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pdbfixer
Commit 951102cd by Peter Eastman Committed by GitHub
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Changes to work with OpenMM 7.6 (#223)

parent 4495086f
Showing with 23 additions and 23 deletions
pdbfixer/pdbfixer.py
...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of ...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org. Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2013-2020 Stanford University and the Authors. Portions copyright (c) 2013-2021 Stanford University and the Authors.
Authors: Peter Eastman Authors: Peter Eastman
Contributors: Contributors:
...@@ -32,18 +32,18 @@ from __future__ import absolute_import ...@@ -32,18 +32,18 @@ from __future__ import absolute_import
__author__ = "Peter Eastman" __author__ = "Peter Eastman"
__version__ = "1.7" __version__ = "1.7"
import simtk.openmm as mm import openmm as mm
import simtk.openmm.app as app import openmm.app as app
import simtk.unit as unit import openmm.unit as unit
from simtk.openmm.app.internal.pdbstructure import PdbStructure from openmm.app.internal.pdbstructure import PdbStructure
from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
from simtk.openmm.app.element import hydrogen, oxygen from openmm.app.element import hydrogen, oxygen
from simtk.openmm.app.forcefield import NonbondedGenerator from openmm.app.forcefield import NonbondedGenerator
# Support Cythonized functions in OpenMM 7.3 # Support Cythonized functions in OpenMM 7.3
# and also implementations in older versions. # and also implementations in older versions.
try: try:
from simtk.openmm.app.internal import compiled from openmm.app.internal import compiled
matchResidue = compiled.matchResidueToTemplate matchResidue = compiled.matchResidueToTemplate
except ImportError: except ImportError:
matchResidue = app.forcefield._matchResidue matchResidue = app.forcefield._matchResidue
...@@ -123,8 +123,8 @@ def _overlayPoints(points1, points2): ...@@ -123,8 +123,8 @@ def _overlayPoints(points1, points2):
Parameters Parameters
---------- ----------
points1 (numpy array of simtk.unit.Quantity with units compatible with distance) - reference set of coordinates points1 (numpy array of openmm.unit.Quantity with units compatible with distance) - reference set of coordinates
points2 (numpy array of simtk.unit.Quantity with units compatible with distance) - set of coordinates to be rotated points2 (numpy array of openmm.unit.Quantity with units compatible with distance) - set of coordinates to be rotated
Returns Returns
------- -------
...@@ -356,11 +356,11 @@ class PDBFixer(object): ...@@ -356,11 +356,11 @@ class PDBFixer(object):
Returns Returns
------- -------
newTopology : simtk.openmm.app.Topology newTopology : openmm.app.Topology
A new Topology object containing atoms from the old. A new Topology object containing atoms from the old.
newPositions : list of simtk.unit.Quantity with units compatible with nanometers newPositions : list of openmm.unit.Quantity with units compatible with nanometers
Atom positions for the new Topology object. Atom positions for the new Topology object.
newAtoms : simtk.openmm.app.Topology.Atom newAtoms : openmm.app.Topology.Atom
New atom objects. New atom objects.
existingAtomMap : dict existingAtomMap : dict
Mapping from old atoms to new atoms. Mapping from old atoms to new atoms.
...@@ -1051,17 +1051,17 @@ class PDBFixer(object): ...@@ -1051,17 +1051,17 @@ class PDBFixer(object):
Parameters Parameters
---------- ----------
boxSize : simtk.openmm.Vec3, optional, default=None boxSize : openmm.Vec3, optional, default=None
The size of the box to fill with water. If specified, padding and boxVectors must not be specified. The size of the box to fill with water. If specified, padding and boxVectors must not be specified.
padding : simtk.unit.Quantity compatible with nanometers, optional, default=None padding : openmm.unit.Quantity compatible with nanometers, optional, default=None
Padding around macromolecule for filling box with water. If specified, boxSize and boxVectors must not be specified. Padding around macromolecule for filling box with water. If specified, boxSize and boxVectors must not be specified.
boxVectors : 3-tuple of simtk.openmm.Vec3, optional, default=None boxVectors : 3-tuple of openmm.Vec3, optional, default=None
Three vectors specifying the geometry of the box. If specified, padding and boxSize must not be specified. Three vectors specifying the geometry of the box. If specified, padding and boxSize must not be specified.
positiveIon : str, optional, default='Na+' positiveIon : str, optional, default='Na+'
The type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'. The type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'.
negativeIon : str, optional, default='Cl-' negativeIon : str, optional, default='Cl-'
The type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. The type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'.
ionicStrength : simtk.unit.Quantity with units compatible with molar, optional, default=0*molar ionicStrength : openmm.unit.Quantity with units compatible with molar, optional, default=0*molar
The total concentration of ions (both positive and negative) to add. This does not include ions that are added to neutralize the system. The total concentration of ions (both positive and negative) to add. This does not include ions that are added to neutralize the system.
Examples Examples
...@@ -1107,7 +1107,7 @@ class PDBFixer(object): ...@@ -1107,7 +1107,7 @@ class PDBFixer(object):
The type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'. The type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'.
negativeIon : str, optional, default='Cl-' negativeIon : str, optional, default='Cl-'
The type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. The type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'.
ionicStrength : simtk.unit.Quantity with units compatible with molar, optional, default=0*molar ionicStrength : openmm.unit.Quantity with units compatible with molar, optional, default=0*molar
The total concentration of ions (both positive and negative) to add. This does not include ions that are added to neutralize the system. The total concentration of ions (both positive and negative) to add. This does not include ions that are added to neutralize the system.
""" """
modeller = app.Modeller(self.topology, self.positions) modeller = app.Modeller(self.topology, self.positions)
......
pdbfixer/ui.py
...@@ -6,9 +6,9 @@ import time ...@@ -6,9 +6,9 @@ import time
import sys import sys
from math import sqrt from math import sqrt
import simtk.openmm.app as app import openmm.app as app
import simtk.unit as unit import openmm.unit as unit
from simtk.openmm.vec3 import Vec3 from openmm.vec3 import Vec3
from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat
from . import uiserver from . import uiserver
......
setup.py
...@@ -34,7 +34,7 @@ from setuptools import setup, find_packages ...@@ -34,7 +34,7 @@ from setuptools import setup, find_packages
DOCLINES = __doc__.split("\n") DOCLINES = __doc__.split("\n")
######################## ########################
__version__ = '1.7' __version__ = '1.8'
VERSION = __version__ VERSION = __version__
ISRELEASED = False ISRELEASED = False
######################## ########################
......
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