babel2 test.sdf out.mol2 babel2 -s test.sdf out.mol2
convert 1cxv.pdb 1cxv.mol2
convert.py \
--i=1cxv.pdb \
--o=1cxv.smi
convert.py (PDB -> SMILES):
mols in: 1 mols out: 1
Total: 1 mols processed.
convert.py \
--i=1cxv.pdb \
--o=1cxv.smi \
--pdbiDefault \
--pdbiTerMask
convert.py (PDB -> SMILES):
mols in: 3 mols out: 3
Total: 3 mols processed.
molcount -i ~/data/3d/MMFF94.mol2 molcnt: 752 confcnt: 753 avg conf/mol: 1.0 752 molcount -i ~/data/3d/MMFF94.mol2 -titles molcnt: 753 confcnt: 753 avg conf/mol: 1.0 753 molcount -i ~/data/3d/MMFF94.mol2 -v ... 744. FE2PW3: 2 confs ... molcount -i ~/data/3d/MMFF94.mol2 -titles ... 744. FE2PW3: 1 confs 745. FE3PW3: 1 confs ...
babel3 \ -i 1cxv.pdb \ -o 1cxv.smi \ -pdbiConnect \ -pdbiTerMask \ -pdbiBondOrder \ -pdbiImplicitH \ -pdbiTerMask babel3: input format: PDB (flavored) babel3: input flavor: 0B07 babel3: mols in: 3 babel3: confs in: 3 babel3: output format: SMILES babel3: output flavor: 4024 (default) babel3: mols out: 3 babel3: errors: 0 babel3: warnings: 0
Use test.sdf for uploaded input.
fixmols.py \
--i=drugs.sdf \
--o=drugs.fixed.sdf \
--v
match: [Nv3X3;!$(N~[!#6;!#1]):1]>>[N+:1] charged amine
CC(C)NCC(COc1ccc(cc1)CC(=O)N)O -> CC(C)[NH+]CC(COc1ccc(cc1)CC(=O)[NH2+])O
match: [O:1]=[C:2]-[O:3][#1:4]>>[O:1]=[C:2]-[O:3] carboxylic acid (1)
match: [O:1]=[C:2][OD1-0:3]>>[O:1]=[C:2][O-:3] carboxylic acid (2)
CC(=O)Oc1ccccc1C(=O)O -> CC(=O)Oc1ccccc1C(=O)[O-]
match: [Nv3X3;!$(N~[!#6;!#1]):1]>>[N+:1] charged amine
c1nc2c(=O)[nH]c(nc2n1COCCO)N -> c1nc2c(=O)[nH]c(nc2n1COCCO)[NH2+]
match: [Nv3X3;!$(N~[!#6;!#1]):1]>>[N+:1] charged amine
CC(C)NCC(COc1ccccc1CC=C)O -> CC(C)[NH+]CC(COc1ccccc1CC=C)O
match: [Nv3X3;!$(N~[!#6;!#1]):1]>>[N+:1] charged amine
Cc1c(c(=O)n(n1C)c2ccccc2)N(C)C -> Cc1c(c(=O)n(n1C)c2ccccc2)[N+](C)C
Cn1cnc2c1c(=O)n(c(=O)n2C)C -> Cn1cnc2c1c(=O)n(c(=O)n2C)C
1 mols fixed by: carboxylic acid (1)
1 mols fixed by: carboxylic acid (2)
4 mols fixed by: charged amine
fixmols.py: 6 mols; 5 fixed
aromodels
OEChem version: 1.3.4 built: 20050812
pi-electrons for each atomtype, aromodel
(dash means non-aromatic)
OpenEye Daylight Tripos MDL MMFF
C( 1): 1 1 1 1 1
C_Exo( 2): 1 1 - - -
C_EnegExo( 3): 0 0 - - -
C2_Minus( 4): 1 1 - - -
C3_Minus( 5): 2 2 - - -
C2_Plus( 6): 1 1 - - -
C3_Plus( 7): 0 0 - - -
N_Pyridine( 8): 1 1 1 1 1
N_Pyrole( 9): 2 2 - - 2
N_Oxide(10): 1 1 - 1 -
N_Oxide_Plus(11): 0 1 - - -
N_Minus(12): 2 2 - - 2
N_Plus(13): 1 1 1 1 1
O(14): 2 2 - - 2
O_Plus(15): 1 1 - - -
S(16): 2 2 - - 2
S_Plus(17): 1 1 - - -
S_Oxide_Plus(18): 2 2 - - -
P_Pyridine(19): 1 1 - - -
P_Pyrole(20): 2 2 - - -
P_Oxide(21): 1 1 - - -
P_Oxide_Plus(22): 0 1 - - -
P_Minus(23): 2 2 - - -
P_Plus(24): 1 1 - - -
Si(25): - - - - -
Se(26): 2 2 - - -
Se_Plus(27): 1 1 - - -
Te(28): 2 - - - -
Te_Plus(29): 1 - - - -
As(30): 2 2 - - -
aromatest.py caffeine.sdf
Canonical SMILES; flavored by aromaticity model:
