CaviTracer tool for detecting channels, tunnels, pores

[karolamik13]

CaviTracer, created by Eryk Trzcinski, as his MSc work under my supervision.
Additional installation of open3D package is required:
pip install open3d

Test functions:
from prody import *

1. Single PDB:
   p = parsePDB('1tqn.pdb')
   atoms = p.select("protein")
   channels, surface = calcChannels(atoms, output_path='channels_output.pdb')
   showCavities(surface)

To create 3D model to display it in ProDy
vmd_path = '/usr/local/bin/vmd'
model = getVmdModel(vmd_path, atoms)

To display channels (all or one by one):
showChannels(channels, surface=surface, model=model)
showChannels(channels, model=model)
getChannelParameters(channels)
showCavities(surface, show_surface=True)

Save all channels independently as PDB:
output = 'chanels_test'
channels, surface = calcChannels(atoms, output, separate=True)

Display channel 1:

showChannels(channels[1], model)

selected_channels = [channels[1], channels[8]]
showChannels(selected_channels, model)

selected_channels = channels[1:4]
lengths, bottlenecks, volumes = getChannelParameters(selected_channels)
selected_channels_atoms = getChannelAtoms(selected_channels)

atoms_protein = getChannelAtoms(channels, atoms)

Extracting residues that are forming channel[1]:
atoms_protein = getChannelAtoms(channels[1], atoms)
len(atoms_protein.getResnames())

distance = 4
residues = atoms_protein.select('same residue as exwithin '+str(distance)+' of resname FIL')
residues.select('name CA').getResnames(), residues.select('name CA').getResnums()
list(zip(residues.select('name CA').getResnames(), residues.select('name CA').getResnums()))

2. Multiple frames:
   p2 = parsePDB('LXmulti.pdb')
   channels2, surfaces2 = calcChannelsMultipleFrames(p2)

To display particular channel:
channels2[4][1]

model2 = getVmdModel(vmd_path, p2)
showChannels(channels2[4][1], model2)
showChannels(channels2[4][2], model2)

3. Trajectories:
   PDBfile = 'L_traj.pdb'
   DCDfile = 'L_traj.dcd'
   atoms = parsePDB(PDBfile)
   dcd = Trajectory(DCDfile)
   dcd.link(atoms)
   dcd.setCoords(atoms)

channels3, surfaces3 = calcChannelsMultipleFrames(atoms, dcd)
all_channels, all_surfaces=calcChannelsMultipleFrames(atoms, dcd, output_path = 'channels_dcd', separate=True)

[karolamik13]

New features are added:
Python 3.9.21 | packaged by conda-forge | (main, Dec 5 2024, 13:51:40)
Type 'copyright', 'credits' or 'license' for more information
IPython 8.12.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from prody import *
In [2]: atoms = parsePDB('align__addH_7lafA.pdb')
In [3]: selectChannelBySelection(atoms, residue_sele='resid 373', residues_file=True, param_file=True)

selectChannelBySelection() selects channels based on the selection.

I still need to add a function that will return residues per channel into a file (the file is used here) and an additional option to return parameters into a file (also used here).
Those will be available in the next commits.

[karolamik13]

getChannelParameters(channels, param_file_name='1tqnA') -> will save the parameters to file called
1tqnA_Parameters_All_channels.txt:
1tqnA_channel0: 56.945124331611794 1.1529255252365347 871.3272015249249
1tqnA_channel1: 48.534803029525044 1.1529255252365347 1113.9480417205011
1tqnA_channel2: 52.793238139469054 1.1529255252365347 1049.5320771190782
1tqnA_channel3: 69.76196724198059 1.1529255252365347 1342.2090130173915
1tqnA_channel4: 36.49901131352283 1.1529255252365347 626.6339281791867
1tqnA_channel5: 33.764800308315536 1.1529255252365347 417.4940800159774
1tqnA_channel6: 11.699064048139602 1.161672543421736 104.08765471789833
1tqnA_channel7: 16.154296930458283 1.3122081535867374 187.24450715204378
1tqnA_channel8: 22.42697614131529 1.2063476851586834 219.87584623622723

