Filter Files

There are two parameter files a user can provide if they would like to override or augment the default parameter sets. The first is the “filter file”. It provides acceptable limits for all of the physical properties and functional groups in the default filter. The second is the “newrule file”. If you have a filter you like, but would like to augment it with a set of additional rules, these can be added with a newrule file.

There are four types of statements that can occur in a filter file:

  • physical property limits
  • rules
  • new rules
  • selections

The statements should occur one-per-line in the filter file.

Note

If the appropriate line is not in the filter file, or the value is false, the respective measure will not be used in filtering and its value will not be included in any table-based output.

Physical Property Limits

There are a large number of physical property limits. They occur as three fields on a line. For example:

MIN_HETEROATOMS 2 "Minimum number of heteroatoms"

The first field is the property keyword, the second field is the value assigned to that keyword, and the third field is a brief informational message. There are a fixed number of physical property keywords. No additional physical property keywords can be added by the user. The current keywords and brief definitions of each are listed below.

Hint

The values listed below are those found in the default BlockBuster filter.

Basic Properties

Molecular Weight

Isotopic molecular weight

MIN_MOLWT 130 "Minimum molecular weight"
MAX_MOLWT 781 "Maximum molecular weight"

Heavy Atom Count

Number of non-hydrogen atoms

MIN_NUM_HVY 9 "Minimum number of heavy atoms"
MAX_NUM_HVY 55 "Maximum number of heavy atoms"

Carbon Count

Number of carbons

MIN_CARBONS 3 "Minimum number of carbons"
MAX_CARBONS 41 "Maximum number of carbons"

Hetero-Count

Number of non-carbon and non-hydrogen atoms

MIN_HETEROATOMS 1 "Minimum number of heteroatoms"
MAX_HETEROATOMS 14 "Maximum number of heteroatoms"

Hetero-Atom to Carbon Ratio

Hetero-count/carbon-count

MIN_Het_C_Ratio 0.04 "Minimum heteroatom to carbon ratio"
MAX_Het_C_Ratio 4.0 "Maximum heteroatom to carbon ratio"

Chiral Count

Number of chiral atoms

MIN_CHIRAL_CENTERS 0 "Minimum chiral centers"
MAX_CHIRAL_CENTERS 21 "Maximum chiral centers"

Hydrogen-bond Acceptors

Number of atoms which match any of the following:

  • degree 2, aromatic, non-positive nitrogens
  • electron rich or negative, valence less than 4, non-aromatic nitrogens
  • negatively charged or not electron withdrawn and neutral oxygens
  • degree 1, double bonded, electron rich sulfur
MIN_HBOND_ACCEPTORS 0 "Minimum number of hydrogen-bond acceptors"
MAX_HBOND_ACCEPTORS 13 "Maximum number of hydrogen-bond acceptors"

Hydrogen-bond Donors

Number of hydrogen atoms on nitrogen, oxygen, or sulfur atoms

MIN_HBOND_DONORS 0 "Minimum number of hydrogen-bond donors"
MAX_HBOND_DONORS 9 "Maximum number of hydrogen-bond donors"

Lipinski Acceptors

Number of nitrogens or oxygens

MIN_LIPINSKI_ACCEPTORS 1 "Minimum number of oxygen & nitrogen atoms"
MAX_LIPINSKI_ACCEPTORS 14 "Maximum number of oxygen & nitrogen atoms"

Lipinski Donors

Number of nitrogens and oxygens with at least one hydrogen attached

MIN_LIPINSKI_DONORS 0 "Minimum number O & N atoms with hydrogens"
MAX_LIPINSKI_DONORS 6 "Maximum number O & N atoms with hydrogens"

Halide Fraction

Percent of molecular weight from halides

MIN_HALIDE_FRACTION 0.0 "Minimum Halide Fraction"
MAX_HALIDE_FRACTION 0.66 "Maximum Halide Fraction"

Formal Count

Number of atoms with a formal charge (excludes dative)

MIN_COUNT_FORMAL_CRG 0 "Minimum number formal charges"
MAX_COUNT_FORMAL_CRG 4 "Maximum number of formal charges"

Formal Sum

Total formal charge

MIN_SUM_FORMAL_CRG -2 "Minimum sum of formal charges"
MAX_SUM_FORMAL_CRG 2 "Maximum sum of formal charges"

Connected Non-Ring

Considers sets of contiguous (bonded) non-ring atoms

MIN_CON_NON_RING 0 "Minimum number of connected non-ring atoms"
MAX_CON_NON_RING 19 "Maximum number of connected non-ring atoms"

Unbranched Chains

The size of the longest chain of either heavy atoms or of all carbons. An unbranched atom is an atom with at most two connections to other heavy atoms and is not in a ring. A set of unbranched atoms which are connected together form a chain. A molecule may contain multiple chains which are isolated from each other by non-chain atoms (eg. ring or branched atoms). The longest chain of heavy atoms and the longest chain of carbons are identified, and the MIN and MAX parameter filters are applied.