caffeine
OEWriteMolecule(): Cn1cnc2c1c(=O)n(c(=O)n2C)C caffeine
OEAroModelOpenEye: Cn1cnc2c1c(=O)n(c(=O)n2C)C
OEAroModelDaylight: Cn1cnc2c1c(=O)n(c(=O)n2C)C
OEAroModelTripos: CN1C=NC2=C1C(=O)N(C(=O)N2C)C
OEAroModelMMFF: Cn1cnc2c1C(=O)N(C(=O)N2C)C
OEAroModelMDL: CN1C=NC2=C1C(=O)N(C(=O)N2C)C
3 cansmi variation[s]
kekule: CN1C=NC2=C1C(=O)N(C(=O)N2C)C
filter -filter filter_allpass.txt -pkanorm true \ -in drugs.sdf \ -out drugs.fixed.sdf
rings \
-i caffeine.sdf \
-vv
1. caffeine
1. ring(5): c1cnc[nH]1 C5 C8 N4 C7 N3
2. ring(6): c1cc[nH]c[nH2]1 N1 C2 N2 C4 C5 C8
3. ring(9): c1c2c([nH]c[nH2]1)nc[nH]2 N1 C2 N2 C4 C5 N3 C7 N4 C8
ringsystem 1: *=c1c2c(ncn2*)n(c(=*)n1*)*
rings: mols in: 1 out: 0 rings: 3 ringsystems: 1
molanalyze.py --i=paxil.mol
-----------------------------------------------------------------------------
MOL# 1
title: Paxil
comment:
atoms: 25 bonds: 27
heavy atoms: 25 heavy atom bonds: 27
mol formula: C19H21ClFNO3
components: 2 Frerejacque: 4
avg molecular weight: 344.659
O: 47.998 (13.9%)
F: 18.998 ( 5.5%)
Cl: 35.453 (10.3%)
C: 228.203 (66.2%)
N: 14.007 ( 4.1%)
ringsystem [1]: c1ccc2c(c1)OCO2
ringsystem [1]: c1ccccc1
ringsystem [1]: C1CC[NH2]CC1
total rings: 3
formal dimension of mol: 2
observed dimension of mol: 2
length of mol (C9 <-> C19): 6.260
path length: 10
chiral atom centers: 2
rotatable bonds: 4
chiral double bonds: 0
mol total formal charge: 0
mol total partial charge: 0.00
screen.py --i=test.sdf --o=z.smi --v
1. CC(C)(C)c1cc[n+](cc1)COC[n+]2ccc(cc2)C(C)(C)C.O.[Cl-].[Cl-]
2. C[N+](C)(C)CCO.O[Si](O)(O)[O-]
rejected (smarts 0)
rejected (minmwt)
3. Cc1cc(nc2c1c(c(cc2NC(C)CCC(=O)O)OC)Oc3cccc(c3)C(F)(F)F)OC.OS(=O)(=O)O
4. CCOC(=O)CCC(C)C1CCC2C1(CCC3C2C(=O)CC4C3(CCC(=O)C4)C)C
5. O.F[Co]F
rejected (smarts 0)
rejected (minmwt)
6. O=S1(=O)O[Eu](O1)OS(=O)(=O)O[Eu]2OS(=O)(=O)O2
rejected (smarts 0)
7. CN1C2CCC1CC(C2)OC(=O)Cc3ccccc3F.Cl
8. C[n+]1c2ccccn2cc1c3ccc(cc3)C=NNC(=O)C(=O)NN=Cc4ccc(cc4)c5cn6ccccc6[n+]5C.[Br-].[Br-]
rejected (maxmwt)
9. Cc1ccc(cc1)S(=O)(=O)[O-].Cc1ccc(cc1)S(=O)(=O)[O-].C[n+]1c2ccccn2cc1c3ccc(cc3)C=NNC(=S)NN=Cc4ccc(cc4)c5cn6ccccc6[n+]5C.O
rejected (maxmwt)
10. CCN(CC)CCCC(C)Nc1ccnc2c1ccc(c2)Cl.CC(CCC(=O)O)C1CCC2C1(C(CC3C2C(CC4C3(CCC(C4)O)C)O)O)C
rejected (maxmwt)
11. c1cc(c(cc1[I+]c2ccc(c(c2)Cl)Cl)Cl)Cl.c1cc(c(cc1[I+]c2ccc(c(c2)Cl)Cl)Cl)Cl.[O-]S(=O)(=O)[O-]
rejected (maxmwt)
12. c1cc(c(cc1[As]=[Bi][As](c2ccc(c(c2)NCS(=O)(=O)[O-])O)[Bi]=[As]c3ccc(c(c3)NCS(=O)(=O)[O-])O)NCS(=O)(=O)[O-])O.[Na+].[Na+].[Na+]
rejected (smarts 0)
rejected (maxmwt)
rejected (maxhbd)
rejected (maxrot)
13. CC(C)(C)c1cc(cc(c1OP(=O)(c2ccccc2)Oc3c(cc(cc3Br)C#N)C(C)(C)C)Br)C#N
rejected (maxmwt)
screen.py: in: 13 out: 4
mwtlo (<200): 2 mwthi(>600): 6
rotlo (<0): 0 rothi (>12): 1
hbdlo (<0): 0 hbdhi (>5): 1
hbalo (<0): 0 hbahi (>10): 0
0. badatoms: 4 [!#1!#6!#7!#8!#15!#16!F!Cl!Br!I]
1. wildcard: 0 [#0]
Upload test.sdf.
