pycharmm (c48b2)
The pycharmm Python interface to CHARMM
This module describes the interface of CHARMM with the Python
programming language. The pycharmm Python package for CHARMM is
compatible with Python versions 3.6 and greater. The package requires
Python installed on the machine. Please see Python documentation for
the basic procedures to set-up and install Python.
The pycharmm interface is under continuing development with
new CHARMM features being added all of the time. The current
implementation supports dynamics and energy calculations.
Special Notice: The pycharmm interface is an evolving interface.
The interface and associated modules have been well
tested, but are likely to contain yet undiscovered limitations,
compared with the full functionality in CHARMM. Users are forewarned to
carry out some pre-testing on their system prior to initiating long
runs. As new features and methods are added to the interface they will be
described in the updated documentation.
* Setup | Building CHARMM and installing pycharmm
* Use | Use and functional support of pycharmm
* Examples | Examples of pycharmm use
This module describes the interface of CHARMM with the Python
programming language. The pycharmm Python package for CHARMM is
compatible with Python versions 3.6 and greater. The package requires
Python installed on the machine. Please see Python documentation for
the basic procedures to set-up and install Python.
The pycharmm interface is under continuing development with
new CHARMM features being added all of the time. The current
implementation supports dynamics and energy calculations.
Special Notice: The pycharmm interface is an evolving interface.
The interface and associated modules have been well
tested, but are likely to contain yet undiscovered limitations,
compared with the full functionality in CHARMM. Users are forewarned to
carry out some pre-testing on their system prior to initiating long
runs. As new features and methods are added to the interface they will be
described in the updated documentation.
* Setup | Building CHARMM and installing pycharmm
* Use | Use and functional support of pycharmm
* Examples | Examples of pycharmm use
Top
BUILDING CHARMM AND INSTALLING PYCHARMM
===========================================
There are two steps to setup pycharmm and CHARMM for use in Python programming.
The first step is to build CHARMM as a shared object. Next, pycharmm must be
installed as a python package using pip.
To interface with pycharmm, CHARMM must be built as shared object.
Add '--as-library' to the configure command and then build as usual.
For example,
$ ./configure --as-library
$ make -j 2 -C build/cmake install
After a build completes successfully, the shared object should be in the lib
subdirectory of the install directory as libcharmm.so or libcharmm.dylib.
To install pycharmm, Python and the Python package installer pip must be
present. Please see Python documentation for the basic procedures to setup and
install Python.
To install pycharmm, use the path to the pycharmm directory as an argument to
pip. For example, from the root of the CHARMM source directory,
$ pip install tool/pycharmm
At run time, set the environment variable CHARMM_LIB_DIR to the path of the
For example,
bash shell: export CHARMM_LIB_DIR=/usr/local/charmm/lib
csh shell: setenv CHARMM_LIB_DIR /usr/local/charmm/lib
This can be added to your .bashrc or .cshrc so that the variable is always
set.
BUILDING CHARMM AND INSTALLING PYCHARMM
===========================================
There are two steps to setup pycharmm and CHARMM for use in Python programming.
The first step is to build CHARMM as a shared object. Next, pycharmm must be
installed as a python package using pip.
To interface with pycharmm, CHARMM must be built as shared object.
Add '--as-library' to the configure command and then build as usual.
For example,
$ ./configure --as-library
$ make -j 2 -C build/cmake install
After a build completes successfully, the shared object should be in the lib
subdirectory of the install directory as libcharmm.so or libcharmm.dylib.
To install pycharmm, Python and the Python package installer pip must be
present. Please see Python documentation for the basic procedures to setup and
install Python.
To install pycharmm, use the path to the pycharmm directory as an argument to
pip. For example, from the root of the CHARMM source directory,
$ pip install tool/pycharmm
At run time, set the environment variable CHARMM_LIB_DIR to the path of the
For example,
bash shell: export CHARMM_LIB_DIR=/usr/local/charmm/lib
csh shell: setenv CHARMM_LIB_DIR /usr/local/charmm/lib
This can be added to your .bashrc or .cshrc so that the variable is always
set.
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USE
===
Before running a Python script or starting a Python environment, set the
environment variable CHARMM_LIB_DIR to the path of the directory containing
the CHARMM shared object (See the Setup section).
In a python interpreter or script, pycharmm modules must be loaded.
In most cases, for each CHARMM command, there is a corresponding Python module
containing a set of functions to do the task of the original command
but from the Python environment.
For example, to do an energy calculation, a portion of a script might look like the
following.
#!/bin/env python3
import os
import sys
try:
charmm_lib_dir = os.environ['CHARMM_LIB_DIR']
charmm_data_dir = os.environ['CHARMM_DATA_DIR']
except KeyError:
print('please set environment variables',
'CHARMM_LIB_DIR and CHARMM_DATA_DIR',
file=sys.stderr)
sys.exit(1)
import pycharmm.energy as energy
import pycharmm.read as read
rtf_fn = charmm_data_dir + '/top_all36_prot.rtf'
read.rtf(rtf_fn)
prm_fn = charmm_data_dir + '/par_all36_prot.prm'
read.prm(prm_fn, flex=True)
energy.show()
USE
===
Before running a Python script or starting a Python environment, set the
environment variable CHARMM_LIB_DIR to the path of the directory containing
the CHARMM shared object (See the Setup section).
In a python interpreter or script, pycharmm modules must be loaded.
In most cases, for each CHARMM command, there is a corresponding Python module
containing a set of functions to do the task of the original command
but from the Python environment.
For example, to do an energy calculation, a portion of a script might look like the
following.
#!/bin/env python3
import os
import sys
try:
charmm_lib_dir = os.environ['CHARMM_LIB_DIR']
charmm_data_dir = os.environ['CHARMM_DATA_DIR']
except KeyError:
print('please set environment variables',
'CHARMM_LIB_DIR and CHARMM_DATA_DIR',
file=sys.stderr)
sys.exit(1)
import pycharmm.energy as energy
import pycharmm.read as read
rtf_fn = charmm_data_dir + '/top_all36_prot.rtf'
read.rtf(rtf_fn)
prm_fn = charmm_data_dir + '/par_all36_prot.prm'
read.prm(prm_fn, flex=True)
energy.show()
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Examples
========
In the tool/pycharmm/tests directory, there is an example script aldidpep_build.inp
written in traditional CHARMM commands that has been ported to Python as aldidpep_build.py.
This pair of files serves as an extended example of using pycharmm.
Examples
========
In the tool/pycharmm/tests directory, there is an example script aldidpep_build.inp
written in traditional CHARMM commands that has been ported to Python as aldidpep_build.py.
This pair of files serves as an extended example of using pycharmm.