/proteins or\nlocal directory.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eC++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao,\nMichelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in\nprody/proteins/hpbmodule folder). Details of the method can be found\nin the Supplementary Material of InSty manuscript (\u003ca href=\"https://doi.org/10.1016/j.jmb.2025.169009\" rel=\"nofollow\"\u003ehttps://doi.org/10.1016/j.jmb.2025.169009\u003c/a\u003e).\u003c/p\u003e\n\n\u003c/article\u003e","loaded":true,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":[{"level":2,"text":"SYNOPSIS","anchor":"synopsis","htmlText":"SYNOPSIS"},{"level":3,"text":"INSTALLING PRODY","anchor":"installing-prody","htmlText":"INSTALLING PRODY"},{"level":2,"text":"MODULES","anchor":"modules","htmlText":"MODULES"},{"level":2,"text":"GETTING PRODY","anchor":"getting-prody","htmlText":"GETTING PRODY"},{"level":2,"text":"DOCUMENTATION","anchor":"documentation","htmlText":"DOCUMENTATION"},{"level":2,"text":"SOURCE CODE","anchor":"source-code","htmlText":"SOURCE 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href="https://github.com/prody/ProDy/actions/workflows/main.yml"><img alt="https://img.shields.io/github/actions/workflow/status/prody/prody/main.yml" src="https://camo.githubusercontent.com/8beca19ca068805e24366b845105571742f50c69e656482dc084e69a67d20356/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f616374696f6e732f776f726b666c6f772f7374617475732f70726f64792f70726f64792f6d61696e2e796d6c" data-canonical-src="https://img.shields.io/github/actions/workflow/status/prody/prody/main.yml" style="max-width: 100%;"></a> <a href="https://pypi.org/project/ProDy/" rel="nofollow"><img src="https://camo.githubusercontent.com/074e97c9c1118d09bfea3499495ba257f1b6e89642a089913144873bcbc521c0/68747470733a2f2f696d672e736869656c64732e696f2f707970692f762f50726f44792e737667" data-canonical-src="https://img.shields.io/pypi/v/ProDy.svg" style="max-width: 100%;"> </a> <a href="https://github.com/prody/ProDy/commits/master"><img src="https://camo.githubusercontent.com/96014a2a41bb9f2e0b9b72d0f5e1783263cc34a24f8a032aa73694f527348896/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f636f6d6d69742d61637469766974792f6d2f70726f64792f50726f44792e737667" data-canonical-src="https://img.shields.io/github/commit-activity/m/prody/ProDy.svg" style="max-width: 100%;"> </a> <a href="http://www.bahargroup.org/prody/downloads/" rel="nofollow"><img src="https://camo.githubusercontent.com/b7d72ef39c7900ddcd2ccc429018c7cdfe1bff0193f7afcb2fab8f27f82cd502/68747470733a2f2f696d672e736869656c64732e696f2f707970692f646d2f50726f44792e737667" data-canonical-src="https://img.shields.io/pypi/dm/ProDy.svg" style="max-width: 100%;"> </a> <a name="user-content-synopsis"></a> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">SYNOPSIS</h2><a id="user-content-synopsis" class="anchor" aria-label="Permalink: SYNOPSIS" href="#synopsis"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well as application development. ProDy also comes with several analysis applications and a graphical user interface for visual analysis.</p> <p dir="auto">Further details are described in the ProDy papers:</p> <blockquote> <div dir="auto"> <div dir="auto">Bakan A, Meireles LM, Bahar I.</div> <div dir="auto"><em>ProDy</em>: Protein Dynamics Inferred from Theory and Experiments.</div> <div dir="auto"><em>Bioinformatics</em> <strong>2011</strong> 27(11):1575-1577.</div> </div> <div dir="auto"> <div dir="auto">Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I.</div> <div dir="auto"><em>Evol</em> and <em>ProDy</em> for Bridging Protein Sequence Evolution and Structural Dynamics.</div> <div dir="auto"><em>Bioinformatics</em> <strong>2014</strong> 30(18):2681-2683.