diff --git a/meeko/data/atomtypes.txt b/meeko/data/atomtypes.txt deleted file mode 100644 index 04c9dfb9..00000000 --- a/meeko/data/atomtypes.txt +++ /dev/null @@ -1,48 +0,0 @@ -# -# All these atom types are used to define interactions with PN (normal lone pairs) of rings and other pi-groups -# TODO: do they need to interact with aromatic carbons (A), too? -# TODO: do planar atoms (Np, Op, etc) interact with each other? see 4BFQ. -# -# -# - atom types are defined according to the SMARTS sequence -# - atoms for which atom types are defined are specified in the second field -# - for SMARTS atoms for which no atom type is defined, '*' is used -# -# TODO: maybe the indices are not necessary if null ('*') are used -# re-consider oxygen types: there are a lot, not sure if all needed -# -# - -[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0,N])[NH2X3] guanidine; 3,4,5,6; *,*,*,Np,Cp,Np,Np - -[*][CX3](=[OX1])[NX3H2] amides; 0,1,2,3; *,Cp,Op,Np - -[*][CX3](=[OX1])[OH0-,OH] carboxylic/carboxylate; 0,1,2,3; *,Cp,Op,Op - -### N-methylpyrrole, etc... (maybe superfluous? Np would be sufficient?) -[n;X3] N aromatic non-HBacc; 0; Nr - -### anyline -[N;X3]~[a] N aromatic amine non-HBacc; 0; Np - -### pyridine -[n;X2] N aromatic HBacc; 0; Nl - -### aromatic hydroxyl/ether/cyclic carbonyl -[#8;!R]~[a] O aromatic OH HBacc; 0; Op - -[s] S aromatic non-HBacc; 0; Sr - -[o] O aromatic non-HBacc; 0; Or - -[NX4] N charged non-HBacc; 0; N+ - -### nitro (NOTE: maybe Or instead of On, since both non HBacc?) -O~[N](~[O])-[a] aromatic nitro (all non-HBAcc); 0,1,2; On,Np,On,* - - -### This might be superfluous? it has pseudo-atoms already... -[CH2X4][SX2][*] S cys/met; 1; *,Sp,* - -[C]=[C] C aliphatic unsaturated; 0,1; Cp,Cp -# TODO: sp1 (do they interact with aromatic? check literature) diff --git a/meeko/data/flexres_templates.json b/meeko/data/flexres_templates.json deleted file mode 100644 index 8cb821e8..00000000 --- a/meeko/data/flexres_templates.json +++ /dev/null @@ -1,64 +0,0 @@ -{ -"LYS": - {"is_atom": [false, true, false, false, true, false, true, false, true, false, true, false, true, true, true, true, false, false, false, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", null, "CD", null, "CE", null, "NZ", "HZ3", "HZ2", "HZ1", null, null, null, null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, "BRANCH 3 4", null, "BRANCH 4 5", null, "BRANCH 5 6", null, null, null, null, "ENDBRANCH 5 6", "ENDBRANCH 4 5", "ENDBRANCH 3 4", "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"ARG": - {"is_atom": [false, true, false, false, true, false, true, false, true, false, true, true, true, true, true, true, true, true, true, false, false, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", null, "CD", null, "NE", "CZ", "NH2", "NH1", "HH22", "HH21", "HH12", "HH11", "HE", null, null, null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, "BRANCH 3 4", null, "BRANCH 4 5", null, null, null, null, null, null, null, null, null, "ENDBRANCH 4 5", "ENDBRANCH 3 4", "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"GLH": - {"is_atom": [false, true, false, false, true, true, true, false, true, true, true, false, true, true, true, true, false, false, false], "atom_name": [null, "CA", null, null, "CB", "HB2", "HB3", null, "CG", "HG3", "HG2", null, "CD", "OE1", "OE2", "HE2", null, null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, null, null, "BRANCH 2 5", null, null, null, "BRANCH 5 8", null, null, null, null, "ENDBRANCH 5 8", "ENDBRANCH 2 5", "ENDBRANCH 1 2"]}, - -"HIP": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "ND1", "HD1", "CE1", "NE2", "CD2", "HE2", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"VAL": - {"is_atom": [false, true, false, false, true, true, true, false], "atom_name": [null, "CA", null, null, "CB", "CG1", "CG2", null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, null, null, "ENDBRANCH 1 2"]}, - -"TYR": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, true, true, false, true, true, false, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "CD1", "CE1", "CZ", "CE2", "CD2", null, "OH", "HH", null, null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, null, null, "BRANCH 6 9", null, null, "ENDBRANCH 6 9", "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"ASH": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "OD1", "OD2", "HD2", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"HIE": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "ND1", "CE1", "NE2", "HE2", "CD2", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"GLU": - {"is_atom": [false, true, false, false, true, false, true, false, true, true, true, false, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", null, "CD", "OE1", "OE2", null, null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, "BRANCH 3 4", null, null, null, "ENDBRANCH 3 