Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Standardize end point to return properties #320

Closed
CS76 opened this issue Aug 24, 2023 · 0 comments · Fixed by #322
Closed

Standardize end point to return properties #320

CS76 opened this issue Aug 24, 2023 · 0 comments · Fixed by #322
Assignees
Labels
enhancement New feature or request

Comments

@CS76
Copy link
Member

CS76 commented Aug 24, 2023

For example, I have a SDF file as follows


  CDK     02012321422D

 26 27  0  0  0  0  0  0  0  0999 V2000
   -0.9788   -0.9177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9691   -0.3171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1665   -0.1068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6312   -0.3171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2164    0.4013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6311    0.0887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0578    1.0782    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9506    0.0974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1577   -0.7865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5818   -1.4996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5830    1.7190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7802    0.0974    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1653    0.8988    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8459    0.4842    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2164   -1.0355    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2177    0.6754    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6875    0.0976    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4164   -0.7125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5542   -1.0355    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7802   -1.1324    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7641   -1.7190    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1671   -0.9515    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8159    0.9963    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1803    1.1217    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1803    2.3163    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0143    2.3163    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0 
  3  4  1  0  0  0  0 
  5  6  1  0  0  0  0 
  3  7  1  0  0  0  0 
  5  7  1  0  0  0  0 
  5  8  1  0  0  0  0 
  4  9  1  0  0  0  0 
  8  9  1  0  0  0  0 
  9 10  2  0  0  0  0 
  7 11  1  0  0  0  0 
  1  6  1  0  0  0  0 
  8 12  1  0  0  0  0 
  8 13  1  0  0  0  0 
  4 14  1  0  0  0  0 
  4 15  1  0  0  0  0 
  6 16  1  0  0  0  0 
  2 17  1  0  0  0  0 
  6 18  1  0  0  0  0 
  2 19  1  0  0  0  0 
  2  3  1  0  0  0  0 
  1 20  1  0  0  0  0 
  1 21  1  0  0  0  0 
  3 22  1  0  0  0  0 
  5 23  1  0  0  0  0 
 11 24  1  0  0  0  0 
 11 25  1  0  0  0  0 
 11 26  1  0  0  0  0 
M  END
> <CHEMNAME>
Pseudopelletierin

> <AUTHOR_LITERATURE>
Georg Heß; Peter Haiss; Dorothee Wistuba; Hans-Ullrich Siehl; Stefan Berger; Dieter Sicker; Klaus-Peter Zeller: Vom Granatapfelbaum zum Cyclooctatetraen, in: Chemie in unserer Zeit, vol. 50/2016, pp. 34 - 43 (DOI: <a href="derefer.jsp?url=http://dx.doi.org/10.1002/ciuz.201500729">10.1002/ciuz.201500729</a>).

> <NMREDATA_VERSION>
1.1\

> <NMREDATA_LEVEL>
1\

> <NMREDATA_ID>
Doi=10.18716/nmrshiftdb2/60001976\
DB_ID=60001976\

> <NMREDATA_SOLVENT>
CDCl3\

> <NMREDATA_TEMPERATURE>
298.0 K\

> <NMREDATA_ASSIGNMENT>
s0, 1.46, 21\
s1, 1.55, 20\
s2, 1.59, 18, 19\
s3, 2.0, 16, 17\
s4, 2.27, 12, 14\
s5, 2.67, 24, 25, 26\
s6, 2.84, 13, 15\
s7, 3.36, 22, 23\
s8, 15.8, 1\
s9, 29.1, 2, 6\
s10, 40.9, 11\
s11, 41.9, 4, 8\
s12, 55.8, 3, 5\
s13, 209.7, 9\
s14, 1.56, 21, 21, 21, 21\


> <NMREDATA_1D_1H>
Spectrum_Location=http://www.nmrshiftdb.org/download/NmrshiftdbServlet/60001116_1H.zip?spectrumid=60001116&nmrshiftdbaction=exportspec&format=rawdata\
Larmor=700.0\
1.46, L=s0\
1.55, L=s1\
1.59, L=s2\
2.0, L=s3\
2.27, L=s4\
2.67, L=s5\
2.84, L=s6\
3.36, L=s7\