MIN_UNBRANCHED 1 "Minimum number of connected unbranched non-ring atoms"
MAX_UNBRANCHED 13 "Maximum number of connected unbranched non-ring atoms"
MIN_UNBRANCHED_C 0 "Minimum number of connected unbranched non-ring carbon"
MAX_UNBRANCHED_C 6 "Maximum number of connected unbranched non-ring carbon"

Total Functional Group Count

Total number of functional groups. Does not count any ring-systems as functional groups. Degree 1 heteroatoms, particularly those with double bonds or dative bonds are considered part of ring systems and do not count as a functional group.

MIN_FCNGRP 0 "Minimum number of functional groups"
MAX_FCNGRP 7 "Maximum number of functional groups"

Note

This is different then the functional group rules.

Ring Systems

Number of ring systems (contiguous systems of ring atoms and bonds)

MIN_RING_SYS 0 "Minimum number of ring systems"
MAX_RING_SYS 5 "Maximum number of ring systems"

Ring Size

Maximum size of any single ring system

MIN_RING_SIZE 0 "Minimum atoms in any ring system"
MAX_RING_SIZE 20 "Maximum atoms in any ring system"

Rotor Count

Number of rotatable bonds. Allows optional adjustment for aliphatic rings following the method of [Oprea-2000].

MIN_ROT_BONDS 0 "Minimum number of rotatable bonds"
MAX_ROT_BONDS 16 "Maximum number of rotatable bonds"
ADJUST_ROT_FOR_RING true "BOOLEAN for whether to estimate degrees of freedom in rings"

Rigid Count

Number of rigid bonds (non-rotatable bonds)

MIN_RIGID_BONDS 4 "Minimum number of rigid bonds"
MAX_RIGID_BONDS 55 "Maximum number of rigid bonds"

Atom Type Checks

Check the validity of atom charges, valences or MMFF atom types for the entire molecule.

TYPECHECK     false "Screen for unusual valences or charges"
MMFFTYPECHECK false "Screen for atoms with unknown MMFF atom types"

LogP

The logP calculation is a derivative of the published XLogP algorithm [Wang-1997-2]., but reparameterized without the dependence on 3D coordinates or the SYBYL/Mol2 aromaticity model.

XLogP

Calculated LogP

MIN_XLOGP -3.0 "Minimum XLogP"
MAX_XLOGP 6.85 "Maximum XLogP"

Solubility

The solubility predictions are based on using the atom-types from the XLogP algorithm, [Wang-1997-2], and reparameterizing them based on available solubility data. Rather than a quantitative cutoff, solubility uses categories. The 6 allowable categories are:

  1. insoluble
  2. poorly
  3. moderately
  4. soluble
  5. very
  6. highly

These categories are keywords used in the filter files as follows.

Solubility

Calculated solubility class

MIN_SOLUBILITY insoluble "Minimum solubility"

Pharmacokinetic Predictors

Several secondary filters that are built upon published combinations of simpler properties are available.

Note

All of these properties are used for filtering in the default filters.

Lipinski Violations

Number of allowable Lipinski violations. A single Lipinski violation is considered acceptable. The published work, [Lipinski-1997], allows compounds to pass with a single violation but not multiple violations.

MAX_LIPINSKI 3 "Maximum number of Lipinski violations"

See also

The Lipinski theory section in the Molecular Properties and Predictors chapter.

PSA

Peter Ertl’s, [Ertl-2000], topological polar surface area (phosphorus and sulfur area is optional).

PSA_USE_SandP false "Count S and P as polar atoms"
MIN_2D_PSA 0.0 "Minimum 2-Dimensional (SMILES) Polar Surface Area"
MAX_2D_PSA 205.0 "Maximum 2-Dimensional (SMILES) Polar Surface Area"

See also

The PSA theory section in the Molecular Properties and Predictors chapter.

GSK/Veber

Veber’s measure of bioavailability (PSA > 140 or Rotatable bonds >10). [Veber-2002].