4", "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"LEU": - {"is_atom": [false, true, false, false, true, false, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "CD2", "CD1", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"PHE": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "CD1", "CE1", "CZ", "CE2", "CD2", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"GLN": - {"is_atom": [false, true, false, false, true, false, true, false, true, true, true, true, true, false, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", null, "CD", "NE2", "HE22", "HE21", "OE1", null, null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, "BRANCH 3 4", null, null, null, null, null, "ENDBRANCH 3 4", "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"ILE": - {"is_atom": [false, true, false, false, true, true, false, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", "CG2", null, "CG1", "CD1", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, null, "BRANCH 2 4", null, null, "ENDBRANCH 2 4", "ENDBRANCH 1 2"]}, - -"MET": - {"is_atom": [false, true, false, false, true, false, true, false, true, true, false, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", null, "SD", "CE", null, null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, "BRANCH 3 4", null, null, "ENDBRANCH 3 4", "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"ASN": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "OD1", "ND2", "HD21", "HD22", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"THR": - {"is_atom": [false, true, false, false, true, true, false, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", "CG2", null, "OG1", "HG1", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, null, "BRANCH 2 4", null, null, "ENDBRANCH 2 4", "ENDBRANCH 1 2"]}, - -"TRP": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, true, true, true, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "CD2", "CE2", "CE3", "CZ2", "NE1", "CH2", "CZ3", "HE1", "CD1", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, null, null, null, null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"CYS": - {"is_atom": [false, true, false, false, true, false, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "SG", "HG", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"SER": - {"is_atom": [false, true, false, false, true, false, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "OG", "HG", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"ASP": - {"is_atom": [false, true, false, false, true, false, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "OD1", "OD2", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]}, - -"HID": - {"is_atom": [false, true, false, false, true, false, true, true, true, true, true, true, false, false], "atom_name": [null, "CA", null, null, "CB", null, "CG", "ND1", "HD1", "CE1", "NE2", "CD2", null, null], "original_line": ["ROOT", null, "ENDROOT", "BRANCH 1 2", null, "BRANCH 2 3", null, null, null, null, null, null, "ENDBRANCH 2 3", "ENDBRANCH 1 2"]} -} diff --git a/meeko/data/pi_non_aromatic.txt b/meeko/data/pi_non_aromatic.txt deleted file mode 100644 index ab019df9..00000000 --- a/meeko/data/pi_non_aromatic.txt +++ /dev/null @@ -1,50 +0,0 @@ -# -# PI_PSEUDO_PATTERNS.txt -# -# patterns used for building pi pseudo-atoms (centroid, normals) for groups that are *not* aromatic -# -# -# SMARTS_PATTERN (space) LABEL PLANE_IDX CENTROID_IDX -# string [ ] string; int, int,... ; int -# -# Indices: -# - are 0-based (this could be changed if necessary) -# - indices are used to define which atoms in the pattern are used to calculate -# centroids and normals; for this reason, they have to be in the order that -# defines the vectors Atom1-Atom2, and Atom3-Atom2, so that they do not define -# a degenerate plane (see code in geomutils.py) -# - centroid idx defines which atom is used used to place the centroid -# -# For example, for guanidine: -# -# [CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0,N])[NH2X3] guanidine; 3,4,5,6; 4 -# -# atoms used to calculate the plane are: -# -# 3: '[NHX3' -# 4: '[CH0X3]' -# 5: '(=[NH2X3+,NHX2+0,N])' -# 6: '[NH2X3]' -# -# and the centroid is place on atom 4 in the pattern ('[CH0X3]') - - -# TODO this pattern can be improved to recognize better actual guanidine group (i.e., smaller pattern) -[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0,N])[NH2X3] guanidine; 3,6,5,4; 4 -[*]~[CX3](=[OX1])[NX3H2] amide; 0,3,1,2; 1 -[*]~[CX3](=[OX1])[OH0-,OH] carboxylic/carboxylate; 0,3,1,2; 1 -# this might be approximated because it places the centroid atoms at 90 degrees sharp, but QM might disagree -[CH2X4][SX2][*] cys/met; 1,0,2; 1 - - - -# TODO -# add delocalized,isolated, double-bonds? (only if they need centroid/normals) -# add nitro-benzene -# add benzoic and benzamide (changing first atom in asn/gln pattern -# the parameter line format might be extended to have a distance value used to set the lenght of the normal vector for different groups -# IMPORTANT: do we really need centroids for these atoms? by looking at structures, it seem we can get away by -# defining interactions between planar atoms (Np, Op, etc.) and aromatic rings. If