> <NMREDATA_2D_1H_NJ_1H>
Spectrum_Location=http://www.nmrshiftdb.org/download/NmrshiftdbServlet/60001117_H,H-COSY.zip?spectrumid=60001117&nmrshiftdbaction=exportspec&format=rawdata\
Larmor=700.0\
CorType=COSY\
s0/s3\
s3/s7\
s6/s7\


> <NMREDATA_2D_1H_NJ_1H#2>
Spectrum_Location=http://www.nmrshiftdb.org/download/NmrshiftdbServlet/60001119_H,H-NOESY.zip?spectrumid=60001119&nmrshiftdbaction=exportspec&format=rawdata\
Larmor=700.0\
CorType=NOESY\
s0/s4\
s2/s4\
s2/s7\
s3/s5\
s3/s7\
s6/s7\


> <NMREDATA_1D_13C>
Spectrum_Location=http://www.nmrshiftdb.org/download/NmrshiftdbServlet/60001112_APT.zip?spectrumid=60001112&nmrshiftdbaction=exportspec&format=rawdata\
Larmor=175.0\
15.8, L=s8\
29.1, L=s9\
40.9, L=s10\
41.9, L=s11\
55.8, L=s12\
209.7, L=s13\


> <NMREDATA_2D_1H_NJ_13C>
Spectrum_Location=molecule/60001976\
Larmor=700.0\
CorType=HMBC\
s0/s9\
s0/s12\
s14/s9\
s14/s12\
s2/s8\
s2/s11\
s3/s8\
s3/s11\
s3/s12\
s4/s9\
s4/s10\
s4/s12\
s5/s12\
s6/s9\
s6/s12\
s7/s8\
s7/s9\
s7/s10\
s7/s11\


> <NMREDATA_2D_1H_NJ_13C#2>
Spectrum_Location=molecule/60001976\
Larmor=700.0\
CorType=HMBC\
s0/s9\
s0/s12\
s14/s9\
s14/s12\
s2/s8\
s2/s11\
s3/s8\
s3/s11\
s3/s12\
s4/s9\
s4/s10\
s4/s12\
s5/s12\
s6/s9\
s6/s12\
s7/s8\
s7/s9\
s7/s10\
s7/s11\


> <NMREDATA_2D_1H_NJ_13C#3>
Spectrum_Location=http://www.nmrshiftdb.org/download/NmrshiftdbServlet/60001120_H,C-ed. HSQC.zip?spectrumid=60001120&nmrshiftdbaction=exportspec&format=rawdata\
Larmor=700.0\
CorType=HSQC\
s0/s8\
s14/s8\
s2/s9\
s3/s9\
s4/s11\
s5/s10\
s6/s11\
s7/s12\


> <NMREDATA_SMILES>
C1(C([H])([H])C2(C(C(C(C(C1([H])[H])(N2C([H])([H])[H])[H])([H])[H])=O)([H])[H])[H])([H])[H]

> <NMREDATA_INCHI>
InChI=1S/C9H15NO/c1-10-7-3-2-4-8(10)6-9(11)5-7/h7-8H,2-6H2,1H3/i1+0H3,2+0H2,3+0H2,4+0H2,5+0H2,6+0H2,7+0H,8+0H,9+0,10+0,11+0

Describe the solution you'd like
Currently, the https://api.naturalproducts.net/latest/chem/standardize endpoint accepts the post request, standardizes the molecule and returns a standard set of key-value pairs in JSON, which is perfect. What would be great is to include all the additional properties in the original SDF file as key-value pairs.

Additional context
This way, we can make most out of the original additional data and don't have to map it separately

@Kohulan Kohulan added the enhancement New feature or request label Aug 24, 2023
Kohulan added a commit that referenced this issue Aug 24, 2023
Kohulan added a commit that referenced this issue Aug 24, 2023
@Kohulan Kohulan linked a pull request Aug 25, 2023 that will close this issue
@CS76 CS76 closed this as completed in #322 Aug 25, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging a pull request may close this issue.

2 participants