Element symbols #78
Element symbols #78
Conversation
Following the discussion in #17, the function strToValidSymbol() inside the Model class has been adjusted. Valid element symbols are a string of alphabetic characters including underscore with the first letter in uppercase and all subsequent letters in lowercase. Any non-alphabetic characters afterwards are ignored. If the symbol begins with a non-alphabetic character then the function returns an empty string. The function is used during structure file and radius file imports and a error message is displayed, in case of an invalid symbol. Resolves: #17
src/model_filereading.cpp
Outdated
| str[i] = tolower(str[i]); | ||
| } | ||
| // allow underscores inside element symbols for custom symbols | ||
| else if (str[i] == '_') {} |
There was a problem hiding this comment.
Underscores don't show properly in unicode chemical formula because it was not considered as a potential character. We should either remove underscore or adapt unicode chemical formula conversion function.
There was a problem hiding this comment.
I'm removing underscores for now. If there's a need it's simple to add them back in and adapt the conversion function.
src/model_filereading.cpp
Outdated
| atom_amounts[valid_symbol]++; // adds one to counter for this symbol | ||
|
|
||
| // as a safety mechanism, if an element symbol is assigned two atomic numbers, default to 0 | ||
| // so it becomes apparent laster on that something is wrong | ||
| // so it becomes apparent later on that something is wrong |
There was a problem hiding this comment.
I think elem_Z is not really used at the moment so I don't know what this safety mechanism will change. There is a similar safety mechanism in readFilePDB(). Better to keep elem_Z for future uses though.
std::stod() is used in the radius file import to import the radius values. To make the import more robust, the invalid argument exception is now handled.
|
Changes have been made. Underscores have been removed as valid symbols, and the app should not be crashing anymore, at least for .xyz and radius files. I'm not equally familiar with .pdb files, so I haven't made all the same changes to that section. |
Skip blank lines in XYZ structure files that were prompting error 105. Fixed unsignedness comparison warning. Moved a comment.
No description provided.