Schrödinger extension for KNIME Workbench version 22.214.171.124005150708 by Schrödinger
Filters structure file, retaining structures that meet the specified criteria. The ligfilter utility filters a structure file based on properties and descriptors. It can filter on any Maestro property, a set of predefined feature counts, or counts of SMARTS patterns for functional groups. This utility supersedes Property Filter, and should be used in preference to it. Input filter files from Property Filter can be read by Ligfilter.
A condition is a one-line expression which describes criteria that a particular descriptor must meet for the for a structure to be retained. Each filter condition describes one or more criteria that a particular To be accepted, a molecule needs to satisfy all specified filter conditions. The syntax for a filter condition expression is <descriptor> <op> <value> [ ['AND'|'OR'] <op> <value> ] ... In case that's hard to decipher, the following are all valid: <descriptor> <op> <value> <descriptor> <op> <value> AND <op2> <value2> <descriptor> <op> <value> OR <op2> <value2> <descriptor> <op> <value> OR <value2> OR <value3> <descriptor> <op> <value> AND <value2> <descriptor> is the name of the descriptor (property name for properties) <op> (conditional operator) must be one of the following: > >= < <= == != NOTE: If a property condition (see below) consists of nothing but the '<descriptor>', then the named property is required to exist, but it may have any value. Multiple conditions a descriptor may be specified in a single expression. The individual conditions may be separated by operators 'AND' or 'OR'. When 'AND' and 'OR' are both used in an expression, the 'AND' operator has higher precedence. For instance, the expression: Num_atoms > 1 AND < 4 OR == 1000 requires that either #atoms be between 1 and 4, or else equal to 1000. Single or double quotes may be used to delimit values containing spaces. There are 2 types of conditions: * PROPERTY CONDITIONS: A property condition allows to retain a ligand only if the specified property exists or is within a specified range. * DEFINITION CONDITIONS: A definition condition is one that allows filtering a ligand by some calculated parameter; like number of atoms, number or aromatic rings, or number of occurrences of a specific SMARTS pattern or a set of patterns (descriptors). Criteria file: If filter conditions are supplied in a separate criteria file, there must be one condition per line. Lines that start with '# ' are treated as comments and blank lines are ignored. Example criteria file: Num_rings == 1 Peroxides > 1 Num_atoms > 100 AND < 1000 r_epik_State_Penalty > 2.5'
H Nitriles Charged_alkylthiols B Sulfonyl_halides Charged_2-nitrophenols C Sulfinyl_halides Charged_4-nitrophenols N Sulfenyl_halides Charged_3,5-nitrophenols O Acyl_halides Acidic_hydrogens F Alkyl_halides Charged_amidines Si Alkyl_halides_wo_fluorine Charged_guanidines P Alkyl_sulfonates Charged_enamines S Halopyrimidines Charged_anilines Cl Anhydrides Charged_dialkyl_anilines Fe 1,2-Dicarbonyls Charged_diaminobenzenes Br Perhalomethylketones Charged_2-aminopyridines I Aliphatic_ketones Charged_4-aminopyridines H-N Epoxides Charged_4-methoxypyridines H-O Aziridines Neutral_amines Charged_amines Aliphatic_esters Tetrazoles Charged_imines Aliphatic_thioesters Catch_for_R-CN4 Charged_amidines Sulphonate_esters Trifluoromethyls Charged_NH-imidazoles Phosphonate_esters Trichloromethyls Charged_imidazoles Imines Tribromomethyls Charged_pyridines Aldehydes Triiodomethyls Aliphatic_carbons Formates t-Butyls Aromatic_carbons Michael_acceptors Neutral_imidazoles Amide_hydrogens beta-Heterosubstituted_carbonyls Neutral_pyridines Amine_or_amide_hydrogens Peroxides Isothiocyanates N-Pyrrole_H R-S-O-R Isocyanates Imines_hydrogens Diazos Isonitriles Heteroaromatic_atoms R-N-S-R Diazoniums Divalent_oxygens Disulfides Carbodiimides Aromatic_basic_nitrogens Guanidines Azides Catch_for_uncharged_guanine_H Amidines Phosphonyl_halides Neutral_sulfones Charged_sulfonamides Phosphinyl_halides Neutral_sulfenes Charged_carboxylic_acids Alkali_metals Neutral_carbonyls Carboxylic_acids_or_carboxylates Alkaline-earth_metals Neutral_P=O-R3 Charged_phosphoric_acids Lanthanide_series Neutral_P(=O)2-R2 Charged_halophosphoric_acids Actinide_series Imines_N_donors Charged_O-PO3 Transition_metals Imines_NH Charged_C-PO3- Other_metals Carbonyls Charged_phosphorylamides Toxic_nonmetals P=O Charged_phosphonic_acids Noble_gases S=O Charged_phosphonamides Silyl_enol_ethers Nitros Charged_sulfuric_acids Nitroalkanes Ethers Charged_sulfenic_acids Phosphines Charged_N-O Charged_sulfonic_acids Neutral_donor_groups Neutral_N-O Charged_hydroxamic_acids Charged_donor_groups Aromatic_N-oxides Aromatic_carboxylate_bioisosteres Neutral_acceptor_groups Neutral_NR3-O Hydroxamates Charged_acceptor_groups Neutral_halophosphoric_acids Acetylhydrazides Donor_groups Alcohols Charged_tetrazoles Acceptor_groups Thiols Charged_alkylthiols Metals Carbon_Thiols Charged_2-nitrophenols Iron_binding_groups Thiones Charged_4-nitrophenols Reactive_groups Tertiary_amines_or_amides Charged_3,5-nitrophenols
To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.
Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to email@example.com, follow @NodePit on Twitter, or chat on Gitter!
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.