GSK_VEBER false "PSA>140 or >10 rot bonds"

Abbott/Martin

Yvonne Martin’s Abbott Bioavailability Score. This is reported as a probability that F>10% in rats. [Martin-2005]

MIN_ABS 0.11 "Minimum probability F>10% in rats"

Pharmacopia/Egan

Egan egg measure of bioavailability (LogP >5.88 or PSA > 131.6). [Egan-2000]

PHARMACOPIA false "LogP > 5.88 or PSA > 131.6"

Aggregators

Aggregators are small molecules that can interfere with assay results by sequestering protein in an aggregation of small molecules in solution. They appear to have activity in many assays, but in fact are usually not specific inhibitors of the protein in question. Includes two measures of whether a molecule is one of the aggregators defined by Shoichet et. al. [McGovern-2003] [Seidler-2003] The first measure, AGGREGATORS, is whether the molecule is an exact match to one of the approximately 400 published aggregators. The second measure, PRED_AGG, is whether the molecule hits in Shoichet’s QSAR model for predicting aggregators.

Aggregators

Whether a compound is known or predicted to aggregate in concentrations common in virtual screening.

AGGREGATORS true "Eliminate known aggregators"
PRED_AGG false "Eliminate predicted aggregators"

Elemental Filters

The elemental filters are applied in this order:

  1. Test for the existence of any of the metals in the ELIMINATE_METALS filter in the molecule.
  2. Remove salts by stripping away all the disconnected components except for the largest.
  3. Test to make sure only atoms specified in ALLOWED_ELEMENTS filter are in the molecule.

The format of the two elemental filter fields is the keyword followed by a comma delimited list of atomic symbols.

Eliminate Metals

Any molecule with the atoms indicated in ELIMINATE_METALS fail to pass the filter.

ELIMINATE_METALS Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd

Allowed Elements

Molecules with atoms other than those specified by ALLOWED_ELEMENTS fail to pass the filter.

ALLOWED_ELEMENTS H,C,N,O,F,P,S,Cl,Br,I

Functional Group Rules

Rules statements set the limits for the maximum number of the specified type of functional group that may be allowed in the molecule.

The first field of a rule statement is the word RULE in all capital letters. The second field is a number indicating the maximum number of the group allowed in a molecule. The third field is the functional group keyword. Functional-group keywords are case sensitive.

RULE 0 acid_halide

The following is a list of functional groups which filter recognizes by default. Three example matches are provided with the atoms that correspond to each other highlighted.

Note

Due to the highly complex nature of the patterns, in particular recursive SMARTS, it is not possible to fully highlight every atom that was included as part of the match.

acetal

../_images/acetal-001.png ../_images/acetal-002.png ../_images/acetal-003.png

acid

../_images/acid-001.png ../_images/acid-002.png ../_images/acid-003.png

acid_chloride

../_images/acid_chloride-001.png ../_images/acid_chloride-002.png ../_images/acid_chloride-003.png

acid_halide

../_images/acid_halide-001.png ../_images/acid_halide-002.png ../_images/acid_halide-003.png

acyclic_NCN

../_images/acyclic_NCN-001.png ../_images/acyclic_NCN-002.png ../_images/acyclic_NCN-003.png

acyclic_NS

../_images/acyclic_NS-001.png ../_images/acyclic_NS-002.png ../_images/acyclic_NS-003.png

acyl_cyanides

../_images/acyl_cyanides-001.png ../_images/acyl_cyanides-002.png ../_images/acyl_cyanides-003.png

acylhydrazide

../_images/acylhydrazide-001.png ../_images/acylhydrazide-002.png ../_images/acylhydrazide-003.png

alcohol

../_images/alcohol-001.png ../_images/alcohol-002.png ../_images/alcohol-003.png

aldehyde

../_images/aldehyde-001.png ../_images/aldehyde-002.png ../_images/aldehyde-003.png

alkene

../_images/alkene-001.png ../_images/alkene-002.png ../_images/alkene-003.png

alkyl

../_images/alkyl-001.png ../_images/alkyl-002.png ../_images/alkyl-003.png

alkyl_halide

../_images/alkyl_halide-001.png ../_images/alkyl_halide-002.png ../_images/alkyl_halide-003.png

alkyl_phosphate

../_images/alkyl_phosphate-001.png ../_images/alkyl_phosphate-002.png ../_images/alkyl_phosphate-003.png

alkylaniline

../_images/alkylaniline-001.png ../_images/alkylaniline-002.png ../_images/alkylaniline-003.png

alkylating_agent

../_images/alkylating_agent-001.png ../_images/alkylating_agent-002.png ../_images/alkylating_agent-003.png