so, we could limit the centroid-normals -# model to rings to create maps, then define weaker pairwise interactions between planar atoms -# As a consequence, this file might become obsolete -# diff --git a/meeko/data/prot_res_params.json b/meeko/data/prot_res_params.json deleted file mode 100644 index 151d143a..00000000 --- a/meeko/data/prot_res_params.json +++ /dev/null @@ -1,3034 +0,0 @@ -{ - "ambiguous": { - "HIS": ["HIE", "HIP", "HID"], - "ASP": ["ASH", "ASP"], - "GLU": ["GLH", "GLU"], - "HOH": ["WAT"], "//": "using HOH as synonym of WAT", - "//": "this can't be used for CYS or LYS because the chosen match is that with fewer missing Hs" - }, - - "TIP3P": { "//": "note that the TIP3P model defines also coordinates", - "epsilon": [ 0.1520, 0.0 , 0.0 ], - "rmin_half": [ 1.7683, 1.0 , 1.0 ], - "q": [-0.834 , 0.417, 0.417], - "smiles": "O([H])[H]" - }, - - "MG": { - "atom_name": [ "OW"], - "atom_type": [ "OA"], - "atom_ignore": [ false], - "ad4_epsii": [ 0.875 ], - "ad4_rii": [ 1.3 ], - "ad4_sol_vol": [ 1.56 ], - "ad4_sol_par": [ -0.00110], - "ad4_hb_rij": [ null], - "ad4_hb_epsij": [ null], - "vina_ri": [ 1.2 ], - "vina_donor": [ true], - "vina_acceptor": [ false], - "vina_hydrophobic": [ false], - "charge": [ 2.0 ], - "smiles": "[Mg]" - }, - - "WAT": { - "atom_name": [ "OW", "HW1", "HW2"], - "atom_type": [ "OA", "HD" , "HD" ], - "atom_ignore": [ false, false, false], - "ad4_epsii": [ 0.2 , 0.02 , 0.02 ], - "ad4_rii": [ 3.2 , 2.0 , 2.0 ], - "ad4_sol_vol": [ 17.1573 , 0.0 , 0.0 ], - "ad4_sol_par": [ -0.00251, 0.00051, 0.00051], - "ad4_hb_rij": [ 1.9 , true, true], - "ad4_hb_epsij": [ 5.0 , true, true], - "vina_ri": [ 1.7 , null, null], - "vina_donor": [ true, false, false], - "vina_acceptor": [ true, true, false], - "vina_hydrophobic": [ false, false, false], - "charge": [ -0.412 , 0.206 , 0.206 ], - "smiles": "O([H])[H]" - }, - - "ALA": { - "atom_name": ["C", "O", "CA", "HA", "N", "H", "CB", "HB1", "HB2", "HB3"], - "atom_type": ["C", "OA", "C", "H", "N", "HD", "C", "H", "H", "H"], - "atom_ignore": [false, false, false, true, false, false, false, true, true, true], - "ad4_epsii": [0.15, 0.2, 0.15, 0.0, 0.16, 0.02, 0.15, 0.0, 0.0, 0.0], - "ad4_rii": [4.0, 3.2, 4.0, 0.0, 3.5, 2.0, 4.0, 0.0, 0.0, 0.0], - "ad4_sol_vol": [33.5103, 17.1573, 33.5103, 0.0, 22.4493, 0.0, 33.5103, 0.0, 0.0, 0.0], - "ad4_sol_par": [-0.00143, -0.00251, -0.00143, 0.0, -0.00162, 0.00051, -0.00143, 0.0, 0.0, 0.0], - "ad4_hb_rij": [null, 1.9, null, null, null, true, null, null, null, null], - "ad4_hb_epsij": [null, 5.0, null, null, null, true, null, null, null, null], - "vina_ri": [1.9, 1.7, 1.9, null, 1.8, null, 1.9, null, null, null], - "vina_donor": [false, false, false, false, true, false, false, false, false, false], - "vina_acceptor": [false, true, false, false, false, false, false, false, false, false], - "vina_hydrophobic": [false, false, false, false, false, false, true, false, false, false], - "charge": [0.243, -0.272, 0.168, 0.0, -0.344, 0.164, 0.041, 0.0, 0.0, 0.0], - "bonds": [ - [0, 1], - [0, 2], - [2, 3], - [2, 4], - [4, 5], - [2, 6], - [6, 7], - [6, 8], - [6, 9] - ], - "bond_cut_atoms": [0, 4], - "smiles": "C(=O)C([H])(N[H])C([H])([H])[H]" - }, - "CYS": { - "atom_name": ["C", "O", "CA", "HA", "N", "H", "CB", "HB2", "HB3", "SG", "HG"], - "atom_type": ["C", "OA", "C", "H", "N", "HD", "C", "H", "H", "SA", "HD"], - "atom_ignore": [false, false, false, true, false, false, false, true, true, false, false], - "ad4_epsii": [0.15, 0.2, 0.15, 0.0, 0.16, 0.02, 0.15, 0.0, 0.0, 0.2, 0.02], - "ad4_rii": [4.0, 3.2, 4.0, 0.0, 3.5, 2.0, 4.0, 0.0, 0.0, 4.0, 2.0], - "ad4_sol_vol": [33.5103, 17.1573, 33.5103, 0.0, 22.4493, 0.0, 33.5103, 0.0, 0.0, 33.5103, 0.0], - "ad4_sol_par": [-0.00143, -0.00251, -0.00143, 0.0, -0.00162, 0.00051, -0.00143, 0.0, 0.0, -0.00214, 0.00051], - "ad4_hb_rij": [null, 1.9, null, null, null, true, null, null, null, 2.5, true], - "ad4_hb_epsij": [null, 5.0, null, null, null, true, null, null, null, 1.0, true], - "vina_ri": [1.9, 1.7, 1.9, null, 1.8, null, 1.9, null, null, 2.0, null], - 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"ad4_sol_par": [-0.00143,-0.00251,-0.00143, 0.00000,-0.00162, 0.00051,-0.00143, 0.00000, 0.00000,-0.00052,-0.00052, 0.00000,-0.00052, 0.00000,-0.00052,-0.00251, 0.00051,-0.00052, 0.00000,-0.00052, 0.00000,-0.00251], - "ad4_hb_rij": [ null, 1.9, null, null, null, true, null, null, null, null, null, null, null, null, null, 1.9, true, null, null, null, null, 1.9], - "ad4_hb_epsij": [ null, 5.0, null, null, null, true, null, null, null, null, null, null, null, null, null, 5.0, true, null, null, null, null, 5.0], - "vina_ri": [ 1.9, 1.7, 1.9, null, 1.8, null, 1.9, null, null, 1.9, 1.9, null, 1.9, null, 1.9, 1.7, null, 1.9, null, 1.9, null, 1.7], - "vina_donor": [ false, false, false, false, true, false, false, false, false, false, false, false, false, false, false, true, false, false, false, false, false, false], - "vina_acceptor": [ false, true, false, false, false, false, false, false, false, false, false, false, false, false, false, true, false, false, false, false, false, true], - "vina_hydrophobic": [ false, false, false, false, false, false, true, false, false, true, true, false, true, false, false, false, false, true, false, true, false, false], - "gasteiger": [ 0.065, -0.538, 0.135, 0.000, -0.341, 0.167, 0.067, 0.000, 0.000, -0.044, 0.007, 0.000, 0.047, 0.000, 0.117, -0.498, 0.299, 0.047, 0.000, 0.007, 0.000, -0.537], - "bonds": [[21, 0], [0, 1], [0, 2], [2, 3], [2, 4], [4, 5], [2, 6], [6, 7], [6, 8], [6, 9], [9, 10], [10, 11], [10, 12], [12, 13], [12, 14], [14, 15], [15, 16], [14, 17], [17, 18], [17, 19], [19, 20], [19, 9]], - "bond_cut_atoms": [4] - }, - "CPRO": { - "atom_names": [ "C", "O", "CA", "HA", "N", "CB", "HB3", "HB2", "CG", "HG2", "HG3", "CD", "HD2", "HD3", "OXT"], - "atom_types": [ "C", "OA", "C", "H", "N", "C", "H", "H", "C", "H", "H", "C", "H", "H", "OA"], - "ad4_epsii": [ 0.15, 0.20, 0.15, 0.00, 0.16, 0.15, 0.00, 0.00, 0.15, 0.00, 0.00, 0.15, 0.00, 0.00, 0.20], - "ad4_rii": [ 4.00, 3.20, 4.00, 0.00, 3.50, 4.00, 0.00, 0.00, 4.00, 0.00, 0.00, 4.00, 0.00, 0.00, 3.20], - "ad4_sol_vol": [ 33.5103, 17.1573, 33.5103, 0.0000, 22.4493, 33.5103, 0.0000, 0.0000, 33.5103, 0.0000, 0.0000, 33.5103, 0.0000, 0.0000, 17.1573], - "ad4_sol_par": [-0.00143,-0.00251,-0.00143, 0.00000,-0.00162,-0.00143, 0.00000, 0.00000,-0.00143, 0.00000, 0.00000,-0.00143, 0.00000, 0.00000,-0.00251], - "ad4_hb_rij": [ null, 1.9, null, null, null, null, null, null, null, null, null, null, null, null, 1.9], - "ad4_hb_epsij": [ null, 5.0, null, null, null, null, null, null, null, null, null, null, null, null, 5.0], - "vina_ri": [ 1.9, 1.7, 1.9, null, 1.8, 1.9, null, null, 1.9, null, null, 1.9, null, null, 1.7], - "vina_donor": [ false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], - "vina_acceptor": [ false, true, false, false, false, false, false, false, false, false, false, false, false, false, true], - "vina_hydrophobic": [ false, false, false, false, false, true, false, false, true, false, false, false, false, false, false], - "gasteiger": [ 0.066, -0.530, 0.135, 0.000, -0.324, 0.034, 0.000, 0.000, 0.025, 0.000, 0.000, 0.124, 0.000, 0.000, -0.530], - "bonds": [[14, 0], [0, 1], [0, 2], [2, 3], [2, 4], [2, 5], [5, 6], [5, 7], [5, 8], [8, 9], [8, 10], [8, 11], [11, 12], [11, 13], [11, 4]], - "bond_cut_atoms": [4] - } -} diff --git a/meeko/data/waterfield.txt b/meeko/data/waterfield.txt deleted file mode 100644 index b0469900..00000000 --- a/meeko/data/waterfield.txt +++ /dev/null @@ -1,101 +0,0 @@ -# -# Water Forcefield 0.1.1 -# - -# Hydrogen -## H -#ATOM H_000 1 0.000 1 1 1.8 [#1] # all hydrogens - -## HC -ATOM H_C_000 0 0.000 1 1 1.8 [#1][#6] # all CH -ATOM H_C_001 1 0.500 1 1 1.8 [#1][#6;X2] # acetylene -ATOM H_C_002 1 0.250 1 1 1.8 [#1][#6;X3] # ethylene / benzene -ATOM H_C_003 1 0.120 1 1 1.8 [#1][#6;X4] # methane - -## OH -ATOM H_O_000 1 0.000 1 1 1.8 [#1][#8] # general hydroxyl (OH) -ATOM H_O_001 1 1.100 1 1 1.8 [#1;X1][#8;X2;v2] # other hydroxyl -ATOM H_O_002 1 1.500 1 1 1.8 [#1;X1][#8;X2;v2;H1][a] # Ar-OH (phenol-like) -ATOM H_O_003 1 1.500 1 1 1.8 [#1;X1][#8;X2;v2;H1]-[#6;X3;v4]=[#8;X1;v2] # carboxylate H -# ATOM H_O_004 1 1.000 1 1 1.8 [] # hydrogen of TIP5P water molecule - -## HN -ATOM H_N_000 1 0.000 1 1 1.8 [#1][#7] # general NH -ATOM H_N_001 1 0.500 1 1 1.8 [#1;X1][#7;X3;v3] # amine -ATOM H_N_002 1 0.800 1 1 1.8 [#1;X1][#7;X2;v3] # nitrogen sp2 (guanidine, immine) -ATOM H_N_003 1 0.800 1 1 1.8 [#1;X1][#7;X3;v3][a] # aniline (matches pyrrole, which follows) -ATOM H_N_004 1 1.300 1 1 1.8 [#1;X1][#7;a;X3;v3;H1] # aromatic nitrogen (pyrrole) -ATOM H_N_005 1 1.100 1 1 1.8 [#1;X1][#7;X3;v3][#6;X3;v4]=[#8;X1;v2] # amide nitrogen donor (overrides pyrrole) - -## HS -ATOM H_S_000 1 0.000 1 1 1.8 [#1][#16] # default SH -ATOM H_S_001 1 0.500 1 1 1.8 [#1;X1][#16;X2;v2] # -SH (general thiol) -ATOM H_S_002 1 0.700 1 1 1.8 [#1;X1][#16;X2;v2;H1][a] # Ar-SH (benzenethiol-like) - -# Oxygen -## O -ATOM O_000 2 0.000 2 2 2.8 [#8] # all oxygens -ATOM O_001 2 0.900 2 2 2.8 [#8;X1;v2]=[#6;X3;v4][*] # in acetone / ester(sp2) / aldehyde -ATOM O_002 2 0.900 2 2 2.8 [#8;X1;v2]=[#6;X3;v4]([#6])[#6,#1] # in acetone / aldehyde -ATOM O_003 2 0.900 2 2 2.8 [#8;X1;v2]=[#6;X3;v4]([a]) # acetophenone -ATOM O_004 2 1.200 2 2 2.8 [#8;X1;v2]=[#6;X3;v4]([#7;X3;v3]) # in amide -ATOM O_006 2 0.600 3 2 2.8 [#8;X2;v2]([!a])[a] # in phenol / anisole -ATOM O_007 2 0.800 3 2 2.8 [#8;X2;v2]([!a])[!a] # in ether (matches hydroxyl/ester(sp3), which follows) -ATOM O_008 2 0.900 3 2 2.8 [#8;X2;v2;H1][!a;!N] # in aliphatic hydroxyl (errnsly match nitro/carboxy) -ATOM O_005 0 0.500 0 0 0.0 [#8;X2;v2](-[*])[#6;X3;v4]=[#8;X1;v2] # in ester(sp3) / acetic acid (sp3) -ATOM O_009 0 0.600 0 0 0.0 [#8;X2;v2]([a])[a] # aromatic oxygen / aromatic ether - -## ON -ATOM O_011_1 2 0.800 2 2 2.8 [#8;X1]~[#7;X3](~[#8;X1]) # nitro group (any) -ATOM O_011_2 2 0.800 2 2 2.8 [#8;X1]~[#7;X3](~[#8;X2;H1]) -ATOM O_012_1 2 0.800 2 2 2.8 [#8;X2;H1]~[#7;X3](~[#8;X1])~[C] # nitro group (aliphatic) -ATOM O_012_2 2 0.800 2 2 2.8 [#8;X1]~[#7;X3](~[#8;X2;H1])~[C] -ATOM O_013_1 2 0.800 2 2 2.8 [#8;X1]~[#7](~[#8;X1])~[c] # nitro group (aromatic) -ATOM O_013_2 2 0.800 2 2 2.8 [#8;X1]~[#7](~[#8;X2;H1])~[c] -ATOM O_019 2 0.600 3 2 2.8 [#8;X2]([#7])[!