mcss \
-qfile NSC13.sdf \
-i NSC13157.mol
N(=C1[C]C=CC=C1)[C]C=[CH] MCSS(NSC 13,NSC 13157) [10a/10b]
mcss: 1 molecules processed
mcss: 1 mcses reported
mcss \
-vv \
-atom_expr AnyAtom \
-bond_expr AnyBond \
-qfile NSC13.sdf \
-i NSC13157.mol
atom expr: AnyAtom (0)
bond expr: AnyBond (0)
molecule 0: NSC 13157
molQ: c1cc2c(ccnc2cc1Cl)N
mol: c1ccc2c(c1)nc3ccccc3n2
match 1/76 (12a/11b): [cH]c[c]c(c[c]Cl)ncc[c]N ->
[cH]cc[c]nc(cc[cH])[c]n[c]
Cl1-> C9 -1.636, 1.122, 0.000 -> 1.706, -0.109, 0.000
N1-> N2 1.070, 0.992, 0.000 -> 1.070, 0.992, 0.000
C1->C12 -0.196, 1.025, 0.000 -> 0.000, 0.000, 0.000
C2->C10 0.440, 0.658, 0.000 -> 1.070, -1.195, 0.000
C3->C11 -0.832, 0.658, 0.000 -> 0.000, 0.000, 0.000
C4-> C8 0.440, -0.077, 0.000 -> 1.706, 0.625, 0.000
C5-> C2 -0.832, -0.077, 0.000 -> 0.440, 0.658, 0.000
C6-> N1 -0.196, -0.444, 0.000 -> -1.636, 1.122, 0.000
C7-> C4 1.070, -0.477, 0.000 -> 0.440, -0.077, 0.000
C8-> C5 1.706, 0.625, 0.000 -> -0.832, -0.077, 0.000
C9-> C6 1.706, -0.109, 0.000 -> -0.196, -0.444, 0.000
N2-> C3 1.070, -1.195, 0.000 -> -0.832, 0.658, 0.000
[CH]C=CC(=N[C]C=C[CH])[C]=N[C] MCSS(NSC 13,NSC 13157) [12a/11b]
mcss: 1 molecules processed
mcss: 1 mcses reported
molalign.py \ --v \ --roulette \ --i=nci_quinolines2d.sdf \ --o=nci_quinolines2d_roulette.sdf roulette spin: 274.3 degrees roulette spin: 203.6 degrees roulette spin: 126.7 degrees roulette spin: 64.3 degrees roulette spin: 197.6 degrees ... molalign.py: in: 19 out: 19 molalign.py \ --v \ --template=NSC13157.mol \ --i=nci_quinolines2d_roulette.sdf \ --o=nci_quinolines2d_aligned2.sdf 1. NSC 3092 rou=274.3 Cc1cc2c(cc1N)nc3cc(ccc3n2)N(C)C.Cl pre-aligned n=14 rms=2.391 match: c1ccc2c(c1)nc3ccccc3n2 (14a/16b) rms=0.033 2. NSC 5009 rou=203.6 *.CCN(CC)c1ccc2=Nc3ccc(cc3N(=c2c1)c4ccccc4)N(CC)CC.[Cl-] pre-aligned n=14 rms=2.798 match: c1ccc2=Nc3ccccc3N=c2c1 (14a/16b) rms=0.047 3. NSC 5493 rou=126.7 c1ccc(cc1)Nc2cc-3nc4ccccc4n(c3cc2=N)c5ccccc5.Cl pre-aligned n=14 rms=3.141 match: c1ccc-2nc3ccccc3[nH]c2c1 (14a/16b) rms=0.015 4. NSC 5756 rou=64.3 Cc1cc2c(cc1N)nc3cc(ccc3n2)N(C)C.Cl pre-aligned n=14 rms=2.802 match: c1ccc2c(c1)nc3ccccc3n2 (14a/16b) rms=0.028 5. NSC 6945 rou=197.6 c1ccc2c(c1)c3ccccc3c4c2nc5ccccc5n4 pre-aligned n=14 rms=0.504 match: c1cc2c(cc1)nc3ccccc3n2 (14a/16b) rms=0.244 ... molalign.py: in: 19 out: 19 aligned: 19Then view compounds with viewmol.
