Fixes#1714 => Functionality for setting size of ghost atom#1911
Fixes#1714 => Functionality for setting size of ghost atom#1911peach280 wants to merge 2 commits intoOpenChemistry:masterfrom
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This looks fine from a Before I merge, it would be great to have a test or two in https://github.com/OpenChemistry/avogadrolibs/blob/master/tests/core/elementtest.cpp |
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Oh, before I forget .. I don't remember if it's mentioned in #1714 but some "ghost" atoms are element 0. That probably needs a special case in your code. |
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I am working on this but I just wanted to clarify a small doubt, does element 0 mean neutronium? Like the edge case should be for neutronium? |
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Most chemistry packages have a element 0 "Xx" or "Du" - it's a placeholder. In Avogadro, it's used to indicate a centroid point, for example. |
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I have committed some changes into this including edge case for element 0. Please review. |
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This pull request has been mentioned on Avogadro Discussion. There might be relevant details there: |
Signed-off-by: Vaishnavi Bhandari <vaishnavibhandari.128@gmail.com>
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| } CustomElementTableInitializer; | ||
| void setCustomElementCovalentRadius(unsigned char atomicNumber, double radius) |
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Unused static function Note
| } | ||
| } | ||
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| void setCustomElementVDWRadius(unsigned char atomicNumber, double radius) |
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| switch (error_handler) | ||
| { | ||
| case error_handler_t::strict: | ||
| { | ||
| JSON_THROW(type_error::create(316, concat("invalid UTF-8 byte at index ", std::to_string(i), ": 0x", hex_bytes(byte | 0)), nullptr)); | ||
| } | ||
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| case error_handler_t::ignore: | ||
| case error_handler_t::replace: | ||
| { | ||
| // in case we saw this character the first time, we | ||
| // would like to read it again, because the byte | ||
| // may be OK for itself, but just not OK for the | ||
| // previous sequence | ||
| if (undumped_chars > 0) | ||
| { | ||
| --i; | ||
| } | ||
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| // reset length buffer to the last accepted index; | ||
| // thus removing/ignoring the invalid characters | ||
| bytes = bytes_after_last_accept; | ||
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| if (error_handler == error_handler_t::replace) | ||
| { | ||
| // add a replacement character | ||
| if (ensure_ascii) | ||
| { | ||
| string_buffer[bytes++] = '\\'; | ||
| string_buffer[bytes++] = 'u'; | ||
| string_buffer[bytes++] = 'f'; | ||
| string_buffer[bytes++] = 'f'; | ||
| string_buffer[bytes++] = 'f'; | ||
| string_buffer[bytes++] = 'd'; | ||
| } | ||
| else | ||
| { | ||
| string_buffer[bytes++] = detail::binary_writer<BasicJsonType, char>::to_char_type('\xEF'); | ||
| string_buffer[bytes++] = detail::binary_writer<BasicJsonType, char>::to_char_type('\xBF'); | ||
| string_buffer[bytes++] = detail::binary_writer<BasicJsonType, char>::to_char_type('\xBD'); | ||
| } | ||
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| // write buffer and reset index; there must be 13 bytes | ||
| // left, as this is the maximal number of bytes to be | ||
| // written ("\uxxxx\uxxxx\0") for one code point | ||
| if (string_buffer.size() - bytes < 13) | ||
| { | ||
| o->write_characters(string_buffer.data(), bytes); | ||
| bytes = 0; | ||
| } | ||
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| bytes_after_last_accept = bytes; | ||
| } | ||
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| undumped_chars = 0; | ||
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| // continue processing the string | ||
| state = UTF8_ACCEPT; | ||
| break; | ||
| } | ||
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| default: // LCOV_EXCL_LINE | ||
| JSON_ASSERT(false); // NOLINT(cert-dcl03-c,hicpp-static-assert,misc-static-assert) LCOV_EXCL_LINE | ||
| } |
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| // previous sequence | ||
| if (undumped_chars > 0) | ||
| { | ||
| --i; |
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| inline std::size_t concat_length(const StringType& str, const Args& ... rest); | ||
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| template<typename... Args> | ||
| inline std::size_t concat_length(const char /*c*/, const Args& ... rest) |
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| inline std::size_t concat_length(const StringType& str, const Args& ... rest); | ||
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| template<typename... Args> | ||
| inline std::size_t concat_length(const char /*c*/, const Args& ... rest) |
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Unused static variable Note library
| } | ||
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| template<typename... Args> | ||
| inline std::size_t concat_length(const char* cstr, const Args& ... rest) |
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Unused local variable Note library
| } | ||
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| template<typename... Args> | ||
| inline std::size_t concat_length(const char* cstr, const Args& ... rest) |
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Unused static variable Note library
| } | ||
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| template<typename StringType, typename... Args> | ||
| inline std::size_t concat_length(const StringType& str, const Args& ... rest) |
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Code scanning / CodeQL
Unused local variable Note library
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This pull request has been mentioned on Avogadro Discussion. There might be relevant details there: |
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@ghutchis Is this worth taking another look at? From your comments, it sounds like it was about ready |
4 participants
Modified elements.cpp to allow for individual radii for each custom element.
Added methods to set the radii for custom elements.
Updated the methods that return the radii to use the vectors instead of the single values.