diff --git a/doc/source/index.rst b/doc/source/index.rst
index bbac12bcb16cfd88ea77fc742ff44d48a3ce4834..94fd76232138995504434cc6119211b2db12250e 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -11,8 +11,6 @@ Contents:
.. toctree::
:maxdepth: 2
- members
-
Features
--------
PyCGTOOL provides a means to quickly and easily generate coarse-grained molecular dynamics models within the MARTINI framework from all-atom or united-atom simulation trajectories.
@@ -29,6 +27,11 @@ PyCGTOOL requires:
Optional:
+- MDTraj for pseudo-CG XTC output (http://mdtraj.org/1.7.2/) with own dependencies:
+
+ - Scipy (https://www.scipy.org/)
+ - Cython (http://cython.org/)
+
- Python testing framework (e.g. Nose2, py.test)
- Numba for increased performance (http://numba.pydata.org/)
- Sphinx to generate documentation yourself (http://www.sphinx-doc.org/en/stable/)
@@ -42,9 +45,9 @@ PyCGTOOL requires four input files to generate a coarse-grained model:
-m PyCGTOOL mapping definition file
-b PyCGTOOL bond definition file
-The program is called by:
-::
- pycgtool.py -g <GRO file> -x <XTC file> -m <MAP file> -b <BND file>
+The program is called by::
+
+ pycgtool.py -g <GRO file> -x <XTC file> -m <MAP file> -b <BND file>
Example mapping and bond definition files are present in the ``test/data`` directory. Their format is explained below.
@@ -58,8 +61,8 @@ Mapping Definition
~~~~~~~~~~~~~~~~~~
An example of mapping definition file for the monosaccharide allose taken from ``test/data/sugar.map`` is shown below.
-Molecule names (as present in the gro coordinate file) are used as section headers inside square brackets. Each of the following lines describes a single coarse-grained bead mapping. The items on a line are: the name of the bead, its MARTINI bead type, a list of all the atom names it should contain. All items on a line are whitespace separated. Multiple molecules may be specified in their own sections. It is not recommended to provide a mapping for water since MARTINI water combines four molecules into a single bead which is not yet supported by PyCGTOOL.
-::
+Molecule names (as present in the gro coordinate file) are used as section headers inside square brackets. Each of the following lines describes a single coarse-grained bead mapping. The items on a line are: the name of the bead, its MARTINI bead type, a list of all the atom names it should contain. All items on a line are whitespace separated. Multiple molecules may be specified in their own sections. It is not recommended to provide a mapping for water since MARTINI water combines four molecules into a single bead which is not yet supported by PyCGTOOL. ::
+
; comments begin with a semicolon
[ALLA]
C1 P3 C1 O1
@@ -78,8 +81,8 @@ An example bond definition file for the monosaccharide allose taken from ``test/
As in the mapping definition file, molecule names are used as section headers inside square brackets. The following lines define bonds lengths, angles and dihedrals between coarse-grained beads. Each line is a list of bead names, using the names defined in the mapping file. Two bead names on a line defines a bond length, three defines an angle, and four defines a dihedral.
-If no angles are defined for a molecule, PyCGTOOL will construct all angles from the list of bonds. This may also be enabled for dihedrals via the ``--interactive`` flag, but is not recommended as in most cases coarse-grained models do not require dihedrals. Additionally, any angles inside a triangle of bond lengths are excluded from the output as they often cause simulation stability issues when used in conjunction with LINCS.
-::
+If no angles are defined for a molecule, PyCGTOOL will construct all angles from the list of bonds. This may also be enabled for dihedrals via the ``--interactive`` flag, but is not recommended as in most cases coarse-grained models do not require dihedrals. Additionally, any angles inside a triangle of bond lengths are excluded from the output as they often cause simulation stability issues when used in conjunction with LINCS. ::
+
; comments begin with a semicolon
[ALLA]
C1 C2
@@ -111,12 +114,12 @@ Modes
~~~~~
PyCGTOOL performs several other functions which may be useful in the testing and use of coarse-grained models.