</div> </div> <div dir="auto"> <div dir="auto">Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I.</div> <div dir="auto"><em>ProDy</em> 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python.</div> <div dir="auto"><em>Bioinformatics</em> <strong>2021</strong> 37(20):3657-3659.</div> </div> </blockquote> <a name="user-content-installing-prody"></a> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">INSTALLING PRODY</h3><a id="user-content-installing-prody" class="anchor" aria-label="Permalink: INSTALLING PRODY" href="#installing-prody"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">ProDy is under active development, so we recommend installing it from source from GitHub to ensure everything works properly.</p> <p dir="auto">We recommend downloading and installing the Anaconda package manager to handle dependencies in controlled environments.</p> <p dir="auto">Then you should download the ProDy code either as a zipped folder to extract or using git as directed at the big green button says code. For example, if you have git installed then you can do the following.</p> <p dir="auto">git clone <a href="https://github.com/prody/ProDy.git">https://github.com/prody/ProDy.git</a></p> <p dir="auto">Then change directory into the ProDy directory tree and install it by running the following commands.</p> <p dir="auto">cd ProDy</p> <p dir="auto">python setup.py build_ext --inplace --force</p> <p dir="auto">pip install -Ue .</p> <p dir="auto">More instructions can be found at <a href="http://bahargroup.org/prody/downloads/" rel="nofollow">http://bahargroup.org/prody/downloads/</a> and <a href="http://bahargroup.org/prody/manual/devel/develop.html" rel="nofollow">http://bahargroup.org/prody/manual/devel/develop.html</a></p> <a name="user-content-modules"></a> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">MODULES</h2><a id="user-content-modules" class="anchor" aria-label="Permalink: MODULES" href="#modules"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">ProDy has a modular structure with modules inside various subpackages.</p> <p dir="auto">The main ones are:</p> <ul dir="auto"> <li><a href="#id1"><span id="user-content-id2">:mod:`~prody.atomic`</span></a> handles all <a href="#id3"><span id="user-content-id4">:class:`~prody.atomic.Atomic`</span></a> objects including <a href="#id5"><span id="user-content-id6">:class:`~prody.atomic.AtomGroup`</span></a> and <a href="#id7"><span id="user-content-id8">:class:`.Selection`</span></a></li> <li><a href="#id9"><span id="user-content-id10">:mod:`~prody.database`</span></a> interfaces with databases such as CATH, DALI, UniProt and Pfam</li> <li><a href="#id11"><span id="user-content-id12">:mod:`~prody.dynamics`</span></a> provides all the modules for normal mode analysis with various elastic network models,</li> </ul> <p dir="auto">as well as PCA, SignDy (<a href="#id13"><span id="user-content-id14">:mod:`~prody.dynamics.signature`</span></a>), hybrid methods such as <a href="#id15"><span id="user-content-id16">:mod:`~prody.dynamics.clustenm`</span></a>, allosteric signal propagation methods <a href="#id17"><span id="user-content-id18">:mod:`~prody.dynamics.perturb`</span></a> (PRS) and <a href="#id19"><span id="user-content-id20">:func:`~prody.dynamics.analysis.calcHitTime`</span></a> (Markovian hitting time), and various analysis and plotting functions.</p> <ul dir="auto"> <li><a href="#id21"><span id="user-content-id22">:mod:`~prody.ensemble`</span></a> enables construction of heterogeneous structural ensembles for exploring dynamics from experiments and simulations</li> <li><a href="#id23"><span id="user-content-id24">:mod:`~prody.proteins`</span></a> provides various modules for parsing different kinds of protein structure files including PDB, mmCIF, MMTF and maps,</li> </ul> <p dir="auto">as well as tools to align and compare structures, and analysis of <a href="#id25"><span id="user-content-id26">:mod:`~prody.proteins.interactions`</span></a> within and between proteins (InSty) and find <a href="#id27"><span id="user-content-id28">:mod:`~prody.proteins.waterbridges`</span></a> (WatFinder).