5.2.1.1. Set temporary files directory

set temp directory {"path"};

Specify the directory MetaSite will use to store temporary files. Notice: path must be enclosed in double quotes.

5.2.1.2. Set system enzymes library path

set system library {"path"};

Specify system library file locations. Notice: path must be enclosed in double quotes.

5.2.1.3. Set user's enzymes library path

set user library {NO | "path"};

Specify if MetaSite has to use an additional custom library, and in case, the path where the corresponding library file is located. Notice: path must be enclosed in double quotes.

5.2.1.4. Conformers generation settings

set conformers {NO | max_number };

Specify if conformational sampling is to be performed as part of the processing of imported structures, and in case it is, the maximum number of generated conformers.

5.2.1.5. Set protonation policy

set protonation {AS_IS | NEUTRALIZE | NORMALIZE {pH}};

Specify if structures are to be imported in the original protonation state, if a neutral form is to be enforced or if protonation is to be determined by the provided pH value.

5.2.1.6. Set minimum mass of generated metabolites

set metabolite minimum mass {mass_value};

Instructs the metabolites generation engine to discard metabolites below a threshold mass value. A null minimum mass disables this filtering option.

5.2.1.7. Set metabolites redundancy policy

set metabolite ignore redundant {NO | mass_fraction};

Some metabolic reaction mechanisms imply the cleavage of specific bonds (e.g dealkylation). In these cases the same reaction may take to the generation of more than one single metabolite. Sometimes, when one of the produced metabolites is much smaller than the other, its presence is not considered significant and the associated information is therefore considered as redundant. This command allows the user to set a threshold value for the metabolite mass percentage respect to the original substrate mass. When this filtering is activated and a group of metabolites is formed from the same reaction, metabolites with a mass fraction below the given the threshold are considered as redundant and discarded.

5.2.1.8. Set metabolites stereochemistry options

set metabolite ignore stereo {YES | NO};

During metabolites generation user has a choice to take tethrahedral stereochemistry into account or not.

5.2.1.9. Enable/disable reaction mechanisms in metabolites generation

set metabolite enable reaction {"reaction1","reaction2",...} {YES | NO};

Specify a list of reactions and whether they should enabled or not during the metabolites generation procedure. All reaction mechanisms are by default enabled, so this command is mostly useful in case the user wants to switch-off a specific subset of metabolit pathways.

Names of reaction mechanism are to be enclosed in double quotes. This is the list of names currently implemented and recognized.

• "Aliphatic Hydroxylation"

• "Aliphatic Hydroxylation"

• "Aromatic Hydroxylation"

• "Acetylenic Hydroxylation (t)"

• "Alkyne Oxidation"

• "Alkyne Hydroxylation"

• "Aldehydic Hydroxylation"

• "Desulphuration"

• "Alcoholic Oxidation"

• "Olefinic Epoxidation"

• "N-Dealkylation"

• "O-Dealkylation"

• "S-Dealkylation"

• "Epoxidic S-Oxidation"

• "Thiolic Hydroxylation"

• "Thioetheric S-Oxidation"

• "Sulphoxidic S-Oxidation"

• "Aliphatic N-Oxidation"

• "Aliphatic N-Hydroxylation"

• "Anilinic Hydroxylation"

• "Aromatic N-Oxidation"

• "Conjugated N-Hydroxylation"

• "Amine Dehydrogenation"

5.2.2.1. New

new;

Creates a new empty document, discarding any eventually unsaved data present in current document.

5.2.2.2. Open

open {"path"};

Opens an existing MetaSite document file. Full path to the file must be specified. Unsaved data eventually present in the current document will be discarded.

5.2.2.3. Save

save [as {"path"} ];

Save current document. If keyword "as" followed by a path to a MetaSite document file is specified, current document will be saved under the given file path. If a file with the same name already exists it will be overwritten. If the "as" clause is omitted, the document will be saved under the current file path; please notice that a current file path only exists only if "save as" or "open" were previously called. A save statement, not followed by an "as" clause, has no effect if a current file path is not defined.

5.2.3.1. Import of MOL2 files

import MOL2 {"path"} [name by [UID | FILE_NAME | STRUCTURE_NAME] ];

Import structures contained in a mol2 or multimol2 file. The path to the file has to be enclosed in double quotes. A policy for object name assignment can be optionally specified; if none is specified, names are based on a unique identified (UID).

5.2.3.2. Import of SDF files

import SDF {"path"} [name by [UID | FILE_NAME | STRUCTURE_NAME | TAG {"tag_name"}] ];

Import structures contained in a mol2 or multimol2 file. The path to the file has to be enclosed in double quotes. A policy for object name assignment can be optionally specified; if none is specified defaults to by UID. If TAG is specified, the exact name of the SD tag must be provided. If any of the structures contained in SDF lacks such tag, the naming procedure for those structures falls back to UID.

5.2.3.3. Import of a SMILES string

import SMILES {"smiles_string"} [name by [UID | string {"name"}] ];

Imports the passed SMILES string. The SMILES string has to be enclosed in double quotes. A policy for object name assignment can be optionally specified; if none is specified defaults to by UID.

5.2.3.4. Import of a SMILES list file

import SMILES list {"path"}format [SMILES | SMILES_NAME | NAME_SMILES];

Import a text file containing a list of SMILES strings; this list must have one of these formats:

• One smiles per line

• Each line contains smiles string and smiles name separated by blanks.

• Each line contains smiles name and smiles string separated by blanks.

5.2.4.1. Compute Site of Metabolism predictions

compute som {LIVER | SKIN | BRAIN | "cypname1","cypname2",};

Performs a site of metabolism prediction on all of the objects in the current dataset. User can specify one of the avaiable consensus models or a list of CYPs.

5.2.4.2. Run metabolites identification

compute metabolite {LIVER | SKIN | BRAIN | "cypname1","cypname2",};

Performs a metabolites identification on all the objects in the current dataset. User can specify one of the avaiable consensus models or a list of CYPs.

5.2.4.3. Run prediction of the MBI character

compute mbi {"cypname1","cypname2",...};

Performs a prediction of the MBI character of all the objects in the current dataset. User should specify the names for one or more CYP models.

5.2.5.1. Export Site of Metabolism predictions

export som as SDF = {"file_path"};

Exports site of metabolism predictions as an SDF file. User must provide the path to a writable output file. In case a file with the same name already exists it is overwritten.

5.2.5.2. Export Metabolite ID data

export metabolite {LIVER | SKIN | BRAIN | "cypname"}as CSV = {"file_path"};

Exports the Metabolite ID results for all of the objects in the current dataset and the given enzyme model. User must provide the path to a writable output file. In case a file with the same name already exists it is overwritten.

5.2.5.3. Export MBI predictions

export mbi as {CSV | SDF}= {"file_path"};

Exports MBI predictions results as either a CSV or an SDF file. User must provide the path to a writable output file. In case a file with the same name already exists it is overwritten.