/
respyte.yml
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/
respyte.yml
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## This file is a sample respyte.yml, input file for resp_optimzer.py
## 'respyte.yml' should be included in 'input' directory', generated from running esp_generator.
## Data structure (generated from running esp_generator.py or can manually be generated with an appropriate data structure):
## input/
## |----respyte.yml
## |----molecules/
## |----mol1/
## |----conf1/
## |----mol1_conf1.pdb(or .mol2) , mol1_conf1.espf
## |----conf2/
## |----mol1_conf2.pdb(or .mol2) , mol1_conf2.espf
## if xyz format has been used for esp generator, the data structure from esp_generator.py is containing pdb format converted from input xyz.
## In molecules, the number of molecules and the number of conformers for each molecule are assigned.
## For example, if the user wants to generate espf data for 2 different molecules with 5 conformers each,
## molecules is like below. (Each coordinate file should be either PDB or Mol2 file format and should be
## located in molecules/mol(i)/mol(j)/ ((i), (j) is integer) with its filename, mol(i)_mol(j).pdb(or .mol2)
## molecules :
## mol1 : 5
## mol2 : 5
molecules :
mol1 : 1
## In charges, user should specify a total charge of each residue.
## If the input molecule is small molecule, should specify net charge of each species.
charges :
mol1 : 0
## In Cheminformatics, user can choose 'openeye' or 'rdkit' or 'None'
## For now, rdkit option is not implemented yet.
cheminformatics : openeye
## If 'symmetry' is set to be True, it will force symmetry between equivalent atoms during the fitting.
symmetry : True
## If 'normalization' is set to be True, the size of A matrix will be normalized so that
## all A matrices have the same scale with methanol A matrix regardless of the size of molecule or grid set.
normalization : True
## In boundary_select, user can select subset of grid.dat
## If boundary_select is not set, it uses all grid points in grid.dat for fitting.
boundary_select:
radii : bondi
inner : 1.4
outer : 2.0
## In restraint, user can specify which restraint(model2, model3 and two-stage fit) to use.
restraint :
# penalty : model2
# a : 0.005
# penalty : model3
# matrices :
# - esp
# # - ef
# a : 0.0005
# b : 0.1
penalty : 2-stg-fit
matrices :
- esp
a1 : 0.0005
a2 : 0.001
b : 0.1
## User can set user-defined constraints on specific charges
## (net charge constraints on residues or atoms, forcing charge equivalence across residues)
#set_charge:
# atom1:
# resname: ALA
# atomname: CA
# charge: -0.2
# atom2:
# resname: ALA
# atomname: HA
# charge: 0.2
#net_set:
# GLU : -1
# charge_equal:
# group1:
# atomname: N
# resname: [LYN, TRP, PRO, GLY, SER, MET, PHE, CYS, ILE,ASN, VAL, HIE, ASH, HID, LEU, ALA, GLN, TYR, THR, GLH]
# group2:
# atomname: C
# resname: [LYN, TRP, PRO, GLY, SER, MET, PHE, CYS, ILE, ASN, VAL, HIE, ASH, HID, LEU, ALA, GLN, TYR, THR, GLH]
# group3:
# atomname: O
# resname: [LYN, TRP, PRO, GLY, SER, MET, PHE, CYS, ILE, ASN, VAL, HIE, ASH, HID, LEU, ALA, GLN, TYR, THR, GLH]
# group4:
# atomname: H
# resname: [LYN, TRP, PRO, GLY, SER, MET, PHE, CYS, ILE, ASN, VAL, HIE, ASH, HID, LEU, ALA, GLN, TYR, THR, GLH]
# group5:
# atomname: N
# resname : [ARG, LYS, HIP]
# group6:
# atomname: N
# resname : [ASP, GLU, CYM]
# group7:
# atomname: C
# resname : [ARG, LYS, HIP]
# group8:
# atomname: C
# resname : [ASP, GLU, CYM]
# group9:
# atomname: O
# resname : [ARG, LYS, HIP]
# group10:
# atomname: O
# resname : [ASP, GLU, CYM]
# group11:
# atomname: H
# resname : [ARG, LYS, HIP]
# group12:
# atomname: H
# resname : [ASP, GLU, CYM]