Command Line Arguments

PIDGINv3 uses a Command Line Interface (CLI) for all available functionality.

This tutorial assumes the PIDGINv3 repository is located at $PV3.

List of available arguments

To see all available options, run

$ python $PV3/ -h
Usage: [options]

  -h, --help            show this help message and exit
  -f FILE               Input smiles or sdf file (required)
  -d DELIM, --smiles_delim=DELIM
                                                Input file (smiles) delimiter char (default: white
                                                space ' ')
                                                Input file (smiles) delimiter column (default: 0)
                                                Input file (smiles) ID column (default: 1)
  -o FILE               Optional output prediction file name
  -t, --transpose       Transpose output (rows are compounds, columns are
  -n NCORES, --ncores=NCORES
                                                No. cores (default: 1)
                                                Bioactivity threshold (can use multiple split by ','.
                                                E.g. '100,10'
  -p PROBA, --proba=PROBA
                                                RF probability threshold (default: None)
  --ad=AD               Applicability Domain (AD) filter using percentile of
                                                weights [float]. Default: 90 (integer for percentile)
  --known_flag          Set known activities (annotate duplicates betweem
                                                input to train with correct label)
  --orthologues         Set to use orthologue bioactivity data in model
  --organism=ORGANISM   Organism filter (multiple can be specified using
                                                commas ',')
                                                Target classification filter
  --min_size=MINSIZE    Minimum number of actives used in model generation
                                                (default: 10)
                                                Comma-seperated performance filtering using following
                                                nomenclature: validation_set[tsscv,l50so,l50po],metric
                                                E.g 'tsscv,bedroc,0.5'
  --se_filter           Optional setting to restrict to models which do not
                                                require Sphere Exclusion (SE)
  --training_log        Optional setting to add training_details to the
                                                prediction file (large increase in output file size)
  --ntrees=NTREES       Specify the minimum number of trees for warm-start
                                                random forest models (N.B Potential large
                                                latency/memory cost)
  --preprocess_off      Turn off preprocessing using the flatkinson (eTox)
                                                standardizer (,
                                                size filter (100 >= Mw >= 1000 and organic mol check
                                                (C count >= 1)
  --std_dev             Turn on matrix calculation for the standard deviation
                                                of prediction across the trees in the forest
  --percentile          Turn on matrix calculation for the percentile of AD

Detailed explanations for the more complicated arguments

SMILES options (-d / –smiles_column / –smiles_id_column)

PIDGINv3 interprets SMILES files (*.smi or *.smiles) using the conventional OpenSMILES specification §4.5), comprising a first column of smiles separated by a white line ( ) character and additional entries as identifiers.

An example of such a file is included in the examples directory for the SMILES file named test.smi, containing two molecules whose SMILES strings are defined as:

COc1cc2c3CN4CCC[C@H]4[C@@H](O)c3c5ccc(O)cc5c2cc1OC CompoundID1
COc1cc2c3CN4CCC[C@H]4[C@@H](O)c3c5ccc(O)c(OC)c5c2cc1OC CompoundID2

The following arguments can alter this behaviour, if desired, to accomodate for different file strcutures:

  • -d (or --smiles_delim)
  • --smiles_column
  • --smiles_id_column

For example test2.smi contains a comma separated file whose first column is the ID and SMILES in the second column.


Thus the following command should be used when running any commands:

$ python $PV3/ -f test2.smi -d ',' --smiles_column 1 --smiles_id_column 0


PIDGINv3 generates a warning message for any user input files which are neither *.smi / *.smi or *.sdf, and will interpret any other file as a SMILES.

Transpose options (-t)

Transposes the prediction matrix from rows as targets and columns as compounds, to rows are columns and columns as compounds.


This will remove the metadata for each target (just the Uniprot name will be used) to ensure only one column header is used.

RF probability theshold (-p)

The continuous probabilities from each model [p(activity)] for input compounds can be converted into binary predictions at a user-specified threshold. The choice of required p(activity) indicates a degree of confidence in predictions when binarizing probabilities.


These probabilities are different from PIDGIN `version 2`_ in that they have not been Platt-scaled, since this increased the number of false positives.

Applicability domain threshold (–ad / –percentile)

PIDGINv3 applies the reliability-density neighbourhood Applicability Domain (AD) analysis by Aniceto et al., from:

In this procedure, three parameters are calculated on a per-compound basis across the training data for each target model. 1.) The nearest-neighbour similarity (sim) [the largest Tanimoto Coefficient (Tc) similarity] to all data points for the target model 2.) The RF probability of activity for the true label of the training compound (i.e. the probability of being active for an active compound or the inactivity prediction for an inactive compound) for the realised models (bias). 3.) The standard deviation (std_dev) of this probability calculation, computed by the deviation of predictions across all trees in the forest (this metric is considered a level prediction certainty). These values are used to compute the weights (w) for each training compound instance using the following equation:


w = sim / (bias * std_dev)

Reliability increases with the increase of w, whereby higher reliability is associated with higher similarity and low bias * std_dev. In practice, this procedure penalizes high similarity which is associated with poor bias and precision observed in the trained model.

