Commit be2fb19f authored by Jacob Durrant's avatar Jacob Durrant

Updated version number to 2.1.

parent 64ef5df4
Pipeline #280 canceled with stages
*.pyc
__pycache__
from_Ben_Patty
......@@ -18,10 +18,10 @@ You should have received a copy of the GNU General Public License along with
this program. If not, see
[https://www.gnu.org/licenses/](https://www.gnu.org/licenses/).
1\. Download POVME 2.0
1\. Download POVME 2.1
----------------------
Begin by downloading POVME 2.0. An example input file is included with the
Begin by downloading POVME 2.1. An example input file is included with the
download (in the 'examples' directory). This input file is heavily commented
and may be even more useful that the information provided on this website.
......
# POVME 2.0 Sample Input File (For Windows)
# POVME 2.1 Sample Input File (For Windows)
# First, we need to define a point field that entirely encompasses all trajectory pockets.
GridSpacing 1.0 # The distance, in Angstroms, between
......@@ -10,9 +10,9 @@ PointsInclusionSphere 65.0 98.0 50.0 16.0 # Add a sphere of poi
# encompassing region, centered on
# (65.0 98.0 50.0) with radius 16.0.
# (65.0 98.0 50.0) is the location of
# the enzymatic active site in the
# the enzymatic active site in the
# sample PDB trajectory file provided
# (4NSS.pdb).
# (4NSS.pdb).
PointsInclusionSphere -100.0 -100.0 -100.0 10.0 # Add a second sphere of points. Note
# that this sphere is included only for
......@@ -23,18 +23,18 @@ PointsInclusionSphere -100.0 -100.0 -100.0 10.0 # Add a second sphere
PointsInclusionBox 100.0 100.0 100.0 10.0 10.0 10.0 # Add a rectangular prism ("box") of
# points to the pocket-encompassing
# region, centered on (100.0 100.0 100.0)
# and spanning 10.0 Angstroms in the x,
# y, and z directions, respectively.
# Again, this box is far from the
# and spanning 10.0 Angstroms in the x,
# y, and z directions, respectively.
# Again, this box is far from the
# 4NSS.pdb structure and is included only
# for demonstration purposes.
PointsExclusionSphere -100.0 -100.0 -100.0 10.0 # Remove all points from the pocket-
# encompassing region that fall within
# a sphere centered at
# (-100.0 -100.0 -100.0) with radius
# 10.0.
PointsExclusionBox 100.0 100.0 100.0 10.0 10.0 10.0 # Remove all points from the pocket-