</p> <ul dir="auto"> <li><a href="#id29"><span id="user-content-id30">:mod:`~prody.sequence`</span></a> has all the sequence alignment and evolutionary analysis tools of Evol</li> </ul> <p dir="auto">Smaller ones include:</p> <ul dir="auto"> <li><a href="#id31"><span id="user-content-id32">:mod:`~prody.chromatin`</span></a> specific to chromatin dynamics (ChromDy) including <a href="#id33"><span id="user-content-id34">:mod:`~prody.chromatin.hic`</span></a> and <a href="#id35"><span id="user-content-id36">:mod:`~prody.chromatin.cluster`</span></a></li> <li><a href="#id37"><span id="user-content-id38">:mod:`~prody.compounds`</span></a> for parsing small molecule compounds/ligands from the PDB and related databases</li> <li><a href="#id39"><span id="user-content-id40">:mod:`~prody.domain_decomposition`</span></a> for Spectrus dynamical domain decomposition</li> <li><a href="#id41"><span id="user-content-id42">:mod:`~prody.trajectory`</span></a> for trajectories in DCD format</li> <li><a href="#id43"><span id="user-content-id44">:mod:`~prody.utilities`</span></a></li> </ul> <a name="user-content-getting-prody"></a> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">GETTING PRODY</h2><a id="user-content-getting-prody" class="anchor" aria-label="Permalink: GETTING PRODY" href="#getting-prody"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">You can run ProDy on all major platforms. For download and installation instructions see:</p> <ul dir="auto"> <li><a href="http://www.bahargroup.org/prody/downloads/" rel="nofollow">http://www.bahargroup.org/prody/downloads/</a></li> </ul> <a name="user-content-documentation"></a> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">DOCUMENTATION</h2><a id="user-content-documentation" class="anchor" aria-label="Permalink: DOCUMENTATION" href="#documentation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li>Homepage: <a href="http://www.bahargroup.org/prody/" rel="nofollow">http://www.bahargroup.org/prody/</a></li> <li>Tutorials: <a href="http://www.bahargroup.org/prody/tutorials" rel="nofollow">http://www.bahargroup.org/prody/tutorials</a></li> <li>Reference: <a href="http://www.bahargroup.org/prody/manual" rel="nofollow">http://www.bahargroup.org/prody/manual</a></li> <li>Applications: <a href="http://www.bahargroup.org/prody/manual/apps" rel="nofollow">http://www.bahargroup.org/prody/manual/apps</a></li> <li>NMWiz GUI: <a href="http://www.bahargroup.org/prody/nmwiz" rel="nofollow">http://www.bahargroup.org/prody/nmwiz</a></li> <li>Changes: <a href="http://www.bahargroup.org/prody/manual/release" rel="nofollow">http://www.bahargroup.org/prody/manual/release</a></li> </ul> <p dir="auto">See also <a href="https://github.com/prody/ProDy-website">https://github.com/prody/ProDy-website</a> for latest versions.</p> <a name="user-content-source-code"></a> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">SOURCE CODE</h2><a id="user-content-source-code" class="anchor" aria-label="Permalink: SOURCE CODE" href="#source-code"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li>Source code: <a href="https://github.com/prody/ProDy">https://github.com/prody/ProDy</a></li> <li>Issue tracker: <a href="https://github.com/prody/ProDy/issues">https://github.com/prody/ProDy/issues</a></li> </ul> <a name="user-content-license"></a> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">LICENSE</h2><a id="user-content-license" class="anchor" aria-label="Permalink: LICENSE" href="#license"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">ProDy is available under MIT License. See LICENSE.txt for more details.