Try good_mcss_example1.sdf and good_mcss_example2.sdf, then try Kekule, then try any-atom matching.
molgeom -i drugs.sdf
atenolol formal dimension of mol: 3 perceived dimension of mol: 3 length of mol (N14,C17): 13.82 bond lengths: 0 1 C:C 1.39 0 2 C:C 1.39 0 3 C-O 1.36 1 4 C:C 1.38 2 5 C:C 1.38 3 6 O-C 1.43 4 7 C:C 1.38 5 7 C:C 1.38 6 8 C-C 1.53 7 9 C-C 1.51 8 10 C-C 1.53 8 11 C-O 1.43 9 12 C-C 1.51 10 13 C-N 1.47 12 14 C-N 1.35 12 15 C=O 1.21 13 16 N-C 1.47 16 17 C-C 1.53 16 18 C-C 1.53 bond angles: 0 1 4 C:C:C 119.94 0 2 5 C:C:C 119.93 0 3 6 C-O-C 106.80 1 0 2 C:C:C 119.89 1 0 3 C:C-O 120.05 1 4 7 C:C:C 120.06 2 0 3 C:C-O 120.05 2 5 7 C:C:C 120.06 3 6 8 O-C-C 109.47 4 7 5 C:C:C 120.11 4 7 9 C:C-C 119.95 5 7 9 C:C-C 119.95 6 8 10 C-C-C 109.47 6 8 11 C-C-O 109.47 7 9 12 C-C-C 109.47 8 10 13 C-C-N 109.47 9 12 14 C-C-N 120.00 9 12 15 C-C=O 120.00 10 8 11 C-C-O 109.47 10 13 16 C-N-C 106.70 13 16 17 N-C-C 109.47 13 16 18 N-C-C 109.47 14 12 15 N-C=O 120.00 17 16 18 C-C-C 109.47 torsion angles: 0 3 6 8 C-O-C-C 180.00 1 0 3 6 C:C-O-C 180.00 2 0 3 6 C:C-O-C 0.21 3 6 8 10 O-C-C-C -180.00 3 6 8 11 O-C-C-O -60.00 4 7 9 12 C:C-C-C 90.00 5 7 9 12 C:C-C-C -90.04 6 8 10 13 C-C-C-N -180.00 7 9 12 14 C-C-C-N -180.00 7 9 12 15 C-C-C=O -0.00 8 10 13 16 C-C-N-C -180.00 10 13 16 17 C-N-C-C 150.00 10 13 16 18 C-N-C-C -90.01 11 8 10 13 O-C-C-N 60.01 6 member ring: c1ccccc1 avg torsion (pucker): 0.48 ...
molgeom.py --i=drugs.sdf
setrotor.py 'O1 C6 C8 C10 0 180 45' atenolol.mol2 out.mol2
rmsd \
-ref dopamine.mol2 \
-i dopamine.om.mol2 \
-o out.mol2 \
-nooverlay
dopamine(0) dopamine(0): rmsd: 1.1483
dopamine(0) dopamine(1): rmsd: 1.4090
dopamine(0) dopamine(2): rmsd: 1.4893
dopamine(0) dopamine(3): rmsd: 1.2453
dopamine(0) dopamine(4): rmsd: 0.8468
dopamine(0) dopamine(5): rmsd: 1.1356
dopamine(0) dopamine(6): rmsd: 0.8936
dopamine(0) dopamine(7): rmsd: 1.0991
rmsd: mols: 1
rmsd \
-ref dopamine.mol2 \
-i dopamine.om.mol2 \
-o out.mol2 \
-nooverlay \
-vv
numconfs=8 maxconfid=8
dopamine(0) dopamine(0): rmsd: 0.6245
trans: 0.33,0.13,-2.07
rot: 0.98,-0.03,0.17,-0.04,0.93,0.37,-0.17,-0.37,0.91
dopamine(0) dopamine(1): rmsd: 1.0270
trans: 0.60,-0.26,-0.02
rot: 1.00,0.09,0.03,-0.08,0.98,-0.19,-0.04,0.19,0.98
dopamine(0) dopamine(2): rmsd: 1.0077
trans: 1.29,-0.35,0.09
rot: 0.96,0.24,0.15,-0.20,0.95,-0.24,-0.20,0.20,0.96
dopamine(0) dopamine(3): rmsd: 0.6133
trans: 0.84,0.17,-1.85
rot: 0.94,0.06,0.33,-0.16,0.94,0.29,-0.30,-0.32,0.90
dopamine(0) dopamine(4): rmsd: 0.0519
trans: 0.77,0.26,-1.49
rot: 0.97,0.05,0.23,-0.10,0.97,0.23,-0.21,-0.24,0.95
dopamine(0) dopamine(5): rmsd: 0.7097
trans: 1.00,-0.03,-0.22
rot: 0.98,0.15,0.12,-0.13,0.98,-0.12,-0.13,0.11,0.99
dopamine(0) dopamine(6): rmsd: 0.5530
trans: 0.46,0.19,-1.26
