ljmartin

## combiningKd_simulation.ipynb

      
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                ljmartin
                / combiningKd_simulation.ipynb
            
            
              Created
              November 20, 2024 06:42
            
          
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## ligand.yaml
sequences:
  - protein:
      id: [A, B]
      sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
      msa: ./seq1.a3m
  - ligand:
      id: [C, D]
      ccd: SAH
  - ligand:
      id: [E, F]

## colorESP.ipynb

      
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                ljmartin
                / colorESP.ipynb
            
            
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              September 3, 2024 20:55
            
          
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## Ultra large benchmarking.ipynb

      
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                ljmartin
                / Ultra large benchmarking.ipynb
            
            
              Created
              August 16, 2024 20:41
            
          
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## mfp_symmetrization.py
#https://github.com/rdkit/rdkit/discussions/6135

from rdkit import Chem
from rdkit.Chem import AllChem

def mol_to_bits(mol, radius=0):
    bi = {}
    fp = AllChem.GetMorganFingerprint(mol, radius, bitInfo=bi,useFeatures=False)
    bits = np.zeros(mol.GetNumAtoms(),dtype=int)
    for key, value in bi.items():

## surfaceness-descriptor.ipynb

      
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                ljmartin
                / surfaceness-descriptor.ipynb
            
            
              Created
              August 1, 2024 07:33
            
          
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## example_for_ricardo.ipynb

      
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                ljmartin
                / example_for_ricardo.ipynb
            
            
              Created
              July 3, 2024 07:32
            
          
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## sasa_in_numpy.ipynb

      
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                ljmartin
                / sasa_in_numpy.ipynb
            
            
              Created
              March 10, 2024 06:28
            
          
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## combiningKi_simulation.ipynb

      
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                ljmartin
                / combiningKi_simulation.ipynb
            
            
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              April 29, 2024 08:10
            
          
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## tautomer_with_fps.ipynb

      
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                ljmartin
                / tautomer_with_fps.ipynb
            
            
              Created
              March 1, 2024 00:28
            
          
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	sequences:
	- protein:
	id: [A, B]
	sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
	msa: ./seq1.a3m
	- ligand:
	id: [C, D]
	ccd: SAH
	- ligand:
	id: [E, F]
	#https://github.com/rdkit/rdkit/discussions/6135

	from rdkit import Chem
	from rdkit.Chem import AllChem

	def mol_to_bits(mol, radius=0):
	bi = {}
	fp = AllChem.GetMorganFingerprint(mol, radius, bitInfo=bi,useFeatures=False)
	bits = np.zeros(mol.GetNumAtoms(),dtype=int)
	for key, value in bi.items():