</p> <p dir="auto">Biopython (<a href="http://biopython.org/" rel="nofollow">http://biopython.org/</a>) KDTree and TreeConstruction modules are distributed with ProDy. Biopython is developed by The Biopython Consortium and is available under the Biopython license (<a href="http://www.biopython.org/DIST/LICENSE" rel="nofollow">http://www.biopython.org/DIST/LICENSE</a>).</p> <p dir="auto">Pyparsing (<a href="https://github.com/pyparsing/pyparsing">https://github.com/pyparsing/pyparsing</a>) module is distributed with ProDy. Pyparsing is developed by Paul T. McGuire and is available under the MIT license (<a href="http://www.opensource.org/licenses/mit-license.php" rel="nofollow">http://www.opensource.org/licenses/mit-license.php</a>).</p> <p dir="auto">CEalign module (<a href="https://pymolwiki.org/index.php/Cealign_plugin" rel="nofollow">https://pymolwiki.org/index.php/Cealign_plugin</a>) is distributed with ProDy. The original CE method was developed by Ilya Shindyalov and Philip Bourne. The Python version which is used by ProDy is developed by Jason Vertrees and available under the New BSD license.</p> <p dir="auto">Hbp module: The calculation of hydrophobic interactions, solvent accessible surface area (SASA) and volume for each residue is using geometric methods based on the information of the atoms in the molecule. The methods have been programmed in C++ and can be compiled as a python module “hpb.so” which is then used by ProDy. Files for compilation are stored at prody/proteins/hpbmodule folder and required C++ and Fortran compiler. After compilation hpb.so file can be stored in prody/proteins folder in ProDy or in the local directory which is used to perform calulations. The precompiled versions for Python 2.7, 3.8, 3.9, and 3.10 are availabe in prody/proteins/hpbmodule. The user can choose the correct version of hpb.so and copy to the prody/proteins or local directory.</p> <p dir="auto">C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in prody/proteins/hpbmodule folder). Details of the method can be found in the Supplementary Material of InSty manuscript (<a href="https://doi.org/10.1016/j.jmb.2025.169009" rel="nofollow">https://doi.org/10.1016/j.jmb.2025.169009</a>).</p> </article></div></div></div></div></div> <!-- --> <!-- --> <script type="application/json" id="__PRIMER_DATA_:R0:__">{"resolvedServerColorMode":"day"}</script></div> </react-partial> <input type="hidden" data-csrf="true" value="1gJC2D4an3WgjKYnfwNg2FxZzn9VhzX3sIvdtwv96T/AyVJFtT92FSW9WqeLyWVPUh5kcW6TJAPD7BD7D2P7zw==" /> </div> <div data-view-component="true" class="Layout-sidebar"> <div class="BorderGrid about-margin" data-pjax> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <div class="hide-sm hide-md"> <h2 class="mb-3 h4">About</h2> <p class="f4 my-3"> A Python Package for Protein Dynamics Analysis </p> <div class="my-3 d-flex flex-items-center"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link flex-shrink-0 mr-2"> <path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path> </svg> <span class="flex-auto min-width-0 css-truncate css-truncate-target width-fit"> <a title="http://prody.csb.pitt.edu" role="link" target="_blank" rel="noopener noreferrer nofollow" class="text-bold" href="http://prody.csb.pitt.edu">prody.csb.pitt.edu</a> </span> </div> <h3 class="sr-only">Topics</h3> <div class="my-3"> <div class="f6"> <a href="/topics/python" title="Topic: python" data-view-component="true" class="topic-tag topic-tag-link"> python </a> <a href="/topics/dynamics" title="Topic: dynamics" data-view-component="true" class="topic-tag topic-tag-link"> dynamics </a> <a href="/topics/protein" title="Topic: protein" data-view-component="true" class="topic-tag