alkyne

../_images/alkyne-001.png ../_images/alkyne-002.png ../_images/alkyne-003.png

alphahalo_amine

../_images/alphahalo_amine-001.png ../_images/alphahalo_amine-002.png ../_images/alphahalo_amine-003.png

alphahalo_ketone

../_images/alphahalo_ketone-001.png ../_images/alphahalo_ketone-002.png ../_images/alphahalo_ketone-003.png

amide

../_images/amide-001.png ../_images/amide-002.png ../_images/amide-003.png

aminal

../_images/aminal-001.png ../_images/aminal-002.png ../_images/aminal-003.png

amine

../_images/amine-001.png ../_images/amine-002.png ../_images/amine-003.png

amino_acid

../_images/amino_acid-001.png ../_images/amino_acid-002.png ../_images/amino_acid-003.png

anhydride

../_images/anhydride-001.png ../_images/anhydride-002.png ../_images/anhydride-003.png

aniline

../_images/aniline-001.png ../_images/aniline-002.png ../_images/aniline-003.png

aniline_unsubstituted

../_images/aniline_unsubstituted-001.png ../_images/aniline_unsubstituted-002.png ../_images/aniline_unsubstituted-003.png

arene

../_images/arene-001.png ../_images/arene-002.png ../_images/arene-003.png

arenesulfonyl

../_images/arenesulfonyl-001.png ../_images/arenesulfonyl-002.png ../_images/arenesulfonyl-003.png

aryl

../_images/aryl-001.png ../_images/aryl-002.png ../_images/aryl-003.png

aryl_halide

../_images/aryl_halide-001.png ../_images/aryl_halide-002.png ../_images/aryl_halide-003.png

aryl_mono_BrI

../_images/aryl_mono_BrI-001.png ../_images/aryl_mono_BrI-002.png ../_images/aryl_mono_BrI-003.png

azide

../_images/azide-001.png ../_images/azide-002.png ../_images/azide-003.png

aziridine

../_images/aziridine-001.png ../_images/aziridine-002.png ../_images/aziridine-003.png

azo

../_images/azo-001.png ../_images/azo-002.png ../_images/azo-003.png

azocyanamides

../_images/azocyanamides-001.png ../_images/azocyanamides-002.png ../_images/azocyanamides-003.png

base

../_images/base-001.png ../_images/base-002.png ../_images/base-003.png

benzyl_ether

../_images/benzyl_ether-001.png ../_images/benzyl_ether-002.png ../_images/benzyl_ether-003.png

benzyloxycarbonyl_CBZ

../_images/benzyloxycarbonyl_CBZ-001.png ../_images/benzyloxycarbonyl_CBZ-002.png ../_images/benzyloxycarbonyl_CBZ-003.png

beta_azo_carbonyl

../_images/beta_azo_carbonyl-001.png ../_images/beta_azo_carbonyl-002.png ../_images/beta_azo_carbonyl-003.png

beta_carbonyl_quat_nitrogen

../_images/beta_carbonyl_quat_nitrogen-001.png ../_images/beta_carbonyl_quat_nitrogen-002.png ../_images/beta_carbonyl_quat_nitrogen-003.png

beta_halo_carbonyl

../_images/beta_halo_carbonyl-001.png ../_images/beta_halo_carbonyl-002.png ../_images/beta_halo_carbonyl-003.png

carbamate

../_images/carbamate-001.png ../_images/carbamate-002.png ../_images/carbamate-003.png

carbamic_acid

../_images/carbamic_acid-001.png ../_images/carbamic_acid-002.png ../_images/carbamic_acid-003.png

carbodiimide

../_images/carbodiimide-001.png ../_images/carbodiimide-002.png ../_images/carbodiimide-003.png

carbonate

../_images/carbonate-001.png ../_images/carbonate-002.png ../_images/carbonate-003.png

carbonyl

../_images/carbonyl-001.png ../_images/carbonyl-002.png ../_images/carbonyl-003.png

carboxylic_acid

../_images/carboxylic_acid-001.png ../_images/carboxylic_acid-002.png ../_images/carboxylic_acid-003.png

cation_C_Cl_I_P_or_S

../_images/cation_C_Cl_I_P_or_S-001.png ../_images/cation_C_Cl_I_P_or_S-002.png ../_images/cation_C_Cl_I_P_or_S-003.png

charge

../_images/charge-001.png ../_images/charge-002.png ../_images/charge-003.png

cyanohydrins

../_images/cyanohydrins-001.png ../_images/cyanohydrins-002.png ../_images/cyanohydrins-003.png