getChannelResidueNames(atoms, channels) -> Provide info about residues that are forming channels
['channel0: LYS173, SER180, VAL183, ILE184, ARG212, PHE302, ALA305, GLY306, THR309, THR310, SER312, SER315, PHE316, TYR319, GLU320, PHE367, ILE369, ALA370, CYS442, GLY444, PHE447, ASN451, LEU475, LEU482, LEU483, GLN484, PRO485, VAL489',
'channel1: ARG106, SER180, VAL183, ILE184, PHE215, THR224, PHE302, ALA305, GLY306, THR310, CYS442, GLY444, PHE447, ASN451',
'channel2: ILE50, LEU51, TYR53, HIS54, PHE57, SER180, VAL183, ILE184, PHE215, LEU216, LEU221, THR224, PHE302, ALA305, GLY306, THR310, CYS442, GLY444, PHE447, ASN451',
'channel3: PHE46, ASP76, GLY77, GLN78, GLN79, ARG106, SER180, VAL183, ILE184, PHE215, THR224, VAL225, PHE226, PRO227, PHE228, PHE302, ALA305, GLY306, THR310, CYS442, GLY444, PHE447, ASN451',
'channel4: SER180, VAL183, ILE184, ARG212, PHE302, ALA305, GLY306, GLU308, THR309, THR310, SER312, ILE369, ALA370, CYS442, GLY444, PHE447, ASN451, LEU482, GLN484',
'channel5: SER180, VAL183, ILE184, THR187, SER188, PHE203, PHE248, SER252, VAL253, ARG255, MET256, PHE271, SER299, PHE302, ILE303, GLY306, THR310, PHE447, ASN451',
'channel6: ILE149, ALA150, GLY153, ASP154, TYR179, PRO344, PRO345, MET450, ASN451, LEU454, ALA455, ARG458',
'channel7: TYR152, LEU156, ASN159, LEU160, GLU163, VAL175, ALA178, TYR179, ASP182, LEU196',
'channel8: LEU132, PRO135, THR136, LYS141, LEU274, MET275, SER278, GLN279, LEU290, LEU295']

To save it in a file:
getChannelResidueNames(atoms, channels, residues_file_name='1tqnA')

The file name is then 1tqnA_Residues_All_channels.txt and contains:
1tqnA_channel0: LYS173, SER180, VAL183, ILE184, ARG212, PHE302, ALA305, GLY306, THR309, THR310, SER312, S
1tqnA_channel1: ARG106, SER180, VAL183, ILE184, PHE215, THR224, PHE302, ALA305, GLY306, THR310, CYS442, G
1tqnA_channel2: ILE50, LEU51, TYR53, HIS54, PHE57, SER180, VAL183, ILE184, PHE215, LEU216, LEU221, THR224
1tqnA_channel3: PHE46, ASP76, GLY77, GLN78, GLN79, ARG106, SER180, VAL183, ILE184, PHE215, THR224, VAL225
1tqnA_channel4: SER180, VAL183, ILE184, ARG212, PHE302, ALA305, GLY306, GLU308, THR309, THR310, SER312, I
1tqnA_channel5: SER180, VAL183, ILE184, THR187, SER188, PHE203, PHE248, SER252, VAL253, ARG255, MET256, P
1tqnA_channel6: ILE149, ALA150, GLY153, ASP154, TYR179, PRO344, PRO345, MET450, ASN451, LEU454, ALA455, A
1tqnA_channel7: TYR152, LEU156, ASN159, LEU160, GLU163, VAL175, ALA178, TYR179, ASP182, LEU196
1tqnA_channel8: LEU132, PRO135, THR136, LYS141, LEU274, MET275, SER278, GLN279, LEU290, LEU295