topic-tag-link"> protein </a> </div> </div> <h3 class="sr-only">Resources</h3> <div class="mt-2"> <a class="Link--muted" data-analytics-event="{"category":"Repository Overview","action":"click","label":"location:sidebar;file:readme"}" href="#readme-ov-file"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-book mr-2"> <path d="M0 1.75A.75.75 0 0 1 .75 1h4.253c1.227 0 2.317.59 3 1.501A3.743 3.743 0 0 1 11.006 1h4.245a.75.75 0 0 1 .75.75v10.5a.75.75 0 0 1-.75.75h-4.507a2.25 2.25 0 0 0-1.591.659l-.622.621a.75.75 0 0 1-1.06 0l-.622-.621A2.25 2.25 0 0 0 5.258 13H.75a.75.75 0 0 1-.75-.75Zm7.251 10.324.004-5.073-.002-2.253A2.25 2.25 0 0 0 5.003 2.5H1.5v9h3.757a3.75 3.75 0 0 1 1.994.574ZM8.755 4.75l-.004 7.322a3.752 3.752 0 0 1 1.992-.572H14.5v-9h-3.495a2.25 2.25 0 0 0-2.25 2.25Z"></path> </svg> Readme </a> </div> <h3 class="sr-only">License</h3> <div class="mt-2"> <a href="#License-1-ov-file" class="Link--muted" data-analytics-event="{"category":"Repository Overview","action":"click","label":"location:sidebar;file:license"}" > <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-law mr-2"> <path d="M8.75.75V2h.985c.304 0 .603.08.867.231l1.29.736c.038.022.08.033.124.033h2.234a.75.75 0 0 1 0 1.5h-.427l2.111 4.692a.75.75 0 0 1-.154.838l-.53-.53.529.531-.001.002-.002.002-.006.006-.006.005-.01.01-.045.04c-.21.176-.441.327-.686.45C14.556 10.78 13.88 11 13 11a4.498 4.498 0 0 1-2.023-.454 3.544 3.544 0 0 1-.686-.45l-.045-.04-.016-.015-.006-.006-.004-.004v-.001a.75.75 0 0 1-.154-.838L12.178 4.5h-.162c-.305 0-.604-.079-.868-.231l-1.29-.736a.245.245 0 0 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16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code-of-conduct mr-2"> <path d="M8.048 2.241c.964-.709 2.079-1.238 3.325-1.241a4.616 4.616 0 0 1 3.282 1.355c.41.408.757.86.996 1.428.238.568.348 1.206.347 1.968 0 2.193-1.505 4.254-3.081 5.862-1.496 1.526-3.213 2.796-4.249 3.563l-.22.163a.749.749 0 0 1-.895 0l-.221-.163c-1.036-.767-2.753-2.037-4.249-3.563C1.51 10.008.007 7.952.002 5.762a4.614 4.614 0 0 1 1.353-3.407C3.123.585 6.223.537 8.048 2.24Zm-1.153.983c-1.25-1.033-3.321-.967-4.48.191a3.115 3.115 0 0 0-.913 2.335c0 1.556 1.109 3.24 2.652 4.813C5.463 11.898 6.96 13.032 8 13.805c.353-.262.758-.565 1.191-.905l-1.326-1.223a.75.75 0 0 1 1.018-1.102l1.48 1.366c.328-.281.659-.577.984-.887L9.99 9.802a.75.75 0 1 1 1.019-1.103l1.384 1.28c.295-.329.566-.661.81-.995L12.92 8.7l-1.167-1.168c-.674-.671-1.78-.664-2.474.03-.268.269-.538.537-.802.797-.893.882-2.319.843-3.185-.032-.346-.35-.693-.697-1.043-1.047a.75.75 0 0 1-.04-1.016c.162-.191.336-.401.52-.623.62-.748 1.356-1.637 2.166-2.417Zm7.112 4.442c.313-.65.491-1.293.491-1.916v-.001c0-.614-.088-1.045-.23-1.385-.143-.339-.357-.633-.673-.949a3.111 3.111 0 0 0-2.218-.915c-1.092.003-2.165.627-3.226 1.602-.823.755-1.554 1.637-2.228 2.45l-.127.154.562.566a.755.755 0 0 0 1.066.02l.794-.79c1.258-1.258 3.312-1.31 4.594-.032.396.394.792.791 1.173 1.173Z"></path> </svg> Code of conduct </a> </div> <include-fragment src="/prody/ProDy/hovercards/citation/sidebar_partial?tree_name=main"> </include-fragment> <div class="mt-2"> <a href="/prody/ProDy/activity" data-view-component="true" class="Link Link--muted"><svg text="gray" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-pulse mr-2"> <path d="M6 2c.306 0 .582.187.696.471L10 10.731l1.304-3.26A.751.751 0 0 1 12 7h3.25a.75.75 0 0 1 0 1.5h-2.742l-1.812 4.528a.751.751 0 0 1-1.392 0L6 4.77 4.696 8.03A.75.75 0 0 1 4 8.5H.75a.75.75 0 0 1 0-1.5h2.742l1.812-4.529A.751.751 0 0 1 6 2Z"></path> </svg> <span class="color-fg-muted">Activity</span></a> </div> <div class="mt-2"> <a href="/prody/ProDy/custom-properties" data-view-component="true" class="Link Link--muted"><svg text="gray" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-note mr-2"> <path