rot: 1.00,0.02,0.01,-0.02,0.99,0.15,-0.00,-0.15,0.99
dopamine(0) dopamine(7): rmsd: 0.4734
trans: 1.37,0.11,-0.66
rot: 0.93,0.19,0.33,-0.19,0.98,-0.03,-0.33,-0.04,0.94
rmsd: mols: 1
rmsd.py \ --ref=dopamine.mol2 \ --i=dopamine.om.mol2 \ --o=out.mol2 \ --overlay \ --v
rmsd_selftest -i dopamine.om.mol2 -vv
1. dopamine: nconfs=8 c1cc(c(cc1CC[NH3+])O)O Minimum global rmsd vs number of conformations rmsd min: nconfs 0.00: 8 0.20: 8 0.40: 8 0.60: 4 0.80: 1 Global pairwise rmsd analysis: min rmsd[4][7]: 0.50 max rmsd[1][3]: 1.23 avg rmsd: 0.80 frequencies: 0.00-0.20: 0 ( 0.0% -> 0.0%) 0.20-0.40: 0 ( 0.0% -> 0.0%) 0.40-0.60: 6 ( 21.4% -> 21.4%) 0.60-0.80: 10 ( 35.7% -> 57.1%) 0.80-1.00: 5 ( 17.9% -> 75.0%) 1.00-1.20: 5 ( 17.9% -> 92.9%) 1.20-1.40: 2 ( 7.1% ->100.0%) 1.40-1.60: 0 ( 0.0% ->100.0%) 1.60-1.80: 0 ( 0.0% ->100.0%) 1.80-2.00: 0 ( 0.0% ->100.0%) 2.00-2.20: 0 ( 0.0% ->100.0%) 2.20-2.40: 0 ( 0.0% ->100.0%) 2.40-2.60: 0 ( 0.0% ->100.0%) 2.60-2.80: 0 ( 0.0% ->100.0%) 2.80-3.00: 0 ( 0.0% ->100.0%) 3.00+: 0 ( 0.0% ->100.0%) total rmsds: 28 Max/min rmsd analysis (near- and far-conformer): avg min rmsd: 0.55 avg max rmsd: 1.09 frequencies: min max 0.00-0.20: 0 ( 0.0% -> 0.0%) 0 ( 0.0% -> 0.0%) 0.20-0.40: 0 ( 0.0% -> 0.0%) 0 ( 0.0% -> 0.0%) 0.40-0.60: 8 (100.0% ->100.0%) 0 ( 0.0% -> 0.0%) 0.60-0.80: 0 ( 0.0% ->100.0%) 0 ( 0.0% -> 0.0%) 0.80-1.00: 0 ( 0.0% ->100.0%) 2 ( 25.0% -> 25.0%) 1.00-1.20: 0 ( 0.0% ->100.0%) 2 ( 25.0% -> 50.0%) 1.20-1.40: 0 ( 0.0% ->100.0%) 4 ( 50.0% ->100.0%) 1.40-1.60: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 1.60-1.80: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 1.80-2.00: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 2.00-2.20: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 2.20-2.40: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 2.40-2.60: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 2.60-2.80: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 2.80-3.00: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) 3.00+: 0 ( 0.0% ->100.0%) 0 ( 0.0% ->100.0%) rmsd_min=0.50 rmsd_max=1.23 Global pairwise variance analysis: min var[4][7]: 0.38 (rmsd[4][7]= 0.50) max var[2][0]: 1.80 (rmsd[2][0]= 1.23) var_min=0.38 var_max=1.80 Global pairwise max-distance analysis: min maxd[4][7]: 2.08 (rmsd[4][7]= 0.50) max maxd[1][3]: 4.38 (rmsd[1][3]= 1.23) maxd_min=2.08 maxd_max=4.38 rmsd_selftest: total mols: 1 confs: 8
movemol \ -i dopamine.mol2 \ -o out.mol2 \ -center \ -rotz 45 \ -trans "5.0,-5.0,1.7" \ -vv c1cc(c(cc1CC[NH3+])O)O formal dimension of mol: 3 centered from: -0.411,-5.093,-2.364 z-rotating: 45.000 deg trans: 5.000,-5.000,1.700
molalign.py \
--v \
--template=NSC13157_3d.mol \
--i=nci_quinolines_3d.oeb \
--o=nci_quinolines_3d_aligned.oeb
...