#1] # ether oxygen in nitrate (NO3) - -## OS -ATOM O_S_000 0 0.000 0 0 0.0 [#8]~[#16] # All O-S -ATOM O_S_001 2 1.400 2 3 2.8 [#8;X1]~[#16;X3] # DMSO (the bond is not always double in openbabel/mol2 files) -ATOM O_S_002 2 1.000 2 3 2.8 [#8;X1]~[#16]~[#8;X1] # Sulfone S(=O)(=O)(C)C / sulfonate S(=O)(=O)(OC)C -ATOM O_S_003 2 0.600 2 3 2.8 [#8;X1]~[#16]([#8;X2])([#8;X2])~[#8;X1] # Sulfate (S(=O)(=O)(OC)OC) -ATOM O_S_004 0 0.750 0 0 0.0 [#8;X2]~[#16] # sulfate/sulfone ether-like oxygen - -## OP -ATOM O_P_000 0 0.000 0 0 0.0 [#8]~[#15] -ATOM O_P_001 2 0.000 2 3 2.8 [#8;X1]~[#15] -ATOM O_P_002 2 1.200 2 3 2.8 [#8]=[#15] -ATOM O_P_003 0 0.750 0 0 0.0 [#8]-[#15] - -## O Lone pairs -# ATOM O_L_000 2 1.000 1 1 2.1 [] # Lone pair of TIP5P water molecule - -# Nitrogen -ATOM N_000 0 0.000 0 0 0.0 [#7] # any nitrogen -ATOM N_001 2 0.900 1 1 2.8 [#7;X1;v3]#[#6;X2;v4] # nitrile -ATOM N_002 2 1.200 2 1 2.8 [#7;X2;v3]=[*] # in immine -ATOM N_003 2 1.200 2 1 2.8 [#7;X2;v3]([a])([a]) # in pyridine -ATOM N_004 2 1.200 3 1 2.8 [#7;X3;v3][!a] # aliphatic amine, ammonia, hydrazine -ATOM N_005 0 0.000 0 0 0.0 [#7;X3;v3][a] # revert anilines erroneously matched in previous smarts -ATOM N_006 0 0.000 0 0 0.0 [#7;X3;v3][#6;X3;v4]=[#8;X1;v2] # revert amides from N_004 - -# Sulfur -ATOM S_000 0 0.000 0 0 0.0 [#16] # any sulfur (in sulfones, sulfates, dmso, therefore weight=0) -ATOM S_001 2 0.500 3 2 2.8 [#16;X2;v2] # generic sp3 sulfur (thioether) -ATOM S_002 0 0.000 0 0 0.0 [#16;X2;v2]([a])[a] # thiophene -ATOM S_003_1 2 0.700 3 2 2.8 [#16;X2;v2]([C;X4;v4])[C;X4;v4] # thioether bound to two sp3 carbons or methanethiol -ATOM S_003_2 2 0.700 3 2 2.8 [#16;X2;v2]([C;X4;v4])[#1] -ATOM S_004 2 0.700 2 3 2.8 [#16;X2;v2;h] # thioketone (in FreeSolv-0.5 occurs as P=S) - -# Carbon -ATOM C_000 0 0.000 0 0 0.0 [#6] # any carbon -ATOM C_001 0 0.300 0 0 0.0 [#6;X2;v4] # sp carbon -ATOM C_002 0 0.300 0 0 0.0 [#6;X3;v4] # sp2 carbon -ATOM C_003 0 0.400 0 0 0.0 [#6;X3;v4;a] # aromatic carbon - -# Halogen -ATOM CL_000 0 0.400 3 1 2.8 [#17] # any chlorine -ATOM F_000 0 0.400 3 1 2.8 [#9] # any fluorine -ATOM BR_000 0 0.400 3 1 2.8 [#35] # any bromine -ATOM I_000 0 0.400 3 1 2.8 [#53] # any iodine -ATOM P_000 0 0.000 0 0 0.0 [#15] # any phosphorus diff --git a/meeko/polymer.py b/meeko/polymer.py index 91b09197..8a549092 100644 --- a/meeko/polymer.py +++ b/meeko/polymer.py @@ -2,6 +2,7 @@ import json import logging import traceback +from importlib_resources import files from os import linesep as os_linesep from sys import exc_info from typing import Union @@ -30,6 +31,7 @@ import numpy as np +data_path = files("meeko.data") periodic_table = Chem.GetPeriodicTable() try: @@ -591,28 +593,86 @@ def from_dict(cls, alldata): as input to allow users to modify the input dict in Python """ - # alldata = json.loads(json_string) - ambiguous = alldata["ambiguous"] + ambiguous = {k: v.copy() for k, v in alldata["ambiguous"].items()} residue_templates = {} padders = {} for key, data in alldata["residue_templates"].items(): - link_labels = None - if "link_labels" in data: - link_labels = { - int(key): value for key, value in data["link_labels"].items() - } - # print(key) - res_template = ResidueTemplate( - data["smiles"], link_labels, data.get("atom_name", None) - ) + res_template = cls.residue_template_from_dict(data) residue_templates[key] = res_template for link_label, data in alldata["padders"].items(): - rxn_smarts = data["rxn_smarts"] - adjacent_res_smarts = data.get("adjacent_res_smarts", None) - auto_blunt = data.get("auto_blunt", False) - padders[link_label] = ResiduePadder(rxn_smarts, adjacent_res_smarts, auto_blunt) + padders[link_label] = cls.padder_from_dict(data) return cls(residue_templates, padders, ambiguous) + @staticmethod + def residue_template_from_dict(data): + if "link_labels" in data: + link_labels = {int(k): v for k, v in data["link_labels"].items()} + else: + link_labels = None + atom_names = data.get("atom_name", None) + return ResidueTemplate(data["smiles"], link_labels, atom_names) + + @staticmethod + def padder_from_dict(data): + rxn_smarts = data["rxn_smarts"] + adjacent_res_smarts = data.get("adjacent_res_smarts", None) + auto_blunt = data.get("auto_blunt", False) + padder = ResiduePadder(rxn_smarts, adjacent_res_smarts, auto_blunt) + return padder + + def add_dict(self, data, overwrite=False): + bad_keys = set(data) - {"ambiguous", "residue_templates", "padders"} + if bad_keys: + raise ValueError("unexpected keys: {bad_keys}") + new_ambiguous = data.get("ambiguous", {}) + if overwrite: + self.ambiguous.update(new_ambiguous) + else: + new_ambiguous = {k: v.copy() for k, v in new_ambiguous.items()} + new_ambiguous.update(self.ambiguous) + self.ambiguous = new_ambiguous + for key, value in