d="M0 3.75C0 2.784.784 2 1.75 2h12.5c.966 0 1.75.784 1.75 1.75v8.5A1.75 1.75 0 0 1 14.25 14H1.75A1.75 1.75 0 0 1 0 12.25Zm1.75-.25a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25v-8.5a.25.25 0 0 0-.25-.25ZM3.5 6.25a.75.75 0 0 1 .75-.75h7a.75.75 0 0 1 0 1.5h-7a.75.75 0 0 1-.75-.75Zm.75 2.25h4a.75.75 0 0 1 0 1.5h-4a.75.75 0 0 1 0-1.5Z"></path> </svg> <span class="color-fg-muted">Custom properties</span></a> </div> <h3 class="sr-only">Stars</h3> <div class="mt-2"> <a href="/prody/ProDy/stargazers" data-view-component="true" class="Link Link--muted"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-star mr-2"> <path d="M8 .25a.75.75 0 0 1 .673.418l1.882 3.815 4.21.612a.75.75 0 0 1 .416 1.279l-3.046 2.97.719 4.192a.751.751 0 0 1-1.088.791L8 12.347l-3.766 1.98a.75.75 0 0 1-1.088-.79l.72-4.194L.818 6.374a.75.75 0 0 1 .416-1.28l4.21-.611L7.327.668A.75.75 0 0 1 8 .25Zm0 2.445L6.615 5.5a.75.75 0 0 1-.564.41l-3.097.45 2.24 2.184a.75.75 0 0 1 .216.664l-.528 3.084 2.769-1.456a.75.75 0 0 1 .698 0l2.77 1.456-.53-3.084a.75.75 0 0 1 .216-.664l2.24-2.183-3.096-.45a.75.75 0 0 1-.564-.41L8 2.694Z"></path> </svg> <strong>462</strong> stars</a> </div> <h3 class="sr-only">Watchers</h3> <div class="mt-2"> <a href="/prody/ProDy/watchers" data-view-component="true" class="Link Link--muted"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-eye mr-2"> <path d="M8 2c1.981 0 3.671.992 4.933 2.078 1.27 1.091 2.187 2.345 2.637 3.023a1.62 1.62 0 0 1 0 1.798c-.45.678-1.367 1.932-2.637 3.023C11.67 13.008 9.981 14 8 14c-1.981 0-3.671-.992-4.933-2.078C1.797 10.83.88 9.576.43 8.898a1.62 1.62 0 0 1 0-1.798c.45-.677 1.367-1.931 2.637-3.022C4.33 2.992 6.019 2 8 2ZM1.679 7.932a.12.12 0 0 0 0 .136c.411.622 1.241 1.75 2.366 2.717C5.176 11.758 6.527 12.5 8 12.5c1.473 0 2.825-.742 3.955-1.715 1.124-.967 1.954-2.096 2.366-2.717a.12.12 0 0 0 0-.136c-.412-.621-1.242-1.75-2.366-2.717C10.824 4.242 9.473 3.5 8 3.5c-1.473 0-2.825.742-3.955 1.715-1.124.967-1.954 2.096-2.366 2.717ZM8 10a2 2 0 1 1-.001-3.999A2 2 0 0 1 8 10Z"></path> </svg> <strong>21</strong> watching</a> </div> <h3 class="sr-only">Forks</h3> <div class="mt-2"> <a href="/prody/ProDy/forks" data-view-component="true" class="Link Link--muted"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo-forked mr-2"> <path d="M5 5.372v.878c0 .414.336.75.75.75h4.5a.75.75 0 0 0 .75-.75v-.878a2.25 2.25 0 1 1 1.5 0v.878a2.25 2.25 0 0 1-2.25 2.25h-1.5v2.128a2.251 2.251 0 1 1-1.5 0V8.5h-1.5A2.25 2.25 0 0 1 3.5 6.25v-.878a2.25 2.25 0 1 1 1.5 0ZM5 3.25a.75.75 0 1 0-1.5 0 .75.75 0 0 0 1.5 0Zm6.75.75a.75.75 0 1 0 0-1.5.75.75 0 0 0 0 1.5Zm-3 8.75a.75.75 0 1 0-1.5 0 .75.75 0 0 0 1.5 0Z"></path> </svg> <strong>159</strong> forks</a> </div> <div class="mt-2"> <a class="Link--muted" href="/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2Fprody%2FProDy&report=prody+%28user%29"> Report repository </a> </div> </div> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame"> <a href="/prody/ProDy/releases" data-view-component="true" class="Link--primary no-underline Link">Releases <span title="13" data-view-component="true" class="Counter">13</span></a></h2> <a class="Link--primary d-flex no-underline" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" href="/prody/ProDy/releases/tag/v2.4.1"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-tag flex-shrink-0 mt-1 color-fg-success"> <path d="M1 7.775V2.75C1 1.784 1.784 1 2.75 1h5.025c.464 0 .91.184 1.238.513l6.25 6.25a1.75 1.75 0 0 1 0 2.474l-5.026 5.026a1.75 1.75 0 0 1-2.474 0l-6.25-6.25A1.752 1.752 0 0 1 1 7.775Zm1.5 0c0 .066.026.13.073.177l6.25 6.25a.25.25 0 0 0 .354 0l5.025-5.025a.25.25 0 0 0 0-.354l-6.25-6.25a.25.25 0 0 0-.177-.073H2.75a.25.25 0 0 0-.25.25ZM6 5a1 1 0 1 1 0 2 1 1 0 0 1 0-2Z"></path> </svg> <div class="ml-2 min-width-0"> <div class="d-flex"> <span