310. NSC 16219
CCN(CC)c1ccc2c(c1)n(c-3cc(=O)c4ccccc4c3n2)c5ccccc5
pre-aligned n=14 rms=6.581
match: c1ccc-2nc3ccccc3[nH]c2c1 (14a/16b) rms=0.105
311. NSC 16219
CCN(CC)c1ccc2c(c1)n(c-3cc(=O)c4ccccc4c3n2)c5ccccc5
pre-aligned n=14 rms=6.581
match: c1ccc-2nc3ccccc3[nH]c2c1 (14a/16b) rms=0.105
312. NSC 16219
CCN(CC)c1ccc2c(c1)n(c-3cc(=O)c4ccccc4c3n2)c5ccccc5
pre-aligned n=14 rms=6.581
match: c1ccc-2nc3ccccc3[nH]c2c1 (14a/16b) rms=0.105
313. NSC 16219
CCN(CC)c1ccc2c(c1)n(c-3cc(=O)c4ccccc4c3n2)c5ccccc5
pre-aligned n=14 rms=6.581
match: c1ccc-2nc3ccccc3[nH]c2c1 (14a/16b) rms=0.105
314. NSC 21661
c1ccc2c(c1)nc3ccc(cc3n2=O)Br
pre-aligned n=14 rms=6.905
match: c1ccc2c(c1)nc3ccccc3n2 (14a/16b) rms=0.105
molalign.py: in: 314 out: 314 aligned: 314
resanalyze.py --i=1cxv.pdb
resanalyze.py --i=1cxv.pdb --v
pdb2lig \ -i 1cxv.pdb \ -outlig 1cxv_lig.mol2 \ -outpro 1cxv_pro.pdb \ -metal \ -v 2953 atom input writing ligand to data/1cxv_lig.mol2 writing protein to data/1cxv_pro.pdb 1153 atom output protein part 131 atom output protein part 1153 atom output protein part 131 atom output protein part [Zn+2] included in protein [Zn+2] included in protein [Zn+2] included in protein [Zn+2] included in protein [Ca+2] included in protein [Ca+2] included in protein [Ca+2] included in protein [Ca+2] included in protein 28 atom output ligand c1cc(ccc1Oc2ccc(cc2)Cl)S(=O)(=O)C3(CCOCC3)CC(=O)NO 28 atom output ligand c1cc(ccc1Oc2ccc(cc2)Cl)S(=O)(=O)C3(CCOCC3)CC(=O)NO pdb2lig: ligand mols: 2 pdb2lig: waters discarded: 320 pdb2lig: other mols discarded: 0
pdb2lig.py \ --i=1cxv.pdb \ --outlig=1cxv_lig.mol2 \ --outpro=1cxv_pro.pdb \ --v writing ligand to 1cxv_lig.mol2 writing protein to 1cxv_pro.pdb 2953 atom input 1153 atom output protein part 131 atom output protein part 1153 atom output protein part 131 atom output protein part discarding [Zn+2] discarding [Zn+2] discarding [Zn+2] discarding [Zn+2] discarding [Ca+2] discarding [Ca+2] discarding [Ca+2] discarding [Ca+2] 28 atom output ligand 28 atom output ligand pdb2lig.py: ligand mols: 2 pdb2lig.py: waters discarded: 321 pdb2lig.py: other mols discarded: 8
bindanalyze.py \
--pro=1cxv_pro.pdb \
--lig=1cxv_lig.mol2
protein: COLLAGENASE-3
ligand: 1cxv.pdb ligand (COLLAGENASE-3)
Nearest 10 residues:
residue pro_atom lig_atom distance
GLU_202 OE2 968 O1 O 0 2.67
LEU_164 N 668 O5 O13 2.70
HIS_211 CE11033 O2 O 3 2.75
ILE_222 O 1111 C18 C25 3.06
HIS_205 NE2 990 O1 O 0 3.17
PHE_220 O 1093 C19 C26 3.22
ALA_165 O 679 N1 N 1 3.24
LEU_218 O 1077 C18 C25 3.25
THR_224 OG11133 Cl1 Cl27 3.26
HIS_201 NE2 959 O1 O 0 3.26
Nearest ionizable residues <10.00 angstroms:
residue pro_atom lig_atom distance
GLU_202 OE2 968 O1 O 0 2.67
HIS_211 CE11033 O2 O 3 2.75
HIS_205 NE2 990 O1 O 0 3.17
