Difference between revisions of "Parser"
| Line 3: | Line 3: | ||
'''Note:''' This is not designed to include ambiguities in the assignment. This is therefore only for use with Level=0. | '''Note:''' This is not designed to include ambiguities in the assignment. This is therefore only for use with Level=0. | ||
| − | = Reading the SDF file = | + | === Reading the SDF file === |
Libraries for divers languages exist to read SDF files. This paragraph is only relevant if you write your own reader/writer | Libraries for divers languages exist to read SDF files. This paragraph is only relevant if you write your own reader/writer | ||
| − | We recommend having in mind, when reading, that an SDF file will have to be written at some point later. We recommend to write them in the same oder, but | + | We recommend having in mind, when reading, that an SDF file will have to be written at some point later. We recommend to write TAGS them in the same oder, but don't expect all reader to do so, so be ready for the TAGS to appear in any order. |
If not too large, the content of the input should be kept in memory so that it can be written later. Since SDF files may contain divers TAGS (not only the NMREDATA tags) they should all be written in the output SDF file. | If not too large, the content of the input should be kept in memory so that it can be written later. Since SDF files may contain divers TAGS (not only the NMREDATA tags) they should all be written in the output SDF file. | ||
| Line 18: | Line 18: | ||
* Analyses/check the molblock (see [[nmredata object structure|possible object structure of NMReDATA]]). Be | * Analyses/check the molblock (see [[nmredata object structure|possible object structure of NMReDATA]]). Be | ||
| − | = Determine how to read the NMREDATA tags = | + | === Determine how to read the NMREDATA tags === |
Scan the tags and list the index of the ones including NMREDATA_ in their name | Scan the tags and list the index of the ones including NMREDATA_ in their name | ||
| Line 28: | Line 28: | ||
* determine the line separator ("\", except for version 1, in which cas the ASCII 10 is the line separator) | * determine the line separator ("\", except for version 1, in which cas the ASCII 10 is the line separator) | ||
| − | = read the NMREDATA tags = | + | === read the NMREDATA tags === |
| − | + | Many simple tags have no particular format. (NMREDATA_SOLVENT, NMREDATA_VERSION, etc.) | |
| − | * in | + | |
| − | + | But most "complex" tags (NMREDATAT_ASSIGNMENT, NMREDATA_J, NMREDATA_1H, etc.) all have a common general structure: | |
| + | |||
| + | Two type of lines should be distinguished: | ||
| + | * property lines | ||
| + | * item in a list | ||
| + | |||
| + | The "property lines" contain a serie of characters (letters) followed the "=" sign followed by the value of the variable. | ||
| + | |||
| + | The "property lines" contain should be identified as such. Property lines should be before the list, but some may follow the lost (not recommended, but possible). | ||
| + | |||
| + | Note that a property may appear more than once. | ||
| + | Excample: | ||
| + | |||
| + | Author=John | ||
| + | Author=Paul | ||
| + | |||
| + | In this case it should be stored as an array. | ||
| + | |||
| + | We recommend the first store the list as an array of array of characters, only later analyse it. | ||
| + | See [[nmredata object structure|possible object structure of NMReDATA]] for more details. | ||
Revision as of 08:47, 29 January 2019
Possible structure of the object including NMReDATA reflecting the format of NMReDATA tags of SDF files.
Note: This is not designed to include ambiguities in the assignment. This is therefore only for use with Level=0.
Reading the SDF file
Libraries for divers languages exist to read SDF files. This paragraph is only relevant if you write your own reader/writer
We recommend having in mind, when reading, that an SDF file will have to be written at some point later. We recommend to write TAGS them in the same oder, but don't expect all reader to do so, so be ready for the TAGS to appear in any order.
If not too large, the content of the input should be kept in memory so that it can be written later. Since SDF files may contain divers TAGS (not only the NMREDATA tags) they should all be written in the output SDF file.
We recommend to
- Open the SDF file
- Read/store the molblock as chain of characters
- Read/store the TAGS as chain of characters
- Close the file
- Analyses/check the molblock (see possible object structure of NMReDATA). Be
Determine how to read the NMREDATA tags
Scan the tags and list the index of the ones including NMREDATA_ in their name
Read the NMReDATA tag. Keep in mind the end of line problem .
First read and analyse the NMREDATA_VERSION to
- determine what character should be ignored (ASCII 10, except for version 1)
- determine the line separator ("\", except for version 1, in which cas the ASCII 10 is the line separator)
read the NMREDATA tags
Many simple tags have no particular format. (NMREDATA_SOLVENT, NMREDATA_VERSION, etc.)
But most "complex" tags (NMREDATAT_ASSIGNMENT, NMREDATA_J, NMREDATA_1H, etc.) all have a common general structure:
Two type of lines should be distinguished:
- property lines
- item in a list
The "property lines" contain a serie of characters (letters) followed the "=" sign followed by the value of the variable.
The "property lines" contain should be identified as such. Property lines should be before the list, but some may follow the lost (not recommended, but possible).
Note that a property may appear more than once. Excample:
Author=John Author=Paul
In this case it should be stored as an array.
We recommend the first store the list as an array of array of characters, only later analyse it. See possible object structure of NMReDATA for more details.