At run time, the user specifies the cut-off for applicability domain (AD) percentile (n) required for input compounds, using the following command:

  • --ad

where int or (n) is a number between 0-100. In this case, the corresponding threshold encapsulating n% of the pre-computed weights is calculated (i.e. n-th percentile of w values). Weights are next calculated on a per-input compound basis by calculating the nearest neighbour similarity to the training set and identifying the corresponding (pre-computed) training compound bias and std_deviation for the near neighbour. The corresponding percentile value for the input compound is calculated in the same manner as above. A percentile value for the input compound above the user-specified percentile threshold means the compound is considered within the applicability domain given the user-specified conditions, and the corresponding probability of activity [p(activity)] (or the binary prediction, if specified) is written in the prediction matrix. Conversely, a weight below the percentile means an input compound is outside the AD, and in this case an NaN (not available) is added to the output matrix.


Higher confidence in the applicability domain (larger n) will increase run-time or latency, since the code will quit looping through training upon identifying a compound within the AD.

This feature can be effectively turned off by specifying the following command (not recommended):

$ python $PV3/ -f test2.smi -d ',' --smiles_column 1 --smiles_id_column 0 --ad 0

If a user would like to obtain a matrix comprising the percentile weights for each of the input compounds, then the command line argument --percentile can be used.

Annotating known activity in ChEMBL or PubChem (–known_flag)

Known actives from ChEMBL and the inactives used from PubChem (possibly only a subset due to undersampling) can be annotated using the command:

  • --known_flag


This requires the full matrix of similarities between input and training compounds to be computed, and hence increases computational cost/latency.

Filtering the models by pre-calculated performance (–performance_filter)

Leave 50% of the random scaffold out (L50SO) and 50% of the ChEMBL publication (from which the bioactivity data has been extracted) ID’s out (L50PO) was performed over 4-splits for the training data as a validation set. The data was also split using time-series split validation (TSSCV). The ROC, BEDROC, Precision-recall curve (PR-AUC) and Brier score were computed over the folds and stored in the file training_log.txt in either the ortho or no_ortho directories. This data can be incorporated into the output prediction file for use as a desired performance value using the command:

  • --performance_filter

where the user should supply comma-seperated performance filtering using following nomenclature: validation_set[tsscv,l50so,l50po], metric[bedroc,roc,prauc,brier], performance_threshold float].

For example the following command would provice predictions for the models with a BEDROC of 0.5 during TSSCV:

$ python $PV3/ -f test.smi --ad 0 --performance_filter tsscv,bedroc,0.5

Incorporating training log with predictions (–training_log)

The results from the above analysis can be appended to the target information columns to provide detailed information to the user for filering. This will increase the file size due to the significant amount of data. The column headings have the following meanings:

  • MODEL_ID: ID of the model (nomenclature defined as 1. the Uniprot IDs annotated in the active/inactive training set, 2. if Sphere exclusion (SE) has been used and 3. an underscore followed by the threshold for activity)
  • FINGERPRINT: Type of molecular fingerprint used
  • N_TREES: Number of trees in the forest (differs depending on the tree optimisation)
  • TRAIN_TIME_SEC: Time taken to train the RF model
  • OUTOFBAG_ERROR_2DP: Out-of-bag (OOB) score for the RF (Sklearn calculated)
  • N_SCAFFOLDS: Number of generic Murcko scaffolds within the chemistry of training data
  • N_PUBLICATIONS: Number of ChEMBL publications across training data

Time-series split (TSSCV) validation, followed by the metric used and the average/median/standard dev. over the 4 folds:


Leave 50% of publications out, followed by the metric used and the average/median/standard dev. over the 4 folds:


Leave 50% of scaffolds out, followed by the metric used and the average/median/standard dev. over the 4 folds:


The training data was then used to benchmark the realised models using all data, to obtain the following metrics:


The average and standard deviations across all probabilities of activity [p(activity)] for each of the actives and inactivity [p(inactivity)] for all inactives were recorded for compared to the realised models:


Increasing the number of trees (–ntrees)

Thanks to the warm_start function of Scikit-learn RF’s, the number of trees in the forests can be globally increased (at the cost of latency/increased CPU) using the command:

  • --ntrees

Turning off pre-processing (–preprocess_off)

PIDGINv3 implements a pre-processing feature which is turned on by default, to ensure all input molecules are standardised using the flatkinson (eTox) standardiser (, and that any molecules outside the applicability domain of the models, defined by the chemical property filters imposed on ChEMBL and PubChem training data [size filter 100 >= Mw >= 1000 / organic mol check (Carbon count >= 1)] are removed. This functionality can be turned off to force PIDGINv3 to give unreliable predictions (in cases when the input space maybe outside the domain of applicability or when molecules have been pre-standardised) using the following command:

  • --preprocess_off

Output the standard dev. of predictions across the trees (–std_dev)

The standard deviation of the predictions across the trees can be output to the prediction matrix (in place of the probability for activity), using the following command:

  • --std_dev