data.get("residue_templates", {}).items(): + if overwrite or key not in self.residue_templates: + res_template = self.residue_template_from_dict(value) + self.residue_templates[key] = res_template + for link_label, value in data.get("padders", {}).items(): + if overwrite or key not in self.padders: + padder = self.padder_from_dict(data) + self.padders[link_label] = padder + return + + @staticmethod + def lookup_filename(filename, data_path): + p = pathlib.Path(filename) + if not p.exists(): + if (data_path / p).exists(): + filename = str(data_path / p) + elif (data_path / (p.name + ".json")).exists(): + filename = str(data_path / (p.name + ".json")) + else: + raise ValueError(f"can't find {filename} in current dir or {data_path}") + return filename + + @classmethod + def from_json_file(cls, filename): + filename = cls.lookup_filename(filename, data_path) + with open(filename) as f: + jsonstr = f.read() + data = json.loads(jsonstr) + return cls.from_dict(data) + + @classmethod + def create_from_defaults(cls): + return cls.from_json_file("residue_chem_templates") + + def add_json_file(self, filename): + filename = self.lookup_filename(filename, data_path) + with open(filename) as f: + jsonstr = f.read() + data = json.loads(jsonstr) + self.add_dict(data) + return + @staticmethod def _check_missing_padders(residue_templates, padders): diff --git a/meeko/receptor_pdbqt.py b/meeko/receptor_pdbqt.py index b87ad3dd..8f2f79f6 100644 --- a/meeko/receptor_pdbqt.py +++ b/meeko/receptor_pdbqt.py @@ -7,8 +7,6 @@ from collections import defaultdict import json from os import linesep as os_linesep -import pathlib -import sys import numpy as np from scipy import spatial @@ -17,25 +15,6 @@ from .utils.autodock4_atom_types_elements import autodock4_atom_types_elements from .reactive import get_reactive_atype -pkg_dir = pathlib.Path(__file__).parents[0] -with open(pkg_dir / "data" / "residue_params.json") as f: - residue_params = json.load(f) -with open(pkg_dir / "data" / "flexres_templates.json") as f: - flexres_templates = json.load(f) -# the above is controversial, see -# https://stackoverflow.com/questions/6028000/how-to-read-a-static-file-from-inside-a-python-package - -def _write_pdbqt_line(atomidx, x, y, z, charge, atom_name, res_name, res_num, atom_type, chain, - alt_id=" ", in_code="", occupancy=1.0, temp_factor=0.0, record_type="ATOM"): - if len(atom_name) > 4: - raise ValueError("max length of atom_name is 4 but atom name is %s" % atom_name) - atom_name = "%-3s" % atom_name - line = "{:6s}{:5d} {:4s}{:1s}{:3s} {:1s}{:4d}{:1s} {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f} {:6.3f} {:<2s}" - line += os_linesep - return line.format(record_type, atomidx, atom_name, alt_id, res_name, chain, - res_num, in_code, x, y, z, - occupancy, temp_factor, charge, atom_type) - atom_property_definitions = {'H': 'vdw', 'C': 'vdw', 'A': 'vdw', 'N': 'vdw', 'P': 'vdw', 'S': 'vdw', 'Br': 'vdw', 'I': 'vdw', 'F': 'vdw', 'Cl': 'vdw', @@ -127,7 +106,6 @@ def _identify_bonds(atom_idx, positions, atom_types): class PDBQTReceptor: - flexres_templates = flexres_templates skip_types=("H",) def __init__(self, pdbqt_string, skip_typing=False): @@ -172,210 +150,6 @@ def get_atom_indices_by_residue(atoms): atom_idx_by_res[res_id].append(atom_index) return atom_idx_by_res - @staticmethod - def get_params_for_residue(resname, atom_names, residue_params=residue_params): - excluded_params = ("atom_names", "bond_cut_atoms", "bonds") - atom_params = {} - atom_counter = 0 - err = "" - ok = True - is_matched = False - for terminus in ["", "N", "C"]: # e.g. "CTYR" for C-term TYR, hard-coded in residue_params - r_id = "%s%s" % (terminus, resname) - if r_id not in residue_params: - err = "residue %s not in residue_params" % r_id + os_linesep - ok = False - return atom_params, ok, err - ref_names = set(residue_params[r_id]["atom_names"]) - query_names = set(atom_names) - if ref_names == query_names: - is_matched = True - break - - if not is_matched: - ok = False - err = "residue %s did not match residue_params" % r_id + os_linesep - err += "ref_names: %s" % ref_names + os_linesep - err += "query_names: %s" % query_names + os_linesep - return atom_params, ok, err - - for atom_name in atom_names: - name_index = residue_params[r_id]["atom_names"].index(atom_name) - for param in residue_params[r_id].keys(): - if param in excluded_params: - continue - if param not in atom_params: - atom_params[param] = [None] * atom_counter - value = residue_params[r_id][param][name_index] - atom_params[param].append(value) - atom_counter += 1 - - return atom_params, ok, err - - def assign_types_charges(self, residue_params=residue_params): - wanted_params = ("atom_types", "gasteiger") - atom_params = {key: [] for key in wanted_params} - ok = True - err = "" - for r_id, atom_indices in self.atom_idxs_by_res.items(): - atom_names = tuple(self.atoms(atom_indices)["name"]) - resname = r_id[1] - params_this_res, ok_, err_ = self.get_params_for_residue(resname, atom_names, residue_params) - ok &= ok_ - err += err_ - if not ok_: - print("did not match %s with template" % str(r_id), file=sys.stderr) - continue - for key in wanted_params: - atom_params[key].extend(params_this_res[key]) - if ok: - self._atoms["partial_charges"] = atom_params["gasteiger"] - self._atoms["atom_type"] = atom_params["atom_types"] - return ok, err - - def write_flexres_from_template(self, res_id, atom_index=0): - success = True - error_msg = "" - branch_offset = atom_index # templates assume first atom is 1 - output = {"pdbqt": "", "flex_indices": [], "atom_index": atom_index} - resname = res_id[1] - if resname not in self.flexres_templates: - success = False - error_msg = "no flexible residue template for resname %s, sorry" % resname - return output, success, error_msg - if res_id not in self.atom_idxs_by_res: - success = False - chains = set(self._atoms["chain"]) - error_msg += "could not find residue with chain='%s', resname=%s, resnum=%d" % res_id + os_linesep - error_msg += "chains in this receptor: %s" % ", ".join("'%s'" % c for c in chains) + os_linesep - if " " in chains: # should not happen because we use strip() when parsing the chain - error_msg += "use ' ' (a space character) for empty chain" + os_linesep - if "" in chains: - error_msg += "use '' (empty string) for empty chain" + os_linesep - return output, success, error_msg - - # collect lines of res_id - atoms_by_name = {} - for i in self.atom_idxs_by_res[res_id]: - name = self._atoms[i]["name"] - if name in ['C', 'N', 'O', 'H', 'H1', 'H2', 'H3', 'OXT']: # skip backbone atoms - continue - atype = self._atoms[i]["atom_type"] - if atype in self.skip_types: - continue - output["flex_indices"].append(i) - atoms_by_name[name] = self.atoms(i) - - # check it was a full match - template = self.flexres_templates[resname] - got_atoms = set(atoms_by_name) - ref_atoms = set() - for i in range(len(template["is_atom"])): - if template["is_atom"][i]: - ref_atoms.add(template["atom_name"][i]) - if got_atoms != ref_atoms: - success = False - error_msg += "mismatch in atom names for residue %s" % str(res_id) + os_linesep - error_msg += "names found but not in template: %s" % str(got_atoms.difference(ref_atoms)) + os_linesep - error_msg += "missing names: %s" % str(ref_atoms.difference(got_atoms)) + os_linesep - return output, success, error_msg - - # create output string - n_lines = len(template['is_atom']) - for i in range(n_lines): - if template['is_atom'][i]: - atom_index += 1 - name = template['atom_name'][i] - atom = atoms_by_name[name] - if atom["atom_type"] not in self.skip_types: - atom["serial"] = atom_index - output["pdbqt"] += self.write_pdbqt_line(atom) - else: - line = template['original_line'][i] - if branch_offset > 0 and (line.startswith("BRANCH") or line.startswith("ENDBRANCH")): - keyword, i, j = line.split() - i = int(i) + branch_offset - j = int(j) + branch_offset - line = "%s %3d %3d" % (keyword, i, j) - output["pdbqt"] += line + os_linesep # e.g. BRANCH keywords - - output["atom_index"] = atom_index - return output, success, error_msg - - @staticmethod - def write_pdbqt_line(atom): - return _write_pdbqt_line(atom["serial"], atom["xyz"][0], atom["xyz"][1], atom["xyz"][2], - atom["partial_charges"], atom["name"], atom["resname"], - atom["resid"], atom["atom_type"], atom["chain"], - atom["alt_id"], atom["in_code"], atom["occupancy"], - atom["temp_factor"], atom["record_type"]) - - - def write_pdbqt_string(self, flexres=()): - ok = True - err = "" - pdbqt = {"rigid": "", - "flex": {}, - "flex_indices": []} - atom_index = 0 - for res_id in set(flexres): - output, ok_, err_ = self.write_flexres_from_template(res_id, atom_index) - atom_index = output["atom_index"] # next residue starts here - ok &= ok_ - err += err_ - pdbqt["flex_indices"].extend(output["flex_indices"]) - pdbqt["flex"][res_id] = "" - pdbqt["flex"][res_id] += "BEGIN_RES %3s %1s%4d" % (res_id) + os_linesep - pdbqt["flex"][res_id] += output["pdbqt"] - pdbqt["flex"][res_id] += "END_RES %3s %1s%4d" % (res_id) + os_linesep - - # use non-flex lines for rigid part - for i, atom in enumerate(self._atoms): - if i not in pdbqt["flex_indices"] and atom["atom_type"] not in self.skip_types: - pdbqt["rigid"] += self.write_pdbqt_line(atom) - - return pdbqt, ok, err - - @staticmethod - def make_flexres_reactive(pdbqtstr, reactive_name, resname, prefix_atype="", residue_params=residue_params): - atom_names = residue_params[resname]["atom_names"] - bonds = residue_params[resname]["bonds"] - def get_neigh(idx, bonds): - neigh = set() - for (i, j) in bonds: - if i == idx: - neigh.add(j) - elif j == idx: - neigh.add(i) - return neigh - react_idx = atom_names.index(reactive_name) - one_bond_away = get_neigh(react_idx, bonds) - two_bond_away = set() - for i in one_bond_away: - for j in get_neigh(i, bonds): - if (j != react_idx) and (j not in one_bond_away): - two_bond_away.add(j) - names_1bond = [atom_names[i] for i in one_bond_away] - names_2bond = [atom_names[i] for i in two_bond_away] - new_pdbqt_str = "" - for i, line in