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Feature het code in pdb from smiles #150

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merged 3 commits into from
Jul 9, 2024

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Jgmedina95
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Hi! this is the first part of the PRs needed to get the simulation working for systems with solvents different than water.
Basically makes it such that the pdb file downloaded from the smiles for small molecules goes from:

HETATM    1  C1  UNL     1      -0.360  -0.003  -0.018  1.00  0.00           C  
HETATM    2  O1  UNL     1       0.914   0.522  -0.078  1.00  0.00           O  
HETATM    3  H1  UNL     1      -0.490  -0.816  -0.757  1.00  0.00           H  
HETATM    4  H2  UNL     1      -0.615  -0.390   0.996  1.00  0.00           H  
HETATM    5  H3  UNL     1      -1.069   0.834  -0.202  1.00  0.00           H  
HETATM    6  H4  UNL     1       1.619  -0.147   0.060  1.00  0.00           H  
CONECT    1    2    3    4    5
CONECT    2    6
END

to

COMPND    ethanol
HETATM    1  C1  EOH     1      -0.953   0.048   0.042  1.00  0.00           C  
HETATM    2  C2  EOH     1       0.489  -0.320  -0.189  1.00  0.00           C  
HETATM    3  O1  EOH     1       1.277   0.325   0.738  1.00  0.00           O  
HETATM    4  H1  EOH     1      -1.357   0.734  -0.733  1.00  0.00           H  
HETATM    5  H2  EOH     1      -1.593  -0.863   0.022  1.00  0.00           H  
HETATM    6  H3  EOH     1      -1.071   0.596   1.011  1.00  0.00           H  
HETATM    7  H4  EOH     1       0.788  -0.138  -1.238  1.00  0.00           H  
HETATM    8  H5  EOH     1       0.590  -1.429  -0.041  1.00  0.00           H  
HETATM    9  H6  EOH     1       1.831   1.047   0.388  1.00  0.00           H  
CONECT    1    2    4    5    6
CONECT    2    3    7    8
CONECT    3    9
END

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@qcampbel qcampbel left a comment

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made some minor suggestions. Overall, LMTG. Thanks for adding this!

mdagent/tools/base_tools/preprocess_tools/pdb_get.py Outdated Show resolved Hide resolved
mdagent/tools/base_tools/preprocess_tools/pdb_get.py Outdated Show resolved Hide resolved
@Jgmedina95 Jgmedina95 merged commit 135926e into main Jul 9, 2024
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@Jgmedina95 Jgmedina95 deleted the feature_het_code_in_pdb_from_smiles branch July 10, 2024 02:13
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2 participants