cycloheximide_derivatives

../_images/cycloheximide_derivatives-001.png ../_images/cycloheximide_derivatives-002.png ../_images/cycloheximide_derivatives-003.png

cyclopropyl

../_images/cyclopropyl-001.png ../_images/cyclopropyl-002.png ../_images/cyclopropyl-003.png

cytochalasin_derivatives

../_images/cytochalasin_derivatives-001.png ../_images/cytochalasin_derivatives-002.png ../_images/cytochalasin_derivatives-003.png

di_peptide

../_images/di_peptide-001.png ../_images/di_peptide-002.png ../_images/di_peptide-003.png

dioxane_6MR

../_images/dioxane_6MR-001.png ../_images/dioxane_6MR-002.png ../_images/dioxane_6MR-003.png

dioxolane_5MR

../_images/dioxolane_5MR-001.png ../_images/dioxolane_5MR-002.png ../_images/dioxolane_5MR-003.png

disulfide

../_images/disulfide-001.png ../_images/disulfide-002.png ../_images/disulfide-003.png

dithioacetal

../_images/dithioacetal-001.png ../_images/dithioacetal-002.png ../_images/dithioacetal-003.png

dye

../_images/dye-001.png ../_images/dye-002.png ../_images/dye-003.png

enamine

../_images/enamine-001.png ../_images/enamine-002.png ../_images/enamine-003.png

enol_ether

../_images/enol_ether-001.png ../_images/enol_ether-002.png ../_images/enol_ether-003.png

epoxide

../_images/epoxide-001.png ../_images/epoxide-002.png ../_images/epoxide-003.png

ester

../_images/ester-001.png ../_images/ester-002.png ../_images/ester-003.png

ether

../_images/ether-001.png ../_images/ether-002.png ../_images/ether-003.png

fluorenylmethoxycarbonyl_Fmoc

../_images/fluorenylmethoxycarbonyl_Fmoc-001.png    

guanidine

../_images/guanidine-001.png ../_images/guanidine-002.png ../_images/guanidine-003.png

halide

../_images/halide-001.png ../_images/halide-002.png ../_images/halide-003.png

halo_alkene

../_images/halo_alkene-001.png ../_images/halo_alkene-002.png ../_images/halo_alkene-003.png

halo_amine

halopyrimidine

../_images/halopyrimidine-001.png ../_images/halopyrimidine-002.png ../_images/halopyrimidine-003.png

hemiacetal

../_images/hemiacetal-001.png ../_images/hemiacetal-002.png ../_images/hemiacetal-003.png

hemiaminal

../_images/hemiaminal-001.png ../_images/hemiaminal-002.png ../_images/hemiaminal-003.png

hemiketal

../_images/hemiketal-001.png ../_images/hemiketal-002.png ../_images/hemiketal-003.png

hetatm

../_images/hetatm-001.png ../_images/hetatm-002.png ../_images/hetatm-003.png

hetero_hetero

HOBT_esters

../_images/HOBT_esters-001.png ../_images/HOBT_esters-002.png  

hydrazine

../_images/hydrazine-001.png ../_images/hydrazine-002.png ../_images/hydrazine-003.png

hydrazone

../_images/hydrazone-001.png ../_images/hydrazone-002.png ../_images/hydrazone-003.png

hydroxamic_acid

../_images/hydroxamic_acid-001.png ../_images/hydroxamic_acid-002.png ../_images/hydroxamic_acid-003.png

hydroxyl

../_images/hydroxyl-001.png ../_images/hydroxyl-002.png ../_images/hydroxyl-003.png

hydroxylamine

../_images/hydroxylamine-001.png ../_images/hydroxylamine-002.png ../_images/hydroxylamine-003.png

imidoyl_chlorides

../_images/imidoyl_chlorides-001.png ../_images/imidoyl_chlorides-002.png ../_images/imidoyl_chlorides-003.png

imine

../_images/imine-001.png ../_images/imine-002.png ../_images/imine-003.png

imino

../_images/imino-001.png ../_images/imino-002.png ../_images/imino-003.png

iodine

../_images/iodine-001.png ../_images/iodine-002.png ../_images/iodine-003.png

iodoso

../_images/iodoso-001.png ../_images/iodoso-002.png ../_images/iodoso-003.png

iodoxy

../_images/iodoxy-001.png ../_images/iodoxy-002.png ../_images/iodoxy-003.png

isocyanate

../_images/isocyanate-001.png ../_images/isocyanate-002.png ../_images/isocyanate-003.png