enumerate(pdbqtstr.split(os_linesep)[:-1]): - if line.startswith("ATOM") or line.startswith("HETATM"): - name = line[12:16].strip() - atype = line[77:].strip() - if name == reactive_name: - new_type = prefix_atype + get_reactive_atype(atype, 1) - elif name in names_1bond: - new_type = prefix_atype + get_reactive_atype(atype, 2) - elif name in names_2bond: - new_type = prefix_atype + get_reactive_atype(atype, 3) - else: - new_type = atype - new_pdbqt_str += line[:77] + new_type + os_linesep - else: - new_pdbqt_str += line + os_linesep - return new_pdbqt_str - - def atoms(self, atom_idx=None): """Return the atom i diff --git a/scripts/mk_prepare_receptor.py b/scripts/mk_prepare_receptor.py index 7ea3dc78..63679e1a 100755 --- a/scripts/mk_prepare_receptor.py +++ b/scripts/mk_prepare_receptor.py @@ -36,11 +36,6 @@ path_to_this_script = pathlib.Path(__file__).resolve() -pkg_dir = pathlib.Path(pkg_init_path).parents[0] -templates_fn = str(pkg_dir / "data" / "residue_chem_templates.json") -with open(templates_fn) as f: - res_chem_templates = json.load(f) - def parse_cmdline_res(string): """ "A:5,7,BB:12C -> "A:5", "A:7", "BB:12C" """ @@ -153,6 +148,7 @@ def get_args(): io_group.add_argument( "--write_pdb", help="prepared receptor (must specify filename)", + nargs="*", metavar="PDB_FILENAME", ) io_group.add_argument( @@ -174,7 +170,7 @@ def get_args(): config_group.add_argument("-n", "--set_template", help="e.g. A:5,7=CYX,B:17=HID") config_group.add_argument("-d", "--delete_residues", help="e.g. A:350,B:15,16,17") config_group.add_argument("-b", "--blunt_ends", help="e.g. A:123,200=2,A:1=0") - config_group.add_argument("--add_templates", help="[.json]", metavar="JSON_FILENAME") + config_group.add_argument("--add_templates", help="[.json]", metavar="JSON_FILENAME", nargs="+", default=[]) config_group.add_argument("--mk_config", help="[.json]", metavar="JSON_FILENAME") config_group.add_argument( "-a", "--allow_bad_res", @@ -479,23 +475,9 @@ def get_args(): mk_prep = MoleculePreparation() # load templates for mapping -if args.add_templates is not None: - with open(args.add_templates) as f: - more_templates = json.load(f) - bad_keys = set() - for key, values in more_templates.items(): - if key not in res_chem_templates: - bad_keys.add(key) - else: - res_chem_templates[key].update(values) - if len(bad_keys): - msg = "Unrecognized keys provided in add_templates:" + os_linesep - msg += f"{bad_keys=}" + os_linesep - msg += f"allowed keys: {res_chem_templates.keys()}" + os_linesep - msg += f"see template file: {templates_fn}" + os_linesep - print(msg, file=sys.stderr) - sys.exit(2) -templates = ResidueChemTemplates.from_dict(res_chem_templates) +templates = ResidueChemTemplates.create_from_defaults() +for fn in args.add_templates: + templates.add_json_file(fn) # create polymers if args.read_with_prody is not None: diff --git a/test/flexres_export_test.py b/test/flexres_export_test.py index 938c0781..38898765 100644 --- a/test/flexres_export_test.py +++ b/test/flexres_export_test.py @@ -13,11 +13,7 @@ j3r_docked = pkgdir / "test/polymer_data/just-three-residues_vina_flexres.pdbqt" j3r_idx_docked = pkgdir / "test/polymer_data/just-three-residues_vina_flexres_idxmap.pdbqt" -meekodir = pathlib.Path(meeko.__file__).parents[0] - -with open(meekodir / "data" / "residue_chem_templates.json") as f: - t = json.load(f) -chem_templates = ResidueChemTemplates.from_dict(t) +chem_templates = ResidueChemTemplates.create_from_defaults() mk_prep = MoleculePreparation( merge_these_atom_types=["H"], charge_model="gasteiger", diff --git a/test/json_serialization_test.py b/test/json_serialization_test.py index b48674f1..217b37ce 100644 --- a/test/json_serialization_test.py +++ b/test/json_serialization_test.py @@ -34,7 +34,6 @@ # from ..meeko.utils.pdbutils import PDBAtomInfo pkgdir = pathlib.Path(meeko.__file__).parents[1] -meekodir = pathlib.Path(meeko.__file__).parents[0] # Test Data ahhy_example = pkgdir / "test/polymer_data/AHHY.pdb" @@ -43,9 +42,7 @@ ) # Polymer creation data -with open(meekodir / "data" / "residue_chem_templates.json") as f: - t = json.load(f) -chem_templates = ResidueChemTemplates.from_dict(t) +chem_templates = ResidueChemTemplates.create_from_defaults() mk_prep = MoleculePreparation() diff --git a/test/polymer_creation_test.py b/test/polymer_creation_test.py index 9f07b871..762b0e00 100644 --- a/test/polymer_creation_test.py +++ b/test/polymer_creation_test.py @@ -14,7 +14,6 @@ pkgdir = pathlib.Path(meeko.__file__).parents[1] -meekodir = pathlib.Path(meeko.__file__).parents[0] ahhy_example = pkgdir / "test/polymer_data/AHHY.pdb" just_one_ALA_missing = ( @@ -35,9 +34,7 @@ # TODO: add checks for untested polymer fields (e.g. input options not indicated here) -with open(meekodir / "data" / "residue_chem_templates.json") as f: - t = json.load(f) -chem_templates = ResidueChemTemplates.from_dict(t) +chem_templates = ResidueChemTemplates.create_from_defaults() mk_prep = MoleculePreparation( merge_these_atom_types=["H"], charge_model="gasteiger",