8.1. Pharmacophore 3D Visualization

The script gen_ph4_3d_vis.py generates 3D visual representations of pharmacophores read from an input file and writes the resulting vector graphics data to one or more (in case of multiple input pharmacophores) output file(s).

Synopsis

python gen_ph4_3d_vis.py [-h] -i <file> -o <file> [-c] [-d] [-t]

Mandatory options

-i <file>

Input pharmacophore file (.pml, .cdf)

-o <file>

3D visualization data output file (.r3d, .stl, .ply, .wrl)

Other options

-h, --help

Show help message and exit

-c

Do not output spheres representing the feature centers (default: false)

-d

Make vector and plane features undirected (default: false)

-t

Disable feature transparency (default: false)

Example

Generation of a Raster3D file for the pharmacophore of ligand MIT (complex 1DWC ):

$ python gen_ph4_3d_vis.py -i 1dwc_MIT_ph4.pml -o 1dwc_MIT_ph4.r3d
1dwc_MIT.sdf
1dwc_MIT_ph4.pml
1dwc_MIT_ph4.r3d
PyMOL visualization example

PyMOL displaying the structure and pharmacophore of ligand MIT

Code

  1import sys
  2import os
  3import argparse
  4
  5import CDPL.Util as Util
  6import CDPL.Pharm as Pharm
  7import CDPL.Vis as Vis
  8
  9
 10def parseArgs() -> argparse.Namespace:
 11    parser = argparse.ArgumentParser(description='Generates 3D vector graphics representations of pharmacophores for the display by external programs.')
 12
 13    parser.add_argument('-i',
 14                        dest='in_file',
 15                        required=True,
 16                        metavar='<file>',
 17                        help='Input pharmacophore file (*.pml, *.cdf)')
 18    parser.add_argument('-o',
 19                        dest='out_file',
 20                        required=True,
 21                        metavar='<file>',
 22                        help='3D visualization data output file (*.r3d, *.stl, *.ply, *.wrl)')
 23    parser.add_argument('-c',
 24                        dest='no_ftr_ctrs',
 25                        required=False,
 26                        action='store_true',
 27                        default=False,
 28                        help='Do not output spheres representing the feature centers (default: false)')
 29    parser.add_argument('-d',
 30                        dest='no_ftr_dir',
 31                        required=False,
 32                        action='store_true',
 33                        default=False,
 34                        help='Make vector and plane features undirected (default: false)')
 35    parser.add_argument('-t',
 36                        dest='no_transp',
 37                        required=False,
 38                        action='store_true',
 39                        default=False,
 40                        help='Disable feature transparency (default: false)')
 41     
 42    return parser.parse_args()
 43    
 44def main() -> None:
 45    args = parseArgs()
 46
 47    # create reader for input pharmacophores (format specified by file extension)
 48    reader = Pharm.PharmacophoreReader(args.in_file) 
 49    
 50    # create an instance of the default implementation of the Pharm.Pharmacophore interface
 51    ph4 = Pharm.BasicPharmacophore()
 52
 53    # instantiate class implementing the creation of visual 3D
 54    # representations of Pharm.FeatureContainer objects
 55    ph4_3d_repr_factory = Vis.FeatureContainerObject3DFactory()
 56
 57    # apply the value of option -c
 58    Vis.setShowFeatureCentersParameter(ph4_3d_repr_factory, not args.no_ftr_ctrs)
 59
 60    # process option -t
 61    if args.no_transp:
 62        ftr_colors = Vis.DefaultFeatureColorTable()
 63
 64        for color in ftr_colors.values():
 65            color.setAlpha(1.0)
 66
 67        Vis.setFeatureColorTableParameter(ph4_3d_repr_factory, ftr_colors)
 68
 69    out_file, out_file_ext = os.path.splitext(args.out_file)
 70    
 71    # read and process pharmacophores one after the other until the end of input has been reached
 72    try:
 73        i = 1
 74        
 75        while reader.read(ph4):
 76            try:
 77                if args.no_ftr_dir:                       # if pharm. features shall be output without orientation information (option -d)
 78                    Pharm.clearOrientations(ph4)          # clear orientation property of all features
 79                    Pharm.removePositionalDuplicates(ph4) # and reduce multiple features having the same type and position to one feature
 80
 81                # create writer for the output file (file format determined by the file extension)
 82                writer = Vis.Object3DWriter(f'{out_file}_{i}{out_file_ext}')
 83
 84                # generate the 3D visual representation of the read pharmacophore
 85                ph4_3d_repr = ph4_3d_repr_factory.create(ph4)
 86
 87                # output the generated visualization data
 88                if not writer.write(ph4_3d_repr):
 89                    sys.exit('Error: output of pharmacophore visualization data failed')
 90
 91                i += 1
 92                writer.close()
 93    
 94            except Exception as e:
 95                sys.exit('Error: generation or output of pharmacophore visualization data failed:\n' + str(e))
 96                
 97    except Exception as e: # handle exception raised in case of severe read errors
 98        sys.exit('Error: reading pharmacophore failed:\n' + str(e))
 99
100    sys.exit(0)
101        
102if __name__ == '__main__':
103    main()

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