isonitrile

../_images/isonitrile-001.png ../_images/isonitrile-002.png ../_images/isonitrile-003.png

isothiocyanate

../_images/isothiocyanate-001.png ../_images/isothiocyanate-002.png ../_images/isothiocyanate-003.png

ketal

../_images/ketal-001.png ../_images/ketal-002.png ../_images/ketal-003.png

ketone

../_images/ketone-001.png ../_images/ketone-002.png ../_images/ketone-003.png

lactam

../_images/lactam-001.png ../_images/lactam-002.png ../_images/lactam-003.png

lactone

../_images/lactone-001.png ../_images/lactone-002.png ../_images/lactone-003.png

lawesson_s_reagent

../_images/lawesson_s_reagent-001.png ../_images/lawesson_s_reagent-002.png ../_images/lawesson_s_reagent-003.png

long_aliphatic_chain

../_images/long_aliphatic_chain-001.png ../_images/long_aliphatic_chain-002.png ../_images/long_aliphatic_chain-003.png

malonic

../_images/malonic-001.png ../_images/malonic-002.png ../_images/malonic-003.png

mercapto

../_images/mercapto-001.png ../_images/mercapto-002.png ../_images/mercapto-003.png

methoxyethoxymethyl_MEM

../_images/methoxyethoxymethyl_MEM-001.png ../_images/methoxyethoxymethyl_MEM-002.png ../_images/methoxyethoxymethyl_MEM-003.png

methyl_ketone

../_images/methyl_ketone-001.png ../_images/methyl_ketone-002.png ../_images/methyl_ketone-003.png

michael_acceptor

../_images/michael_acceptor-001.png ../_images/michael_acceptor-002.png ../_images/michael_acceptor-003.png

monensin_derivatives

../_images/monensin_derivatives-001.png    

mono_alkene

../_images/mono_alkene-001.png ../_images/mono_alkene-002.png ../_images/mono_alkene-003.png

mono_alkyne

../_images/mono_alkyne-001.png ../_images/mono_alkyne-002.png ../_images/mono_alkyne-003.png

nitrile

../_images/nitrile-001.png ../_images/nitrile-002.png ../_images/nitrile-003.png

nitro

../_images/nitro-001.png ../_images/nitro-002.png ../_images/nitro-003.png

nitroso

../_images/nitroso-001.png ../_images/nitroso-002.png ../_images/nitroso-003.png

N_methoyl

../_images/N_methoyl-001.png ../_images/N_methoyl-002.png ../_images/N_methoyl-003.png

nonacylhydrazone

../_images/nonacylhydrazone-001.png ../_images/nonacylhydrazone-002.png ../_images/nonacylhydrazone-003.png

noxide

../_images/noxide-001.png ../_images/noxide-002.png ../_images/noxide-003.png

N_P_S_Halides

../_images/N_P_S_Halides-001.png ../_images/N_P_S_Halides-002.png ../_images/N_P_S_Halides-003.png

NS_beta_halothyl

../_images/NS_beta_halothyl-001.png ../_images/NS_beta_halothyl-002.png ../_images/NS_beta_halothyl-003.png

nucleophile

../_images/nucleophile-001.png ../_images/nucleophile-002.png ../_images/nucleophile-003.png

organometallic

../_images/organometallic-001.png ../_images/organometallic-002.png ../_images/organometallic-003.png

oxalyl

../_images/oxalyl-001.png ../_images/oxalyl-002.png ../_images/oxalyl-003.png

oxaziridine

../_images/oxaziridine-001.png ../_images/oxaziridine-002.png ../_images/oxaziridine-003.png

oxime

../_images/oxime-001.png ../_images/oxime-002.png ../_images/oxime-003.png

oxygen_cation

../_images/oxygen_cation-001.png ../_images/oxygen_cation-002.png ../_images/oxygen_cation-003.png

paranitrophenyl_esters

../_images/paranitrophenyl_esters-001.png ../_images/paranitrophenyl_esters-002.png ../_images/paranitrophenyl_esters-003.png

pentafluorophenyl_esters

../_images/pentafluorophenyl_esters-001.png ../_images/pentafluorophenyl_esters-002.png ../_images/pentafluorophenyl_esters-003.png

perhalo_ketone

../_images/perhalo_ketone-001.png ../_images/perhalo_ketone-002.png ../_images/perhalo_ketone-003.png

peroxide

../_images/peroxide-001.png ../_images/peroxide-002.png ../_images/peroxide-003.png