-Mapping-only mode performs a coarse-grain mapping on a single frame and may be used to generate initial coordinates for a coarse-grain simulation, whether the model being used was created by PyCGTOOL or not. In this respect it functions similarly to the MARTINI tool MARTINIZE. This mode may be invoked by:
-::
+Mapping-only mode performs a coarse-grain mapping on a single frame and may be used to generate initial coordinates for a coarse-grain simulation, whether the model being used was created by PyCGTOOL or not. In this respect it functions similarly to the MARTINI tool MARTINIZE. This mode may be invoked by::
+
pycgtool.py -g <GRO file> -m <MAP file>
-Measure-only mode may be used to aid in the testing of a coarse-grained model by making measurements of bonds from a true corase-grained simulation trajectory. These bond measurements are those collected from the pseudo-coarse-grained trajectory used to generate the model, so are a directly comparable measure of model accuracy. This mode may be invoked by:
-::
+Measure-only mode may be used to aid in the testing of a coarse-grained model by making measurements of bonds from a true corase-grained simulation trajectory. These bond measurements are those collected from the pseudo-coarse-grained trajectory used to generate the model, so are a directly comparable measure of model accuracy. This mode may be invoked by::
+
pycgtool.py -g <GRO file> -x <XTC file> -b <BND file>
Options
@@ -126,7 +129,9 @@ By passing the flag ``--interactive`` to PyCGTOOL several advanced options are a
================== ========================================== =======================
Option Description Values
================== ========================================== =======================
+output_name Base name of output files **out**, any string
output Coordinate output format **gro**
+output_xtc Should a pseudo-CG XTC be created **False**, True
map_only Run in mapping-only mode **False**, True
map_center Mapping method **geom**, mass
constr_threshold Convert stiff bonds to constraints over **100000**, any number
diff --git a/pycgtool.py b/pycgtool.py
index 0bc112391d17040023a19afd2f55c29921629530..6eb7ca03169c8c0e437da63bf7ed7e7b2c8bc675 100755
--- a/pycgtool.py
+++ b/pycgtool.py
@@ -95,24 +95,21 @@ if __name__ == "__main__":
args = parser.parse_args()
config = Options([("output_name", "out"),
("output", "gro"),
- ("map_only", False),
+ ("output_xtc", args.outputxtc),
+ ("map_only", bool(args.bnd)),
("map_center", "geom"),
("constr_threshold", 100000),
- ("dump_measurements", False),
+ ("dump_measurements", bool(args.bnd) and not bool(args.map)),
("dump_n_values", 100000),
("output_forcefield", False),
("temperature", 310),
("angle_default_fc", True),
("generate_angles", True),
- ("generate_dihedrals", False),
- ("output_xtc", args.outputxtc)],
+ ("generate_dihedrals", False)],
args)
if not args.bnd:
config.set("map_only", True)
- if args.bnd and not args.map:
- config.set("dump_measurements", True)
-
if not args.map and not args.bnd:
parser.error("One or both of -m and -b is required.")
diff --git a/pycgtool/mapping.py b/pycgtool/mapping.py
index d0f3e78a7df5d0a490415bb6c3afd80a45bfa418..16828db316987aa2b3b3653d80d28b603939602e 100644
--- a/pycgtool/mapping.py
+++ b/pycgtool/mapping.py
@@ -126,12 +126,14 @@ class Mapping:
"""
if cgframe is None:
cgframe = Frame()
- cgframe.name = frame.name
- cgframe.number = frame.number
- cgframe.box = frame.box
+ cgframe.name = frame.name
+
cgframe.natoms = 0
cgframe.residues = []
+ cgframe.number = frame.number
+ cgframe.box = frame.box
+
for aares in frame:
if aares.name not in self._mappings:
continue