HIS_201 NE2 959 O1 O 0 3.26
HIS_166 CA 682 N1 N 1 4.09
ASP_210 OD11023 O2 O 3 7.25
ASP_158 OD1 637 O5 O13 7.34
HIS_179 O 776 O1 O 0 7.44
ASP_181 CB 798 O5 O13 7.45
ASP_237 OD21211 Cl1 Cl27 7.72
ASP_214 O 1053 C18 C25 7.97
GLU_184 OE2 826 O5 O13 7.99
ASP_177 O 763 O1 O 0 9.21
Possible hydrogen bonds <6.00 angstroms:
protein-ligand donor-acceptor pairs:
residue pro_atom lig_atom distance
TYR_155 OH 612 O2 0 5.05
HIS_211 ND11031 O2 0 4.06
protein-ligand acceptor-donor pairs:
residue pro_atom lig_atom distance
ALA_165 O 679 O1 0 3.60
HIS_201 O 953 O1 0 5.73
GLU_202 OE1 967 O1 0 3.32
ALA_165 O 679 N1 0 3.24
GLU_202 OE1 967 N1 0 4.12
ligand: 1cxv.pdb ligand (COLLAGENASE-3)
Nearest 10 residues:
residue pro_atom lig_atom distance
GLU_502 OE22253 O1 O 0 2.61
LEU_464 N 1953 O5 O13 2.67
HIS_511 CE12318 O2 O 3 2.77
ILE_522 O 2396 C18 C25 3.10
HIS_505 NE22275 O1 O 0 3.15
PHE_520 O 2378 C19 C26 3.20
ALA_465 O 1964 N1 N 1 3.23
THR_524 OG12418 Cl1 Cl27 3.26
HIS_501 NE22244 O1 O 0 3.27
LEU_518 O 2362 C18 C25 3.27
Nearest ionizable residues <10.00 angstroms:
residue pro_atom lig_atom distance
GLU_502 OE22253 O1 O 0 2.61
HIS_511 CE12318 O2 O 3 2.77
HIS_505 NE22275 O1 O 0 3.15
HIS_501 NE22244 O1 O 0 3.27
HIS_466 CA 1967 N1 N 1 4.15
ASP_510 OD12308 O2 O 3 7.28
ASP_458 OD21923 C4 C 6 7.35
ASP_481 CB 2083 O5 O13 7.45
HIS_479 O 2061 O1 O 0 7.47
ASP_537 OD22496 Cl1 Cl27 7.75
GLU_484 OE22111 O5 O13 7.89
ASP_514 O 2338 C18 C25 7.95
ASP_477 O 2048 O1 O 0 9.23
Possible hydrogen bonds <6.00 angstroms:
protein-ligand donor-acceptor pairs:
residue pro_atom lig_atom distance
HIS_511 ND12316 O2 0 4.06
protein-ligand acceptor-donor pairs:
residue pro_atom lig_atom distance
ALA_465 O 1964 O1 0 3.58
HIS_501 O 2238 O1 0 5.72
GLU_502 OE12252 O1 0 3.40
ALA_465 O 1964 N1 0 3.23
GLU_502 OE12252 N1 0 4.20
flipper.py \ --i=aspartame.smi \ --o=.ism \ --flipall COC(=O)[C@@H](Cc1ccccc1)NC(=O)[C@H](CC(=O)O)N Aspartame COC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(=O)O)N Aspartame COC(=O)[C@@H](Cc1ccccc1)NC(=O)[C@@H](CC(=O)O)N Aspartame COC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](CC(=O)O)N Aspartame RESULTS: 1 in -> 1 processed RESULTS: 4 stereoisomers out
frag.py \
--smarts="N1CCCCC1" \
--i=data/paxil.mol \
--addrgroups \
--v
1. Paxil
c1cc(ccc1F)[R2] Paxil
C1(CCNCC1[R1])[R2] Paxil
C(Oc1ccc2c(c1)OCO2)[R1] Paxil
Cl Paxil
nfrags=4
frag.py: 1 mols in; 4 frags out
frag.py \
--smarts="N1CCCCC1" \
--i=data/paxil.mol \
--monomersmi \
--v
1. Paxil
c1cc&2ccc1F Paxil
C&21CCNCC&11 Paxil
C&1Oc1ccc2c(c1)OCO2 Paxil
Cl Paxil
nfrags=4
frag.py: 1 mols in; 4 frags out