# encompassing region that fall within a
# box, centered at (100.0 100.0 100.0)
......@@ -64,7 +64,7 @@ SavePoints true # You can optionally
# it from scratch is more efficient. Note
# that POVME also saves a NPY file, which
# contains the same data as the PDB file
# but can be loaded much faster in
# but can be loaded much faster in
# subsequent POVME runs. The point-field
# PDB file is saved to
# {PREFIX}point_field.pdb (see
......@@ -83,11 +83,11 @@ SavePoints true # You can optionally
# them using the comamnds above. Note
# that you should use the .pdb.npy file,
# not the pdb file.
# Load the PDB trajectory file
PDBFileName 4NSS.pdb # Load in the PDB trajectory file with
# the pocket you want to analyze.
# Tell POVME how to identify points that are within the binding pocket.
DistanceCutoff 1.09 # Any point that comes within this
# distance of any receptor atom's van der
......@@ -181,8 +181,8 @@ OutputEqualNumPointsPerFrame true # Some visualization
SaveTabbedVolumeFile true # If true, POVME saves the calculated
# volumes to a file in a simple tabular
# format that can be easily pasted into
# popular spreadsheet programs like
# Microsoft Excel. The file is named
# popular spreadsheet programs like
# Microsoft Excel. The file is named
# {PREFIX}volumes.tabbed.txt
SaveVolumetricDensityMap true # If true, POVME saves a volumetric
......@@ -191,11 +191,9 @@ SaveVolumetricDensityMap true # If true, POVME save
# with each of the pocket-occupying
# points by calculating the fraction of
# all trajectory pocket volumes that
# include the given point. The file is
# include the given point. The file is
# named {PREFIX}volumetric_density.dx.
CompressOutput true # If you're short on disk space, POVME
# can automatically compress all output
# files using gz compression.
# POVME 2.0 Sample Input File
# POVME 2.1 Sample Input File
# First, we need to define a point field that entirely encompasses all trajectory pockets.
GridSpacing 1.0 # The distance, in Angstroms, between
......@@ -10,9 +10,9 @@ PointsInclusionSphere 65.0 98.0 50.0 16.0 # Add a sphere of poi
# encompassing region, centered on
# (65.0 98.0 50.0) with radius 16.0.
# (65.0 98.0 50.0) is the location of
# the enzymatic active site in the
# the enzymatic active site in the
# sample PDB trajectory file provided
# (4NSS.pdb).
# (4NSS.pdb).
PointsInclusionSphere -100.0 -100.0 -100.0 10.0 # Add a second sphere of points. Note
# that this sphere is included only for
......@@ -23,18 +23,18 @@ PointsInclusionSphere -100.0 -100.0 -100.0 10.0 # Add a second sphere
PointsInclusionBox 100.0 100.0 100.0 10.0 10.0 10.0 # Add a rectangular prism ("box") of
# points to the pocket-encompassing
# region, centered on (100.0 100.0 100.0)
# and spanning 10.0 Angstroms in the x,
# y, and z directions, respectively.
# Again, this box is far from the
# and spanning 10.0 Angstroms in the x,
# y, and z directions, respectively.
# Again, this box is far from the
# 4NSS.pdb structure and is included only
# for demonstration purposes.
PointsExclusionSphere -100.0 -100.0 -100.0 10.0 # Remove all points from the pocket-
# encompassing region that fall within
# a sphere centered at
# (-100.0 -100.0 -100.0) with radius
# 10.0.
PointsExclusionBox 100.0 100.0 100.0 10.0 10.0 10.0 # Remove all points from the pocket-
# encompassing region that fall within a
# box, centered at (100.0 100.0 100.0)
......@@ -64,7 +64,7 @@ SavePoints true # You can optionally
# it from scratch is more efficient. Note
# that POVME also saves a NPY file, which
# contains the same data as the PDB file
# but can be loaded much faster in
# but can be loaded much faster in
# subsequent POVME runs. The point-field
# PDB file is saved to
# {PREFIX}point_field.pdb (see
......@@ -83,11 +83,11 @@ SavePoints true # You can optionally
# them using the comamnds above. Note
# that you should use the .pdb.npy file,
# not the pdb file.
# Load the PDB trajectory file
PDBFileName 4NSS.pdb # Load in the PDB trajectory file with
# the pocket you want to analyze.
# Tell POVME how to identify points that are within the binding pocket.
DistanceCutoff 1.09 # Any point that comes within this
# distance of any receptor atom's van der
......@@ -181,8 +181,8 @@ OutputEqualNumPointsPerFrame true # Some visualization
SaveTabbedVolumeFile true # If true, POVME saves the calculated
# volumes to a file in a simple tabular
# format that can be easily pasted into
# popular spreadsheet programs like
# Microsoft Excel. The file is named
# popular spreadsheet programs like
# Microsoft Excel. The file is named
# {PREFIX}volumes.tabbed.txt
SaveVolumetricDensityMap true # If true, POVME saves a volumetric
......@@ -191,10 +191,9 @@ SaveVolumetricDensityMap true # If true, POVME save
# with each of the pocket-occupying
# points by calculating the fraction of
# all trajectory pocket volumes that
# include the given point. The file is
# include the given point. The file is
# named {PREFIX}volumetric_density.dx.
CompressOutput true # If you're short on disk space, POVME
# can automatically compress all output
# files using gz compression.
......@@ -20,8 +20,8 @@
If you use pymolecule in your work, please cite [REFERENCE HERE]"""
"""Note: This is a beta version of pymolecule 2.0. Not intended for distribution
independent of POVME 2.0!!!"""
"""Note: This is a beta version of pymolecule. Not intended for distribution
independent of POVME 2.1!!!"""
import os
......@@ -37,7 +37,7 @@ import sys
import pickle as pickle
import shutil
version = "2.0"
version = "beta"
if __name__ == "__main__":
print("\npymolecule " + version + "\n")
......
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