phenol

../_images/phenol-001.png ../_images/phenol-002.png ../_images/phenol-003.png

phosphanes

../_images/phosphanes-001.png ../_images/phosphanes-002.png ../_images/phosphanes-003.png

phosphinic_acid

../_images/phosphinic_acid-001.png ../_images/phosphinic_acid-002.png ../_images/phosphinic_acid-003.png

phosphonamide

../_images/phosphonamide-001.png ../_images/phosphonamide-002.png ../_images/phosphonamide-003.png

phosphonic_acid

../_images/phosphonic_acid-001.png ../_images/phosphonic_acid-002.png ../_images/phosphonic_acid-003.png

phosphonic_ester

../_images/phosphonic_ester-001.png ../_images/phosphonic_ester-002.png ../_images/phosphonic_ester-003.png

phosphonylnitrile

../_images/phosphonylnitrile-001.png    

phosphoramides

../_images/phosphoramides-001.png ../_images/phosphoramides-002.png ../_images/phosphoramides-003.png

phosphoranes

../_images/phosphoranes-001.png ../_images/phosphoranes-002.png ../_images/phosphoranes-003.png

phosphoric_acid

../_images/phosphoric_acid-001.png ../_images/phosphoric_acid-002.png ../_images/phosphoric_acid-003.png

phosphoric_ester

../_images/phosphoric_ester-001.png ../_images/phosphoric_ester-002.png ../_images/phosphoric_ester-003.png

phosphoryl

../_images/phosphoryl-001.png ../_images/phosphoryl-002.png ../_images/phosphoryl-003.png

phosphoryl

../_images/phosphoryl-001.png ../_images/phosphoryl-002.png ../_images/phosphoryl-003.png

phthalimides_PHT

../_images/phthalimides_PHT-001.png ../_images/phthalimides_PHT-002.png ../_images/phthalimides_PHT-003.png

polyenes

../_images/polyenes-001.png ../_images/polyenes-002.png ../_images/polyenes-003.png

primary_amine

../_images/primary_amine-001.png ../_images/primary_amine-002.png ../_images/primary_amine-003.png

propiolactones

../_images/propiolactones-001.png ../_images/propiolactones-002.png ../_images/propiolactones-003.png

pseudo_amine

../_images/pseudo_amine-001.png ../_images/pseudo_amine-002.png ../_images/pseudo_amine-003.png

quinone

../_images/quinone-001.png ../_images/quinone-002.png ../_images/quinone-003.png

ring

../_images/ring-001.png ../_images/ring-002.png ../_images/ring-003.png

saponin_derivatives

../_images/saponin_derivatives-001.png    

SCN2

../_images/SCN2-001.png ../_images/SCN2-002.png ../_images/SCN2-003.png

secondary_amine

../_images/secondary_amine-001.png ../_images/secondary_amine-002.png ../_images/secondary_amine-003.png

squalestatin_derivatives

../_images/squalestatin_derivatives-001.png    

sulfide

../_images/sulfide-001.png ../_images/sulfide-002.png ../_images/sulfide-003.png

sulfinimine

../_images/sulfinimine-001.png ../_images/sulfinimine-002.png ../_images/sulfinimine-003.png

sulfinylthio

../_images/sulfinylthio-001.png ../_images/sulfinylthio-002.png ../_images/sulfinylthio-003.png

sulfonamide

../_images/sulfonamide-001.png ../_images/sulfonamide-002.png ../_images/sulfonamide-003.png

sulfone

../_images/sulfone-001.png ../_images/sulfone-002.png ../_images/sulfone-003.png

sulfonic_acid

../_images/sulfonic_acid-001.png ../_images/sulfonic_acid-002.png ../_images/sulfonic_acid-003.png

sulfonic_ester

../_images/sulfonic_ester-001.png ../_images/sulfonic_ester-002.png ../_images/sulfonic_ester-003.png

sulfonimine

../_images/sulfonimine-001.png ../_images/sulfonimine-002.png ../_images/sulfonimine-003.png

sulfonyl_halide

../_images/sulfonyl_halide-001.png ../_images/sulfonyl_halide-002.png ../_images/sulfonyl_halide-003.png

sulfonylnitrile

../_images/sulfonylnitrile-001.png ../_images/sulfonylnitrile-002.png ../_images/sulfonylnitrile-003.png

sulfonylurea

../_images/sulfonylurea-001.png ../_images/sulfonylurea-002.png ../_images/sulfonylurea-003.png

sulfoxide

../_images/sulfoxide-001.png ../_images/sulfoxide-002.png ../_images/sulfoxide-003.png