cat frankenmol.in S&1&2&3 [H]&1 C&1 F&2 Br&2 N&3 O&3 C&1CCN&2 [H]&1 N&1 O&1 F&2 Br&2 C&2(=O)O N&11C(=O)N&2C(=O)C(N&3C=N2)=C12 [H]&1 C&1 [H]&2 C&2 C&3 C&3(=O)O frankenmol.py \ --i=frankenmol.in \ --o=.ism N[SH+]F O[SH+]F N[SH+]Br O[SH+]Br C[S+](N)F C[S+](O)F C[S+](N)Br C[S+](O)Br [CH]CCNF [CH]CCNBr [CH]CCNC(=O)[O-] C(C[NH3+])CNF C(C[NH3+])CNBr C(C[NH3+])CNC(=O)[O-] C(CNF)CO C(CNBr)CO C(CNC(=O)[O-])CO Cn1cnc2c1c(=O)[nH]c(=O)[nH]2 c1nc2c(n1C(=O)[O-])c(=O)[nH]c(=O)[nH]2 Cn1cnc2c1c(=O)n(c(=O)[nH]2)C Cn1c(=O)c2c([nH]c1=O)ncn2C(=O)[O-] Cn1cnc2c1c(=O)[nH]c(=O)n2C Cn1c2c(c(=O)[nH]c1=O)n(cn2)C(=O)[O-] Cn1cnc2c1c(=O)n(c(=O)n2C)C Cn1c2c(c(=O)n(c1=O)C)n(cn2)C(=O)[O-] frankenmol.py results: in: 3 out: 25
echo 'Oc1ccccc1' \ | react \ -i .smi \ -smirks '[c:1][H]>>[n:1]' \ -uniq Oc1ccccc1>>Oc1ncccc1.Oc1cnccc1.Oc1ccncc1 react: in: 1 products: 3. echo 'Oc1ccccc1' \ | react \ -i .smi \ -smirks '[c:1][H]>>[n:1]' \ -uniq \ -maps \ -v smirks ok: "[c:1][H]>>[n:1]" (nreac=1) pcount: 3 Oc1[cH:1]cccc1>>Oc1[n:1]cccc1.Oc1c[n:1]ccc1.Oc1cc[n:1]cc1 react: in: 1 products: 3.
cansmi.py \ --i=caffeine.sdf cansmi.py \ --i=caffeine.sdf \ --kekule Cn1cnc2c1c(=O)n(c(=O)n2C)C caffeine Total: 1 mols processed. cansmi.py: in: 1 out: 1 errors: 0 cansmi.py \ --isomeric \ --i=aspartame.mol2 \ --from3d CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine Total: 1 mols processed. cansmi.py: in: 1 out: 1 errors: 0
rename.py 'Color' drugs.sdf .smi
renaming input file: data/drugs.sdf
using field: Color
output to: .smi
c1(ccc(cc1)CC(=O)N)OCC(CNC(C)C)O purple
c1(c(cccc1)OC(=O)C)C(=O)O red
c12c(ncn1COCCO)c(=O)[nH]c(n2)N blue
c1(c(cccc1)CC=C)OCC(CNC(C)C)O green
n1(c(=O)c(c(n1C)C)N(C)C)c2ccccc2 aminopy
c12c(n(c(=O)n(c1=O)C)C)ncn2C black
5 molecules renamed.
Total: 6 molecules processed.
sdf2csv.py drugs.sdf
Title,Energy,Color atenolol,-3.5,purple acetsali,1,red acyclovi,2,blue alprenol,3,green aminopy,4.5, caffeine,0,black
bitvectest
bv1 size=160...bitcount=55...recount=55 bv2 size=160...bitcount=75...recount=75 FP1 is 408713C1E87C000BD18187000F70000000FFB807 orig= 408713C1E87C000BD18187000F70000000FFB807 FP2 is 78EF93C1EE7FFF48018000005FF840BD9C0F9807 orig= 78EF93C1EE7FFF48018000005FF840BD9C0F9807 OETanimoto(bv1,bv2)=0.444 00000000111111110000111100000001->80FFFF07-> 11100000111111111111111100000001 bv1 = FFFF0000 = 00000000000000001111111111111111 bv1[0]=0 bv1[1]=0 bv1[15]=0 bv1[16]=1 bv1[31]=1 bv1[32]=0 ~bv1 = 0000FFFF = 11111111111111110000000000000000 bv2 = 00FF0011 = 10001000000000001111111100000000 bv1 & bv2 = 00FF0000 = 00000000000000001111111100000000 bv1 | bv2 = FFFF0011 = 10001000000000001111111111111111 OEBitVectorXor(bv1,bv2) = FF000011 = 10001000000000000000000011111111 OEBitVectorSub(bv1,bv2) = FF000000 = 00000000000000000000000011111111 bv1 = 00000000000000000000111100000000 OEBitVectorSub(bv1,bv2).IsEmpty()=1 (bv1 subset of bv2)