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Fix CHARMM files parsing and system building #23

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merged 7 commits into from
Oct 20, 2022
Merged

Fix CHARMM files parsing and system building #23

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9c02158
Fix CHARMM files parsing and system building
mdpoleto Sep 1, 2022
3cafee6
Small fix - setPeriodicBoxVectors() and CHARMM
mdpoleto Sep 2, 2022
699151e
Merge branch 'MiaoLab20:main' into main
mdpoleto Oct 13, 2022
0418c0e
Move parameter file parsing and box vector parsing to parser.py.
mdpoleto Oct 13, 2022
5ab5fa4
Including explicit variables for box-vectors. Parameter file attribut…
mdpoleto Oct 14, 2022
a276d69
Creating parse_charmm_gui_toppar method and organizing box vector par…
mdpoleto Oct 19, 2022
46f1a76
Moving parse_and_assign_charmm_gui_toppar() to parser.py
mdpoleto Oct 19, 2022
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49 changes: 24 additions & 25 deletions gamd/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ def assign_tag(root, tagname, value, attributes=None):
xmlTag.text = str(value)
for attribute in attributes:
xmlTag.set(attribute, attributes[attribute])

return

class SystemConfig:
Expand All @@ -31,7 +31,7 @@ def __init__(self):
self.nonbonded_cutoff = 0.9*unit.nanometer
self.constraints = "HBonds"
return

def serialize(self, root):
assign_tag(root, "nonbonded-method", self.nonbonded_method)
assign_tag(root, "nonbonded-cutoff", self.nonbonded_cutoff.value_in_unit(unit.nanometers))
Expand All @@ -43,7 +43,7 @@ def __init__(self):
self.pressure = 1.0 * unit.bar
self.frequency = 25
return

def serialize(self, root):
assign_tag(root, "pressure", self.pressure.value_in_unit(unit.bar))
assign_tag(root, "frequency", self.frequency)
Expand All @@ -54,7 +54,7 @@ def __init__(self):
self.primary = 6.0 * unit.kilocalories_per_mole
self.secondary = 6.0 * unit.kilocalories_per_mole
return

def serialize(self, root):
assign_tag(root, "primary", self.primary.value_in_unit(unit.kilocalories_per_mole))
assign_tag(root, "secondary", self.secondary.value_in_unit(unit.kilocalories_per_mole))
Expand All @@ -70,7 +70,7 @@ def __init__(self):
self.total_simulation_length = 0
self.averaging_window_interval = 0
return

def serialize(self, root):
assign_tag(root, "conventional-md-prep", self.conventional_md_prep)
assign_tag(root, "conventional-md", self.conventional_md)
Expand All @@ -80,7 +80,7 @@ def serialize(self, root):
#assign_tag(root, "total-simulation-length", self.total_simulation_length)
assign_tag(root, "averaging-window-interval", self.averaging_window_interval)
return

def compute_total_simulation_length(self):
self.total_simulation_length = self.conventional_md \
+ self.gamd_equilibration + self.gamd_production
Expand All @@ -95,7 +95,7 @@ def __init__(self):
self.friction_coefficient = 1.0 * unit.picoseconds ** -1
self.number_of_steps = IntegratorNumberOfStepsConfig()
return

def serialize(self, root):
assign_tag(root, "algorithm", self.algorithm)
assign_tag(root, "boost-type", self.boost_type)
Expand All @@ -114,26 +114,25 @@ def __init__(self):
self.coordinates = ""
self.coordinates_filetype = ""
return

def serialize(self, root):
assign_tag(root, "topology", self.topology)
assign_tag(root, "coordinates", self.coordinates, {"type": self.coordinates_filetype})
return


class CharmmConfig:
def __init__(self):
self.topology = ""
self.coordinates = ""
self.parameters = []
self.parameters = ""
self.box_vector = ""
return

def serialize(self, root):
assign_tag(root, "topology", self.topology)
assign_tag(root, "coordinates", self.coordinates)
xmlParams = ET.SubElement(root, 'parameters')
for params_filename in self.parameters:
assign_tag(xmlParams, "file", params_filename)
assign_tag(root, "parameters", self.parameters)
assign_tag(root, "box_vector", self.box_vector)
return

class GromacsConfig:
Expand All @@ -142,7 +141,7 @@ def __init__(self):
self.coordinates = ""
self.include_dir = ""
return

def serialize(self, root):
assign_tag(root, "topology", self.topology)
assign_tag(root, "coordinates", self.coordinates)
Expand All @@ -155,7 +154,7 @@ def __init__(self):
self.forcefield_list_native = []
self.forcefield_list_external = []
return

def serialize(self, root):
assign_tag(root, "coordinates", self.coordinates)
xmlForcefields = ET.SubElement(root, "forcefields")
Expand All @@ -174,7 +173,7 @@ def __init__(self):
self.gromacs = None
self.forcefield = None
return

def serialize(self, root):
if self.amber is not None:
xml_amber_tags = ET.SubElement(root, "amber")
Expand All @@ -198,13 +197,13 @@ def __init__(self):
self.restart_checkpoint_interval = 50000
self.statistics_interval = 500
return

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def compute_chunk_size(self):
gcd = np.gcd.reduce(
[self.energy_interval, self.coordinates_interval,
self.restart_checkpoint_interval, self.statistics_interval])
return gcd

def serialize(self, root):
xml_energy_tags = ET.SubElement(root, "energy")
assign_tag(xml_energy_tags, "interval", self.energy_interval)
Expand All @@ -220,7 +219,7 @@ def __init__(self):
self.overwrite_output = True
self.reporting = OutputsReportingConfig()
return

def serialize(self, root):
assign_tag(root, "directory", self.directory)
assign_tag(root, "overwrite-output", self.overwrite_output)
Expand All @@ -231,15 +230,15 @@ def serialize(self, root):
class Config:
def __init__(self):
# set all the default values

self.temperature = 298.15 * unit.kelvin
self.system = SystemConfig()
self.barostat = None #BarostatConfig()
self.run_minimization = True
self.integrator = IntegratorConfig()
self.input_files = InputFilesConfig()
self.outputs = OutputsConfig()

def serialize(self, filename):
root = ET.Element('gamd')
assign_tag(root, "temperature", self.temperature.value_in_unit(unit.kelvin))
Expand All @@ -255,13 +254,13 @@ def serialize(self, filename):
self.input_files.serialize(xml_input_files)
xml_outputs = ET.SubElement(root, "outputs")
self.outputs.serialize(xml_outputs)

xmlstr = minidom.parseString(ET.tostring(root)).toprettyxml(
indent=" ")
our_file=open(filename, 'w')
our_file.write(xmlstr)
our_file.close()


if __name__ == "__main__":
pass
pass
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