t_butyldimethylsilyl_TBDMS

../_images/t_butyldimethylsilyl_TBDMS-001.png ../_images/t_butyldimethylsilyl_TBDMS-002.png ../_images/t_butyldimethylsilyl_TBDMS-003.png

t_butyldiphenylsilyl_TBDPS

../_images/t_butyldiphenylsilyl_TBDPS-001.png ../_images/t_butyldiphenylsilyl_TBDPS-002.png  

t_butyl_ether

../_images/t_butyl_ether-001.png ../_images/t_butyl_ether-002.png ../_images/t_butyl_ether-003.png

t_butoxycarbonyl_tBOC

../_images/t_butoxycarbonyl_tBOC-001.png ../_images/t_butoxycarbonyl_tBOC-002.png ../_images/t_butoxycarbonyl_tBOC-003.png

terminal_vinyl

../_images/terminal_vinyl-001.png ../_images/terminal_vinyl-002.png ../_images/terminal_vinyl-003.png

tertiary_amine

../_images/tertiary_amine-001.png ../_images/tertiary_amine-002.png ../_images/tertiary_amine-003.png

tetrahydropyran_THP

../_images/tetrahydropyran_THP-001.png ../_images/tetrahydropyran_THP-002.png ../_images/tetrahydropyran_THP-003.png

thioamide

../_images/thioamide-001.png ../_images/thioamide-002.png ../_images/thioamide-003.png

thiocarbamate

../_images/thiocarbamate-001.png ../_images/thiocarbamate-002.png ../_images/thiocarbamate-003.png

thiocarbonyl

../_images/thiocarbonyl-001.png ../_images/thiocarbonyl-002.png ../_images/thiocarbonyl-003.png

thioester

../_images/thioester-001.png ../_images/thioester-002.png ../_images/thioester-003.png

thiol

../_images/thiol-001.png ../_images/thiol-002.png ../_images/thiol-003.png

thiourea

../_images/thiourea-001.png ../_images/thiourea-002.png ../_images/thiourea-003.png

triacyloxime

../_images/triacyloxime-001.png ../_images/triacyloxime-002.png ../_images/triacyloxime-003.png

triazine

../_images/triazine-001.png ../_images/triazine-002.png ../_images/triazine-003.png

tricarbo_phosphene

../_images/tricarbo_phosphene-001.png ../_images/tricarbo_phosphene-002.png ../_images/tricarbo_phosphene-003.png

triflates

triisopropylsilyl_TIPS

../_images/triisopropylsilyl_TIPS-001.png ../_images/triisopropylsilyl_TIPS-002.png ../_images/triisopropylsilyl_TIPS-003.png

trimethylsilyl_TMS

../_images/trimethylsilyl_TMS-001.png ../_images/trimethylsilyl_TMS-002.png ../_images/trimethylsilyl_TMS-003.png

unbranched_chain

../_images/unbranched_chain-001.png ../_images/unbranched_chain-002.png ../_images/unbranched_chain-003.png

urea

../_images/urea-001.png ../_images/urea-002.png ../_images/urea-003.png

New Rules

New rules specify additional functional groups or substructures that may be used. They must specify a substructure definition in the form of a SMARTS in addition to the substructure name and maximum limit. For example:

NEWRULE norbornane 1 C1CC2CCC1C2

The first field is the NEWRULE keyword. The second field defines the name associated with the substructure (primarily for logging purposes). The third field indicates the maximum number of the substructure that can be allowed. The fourth field is the SMARTS string for the substructure, norbornane in this case. This example rule would indicate that molecules with a single norbornane substructure would be allowable, but that those with 2 or more norbornanes would be eliminated.

New rules that have a name that is identical with one of the original rules take precedence over the original rule.

Selection Statements

The select statement allows a filter file to specify the required number of substructures in order to be able to pass the filter. These statements are similar to new rules except that they list a required range for passing the filter rather than the range for failing to pass the filter. For example:

SELECT amine 1 1 [N;!$(*-*[!#6;!#1]);!$(*-a);!$(*=,#*)]

The first field is the SELECT keyword. The second field indicates the name for the selection (again for logging purposes). The third field is the minimum number of substructures required to be in the molecule. The fourth field is the maximum number of substructures allowed in the molecule. The fifth field is the substructure defined by a SMARTS pattern. The example requires that molecules contain exactly one amine. Currently, only a single SELECT statement is allowed in the filter file. Any complex boolean substructure statements can be incorporated directly into the SMARTS. If multiple SELECT statements occur in a filter file, only the final one will be applied.