class="css-truncate css-truncate-target text-bold mr-2" style="max-width: none;">v2.4.1</span> <span title="Label: Latest" data-view-component="true" class="Label Label--success flex-shrink-0"> Latest </span> </div> <div class="text-small color-fg-muted"><relative-time datetime="2023-08-13T08:59:42Z" class="no-wrap">Aug 13, 2023</relative-time></div> </div> </a> <div data-view-component="true" class="mt-3"> <a text="small" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" href="/prody/ProDy/releases" data-view-component="true" class="Link">+ 12 releases</a></div> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3"> <a href="/orgs/prody/packages?repo_name=ProDy" data-view-component="true" class="Link--primary no-underline Link d-flex flex-items-center">Packages <span title="0" hidden="hidden" data-view-component="true" class="Counter ml-1">0</span></a></h2> <div class="text-small color-fg-muted" > No packages published <br> </div> </div> </div> <div class="BorderGrid-row" > <div class="BorderGrid-cell"> <h2 class="h4 mb-3"> <a href="/prody/ProDy/network/dependents" data-view-component="true" class="Link--primary no-underline Link">Used by <span title="273" data-view-component="true" class="Counter">273</span></a> </h2> <a class="d-flex flex-items-center" href="/prody/ProDy/network/dependents"> <ul class="hx_flex-avatar-stack list-style-none min-width-0"> <li class="hx_flex-avatar-stack-item"> <img class="avatar" src="https://avatars.githubusercontent.com/u/108711021?s=64&v=4" width="32" height="32" alt="@23AIBox" /> </li> <li class="hx_flex-avatar-stack-item"> <img class="avatar avatar-user" src="https://avatars.githubusercontent.com/u/84638149?s=64&v=4" width="32" height="32" alt="@Stepanvar" /> </li> <li class="hx_flex-avatar-stack-item"> <img class="avatar avatar-user" src="https://avatars.githubusercontent.com/u/70264920?s=64&v=4" width="32" height="32" alt="@NilsDunlop" /> </li> <li class="hx_flex-avatar-stack-item"> <img class="avatar avatar-user" src="https://avatars.githubusercontent.com/u/201316341?s=64&v=4" width="32" height="32" alt="@WZY-0814" /> </li> <li class="hx_flex-avatar-stack-item"> <img class="avatar avatar-user" src="https://avatars.githubusercontent.com/u/71889838?s=64&v=4" width="32" height="32" alt="@Kalyani02072003" /> </li> <li class="hx_flex-avatar-stack-item"> <img class="avatar" src="https://avatars.githubusercontent.com/u/35711315?s=64&v=4" width="32" height="32" alt="@brineylab" /> </li> <li class="hx_flex-avatar-stack-item"> <img class="avatar avatar-user" src="https://avatars.githubusercontent.com/u/36792948?s=64&v=4" width="32" height="32" alt="@KoubaPetr" /> </li> <li class="hx_flex-avatar-stack-item"> <img class="avatar avatar-user" src="https://avatars.githubusercontent.com/u/200225360?s=64&v=4" width="32" height="32" alt="@shuiyouyuan" /> </li> </ul> <span class="px-2 text-bold text-small no-wrap"> + 265 </span> </a> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3"> <a href="/prody/ProDy/graphs/contributors" data-view-component="true" class="Link--primary no-underline Link d-flex flex-items-center">Contributors <span title="50" data-view-component="true" class="Counter ml-1">50</span></a></h2> <ul class="list-style-none d-flex flex-wrap mb-n2"> <li class="mb-2 mr-2" > <a href="https://github.com/jamesmkrieger" class="" data-hovercard-type="user" data-hovercard-url="/users/jamesmkrieger/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/13259162?s=64&v=4" alt="@jamesmkrieger" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/lordnapi" class="" data-hovercard-type="user" data-hovercard-url="/users/lordnapi/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/12455039?s=64&v=4" alt="@lordnapi" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/SHZ66" class="" data-hovercard-type="user" data-hovercard-url="/users/SHZ66/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/8532098?s=64&v=4" alt="@SHZ66" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/karolamik13" class="" data-hovercard-type="user" data-hovercard-url="/users/karolamik13/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/17188432?s=64&v=4" alt="@karolamik13" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/cihankayacihan" class="" data-hovercard-type="user" data-hovercard-url="/users/cihankayacihan/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/8656307?s=64&v=4" alt="@cihankayacihan" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/fongchun" class="" data-hovercard-type="user" data-hovercard-url="/users/fongchun/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/10843043?s=64&v=4" alt="@fongchun" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/kaynakb" class="" data-hovercard-type="user" data-hovercard-url="/users/kaynakb/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/38768573?s=64&v=4" alt="@kaynakb" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/fdoljanin" class="" data-hovercard-type="user" data-hovercard-url="/users/fdoljanin/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/73669815?s=64&v=4" alt="@fdoljanin" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/yaz62" class="" data-hovercard-type="user" data-hovercard-url="/users/yaz62/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/15043911?s=64&v=4" alt="@yaz62" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/anindita85" class="" data-hovercard-type="user" data-hovercard-url="/users/anindita85/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/1508922?s=64&v=4" alt="@anindita85" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/dkoes" class="" data-hovercard-type="user" data-hovercard-url="/users/dkoes/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/2342142?s=64&v=4" alt="@dkoes" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/luponzo86" class="" data-hovercard-type="user" data-hovercard-url="/users/luponzo86/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/16854208?s=64&v=4" alt="@luponzo86" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/abakan-zz" class="" data-hovercard-type="user" data-hovercard-url="/users/abakan-zz/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/202265?s=64&v=4" alt="@abakan-zz" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/wem22" class="" data-hovercard-type="user" data-hovercard-url="/users/wem22/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/2672664?s=64&v=4" alt="@wem22" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> </ul> <div data-view-component="true" class="mt-3"> <a text="small" href="/prody/ProDy/graphs/contributors" data-view-component="true" class="Link--inTextBlock Link">+ 36 contributors</a></div> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3">Languages</h2> <div class="mb-2"> <span data-view-component="true" class="Progress"> <span style="background-color:#3572A5 !important;;width: 71.4%;" itemprop="keywords" data-view-component="true" class="Progress-item color-bg-success-emphasis"></span> <span style="background-color:#555555 !important;;width: 13.9%;" itemprop="keywords" data-view-component="true" class="Progress-item color-bg-success-emphasis"></span> <span style="background-color:#4d41b1 !important;;width: 7.4%;" itemprop="keywords" data-view-component="true" class="Progress-item color-bg-success-emphasis"></span> <span style="background-color:#f34b7d !important;;width: 7.1%;" itemprop="keywords" data-view-component="true" class="Progress-item color-bg-success-emphasis"></span> <span style="background-color:#ecdebe !important;;width: 0.2%;" itemprop="keywords" 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