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orionarcher / pymatgen-io-openmm

A Pymatgen IO module for setting up OpenMM simulations.
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get unnecessary output from openmm_generator.get_input_set #4

Open SophiaRuan opened 2 years ago

SophiaRuan commented 2 years ago 
trimer_smile = "O=C1CC(OC(O)=C1/C(CCCCCCCC/C(O[H])=C2C(CC(OC/2=O)(C)C)=O)=[N+]([H])/CC[NH+](CC/[N+]([H])=C(CCCCCCCC/C(O[H])=C3C(CC(OC/3=O)(C)C)=O)/C4=C(O)OC(CC4=O)(C)C)CC/[N+]([H])=C(CCCCCCCC/C(O[H])=C5C(CC(OC/5=O)(C)C)=O)/C6=C(O)OC(CC6=O)(C)C)(C)C"
molecules = {"O": 3640,"[Cl-]":560, "[OH3+]": 360, trimer_smile: 50}

input_set = openmm_generator.get_input_set(molecules, density = 0.1)

This code will generate unnecessary output like this: Also, it doesn't print a Packmol set generated.

<ForceField>
  <AtomTypes>
    <Type name="[H][O][H]$O1#0" element="O" mass="15.99943" class="[H][O][H]$O1#0"/>
    <Type name="[H][O][H]$H1#1" element="H" mass="1.007947" class="[H][O][H]$H1#1"/>
    <Type name="[H][O][H]$H2#2" element="H" mass="1.007947" class="[H][O][H]$H2#2"/>
  </AtomTypes>
  <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
    <UseAttributeFromResidue name="charge"/>
    <Atom sigma="0.31507" epsilon="0.6363864000000001" class="[H][O][H]$O1#0"/>
    <Atom sigma="0.1" epsilon="0.0" class="[H][O][H]$H1#1"/>
    <Atom sigma="0.1" epsilon="0.0" class="[H][O][H]$H2#2"/>
  </NonbondedForce>
  <HarmonicBondForce>
    <Bond class1="[H][O][H]$O1#0" class2="[H][O][H]$H1#1" length="0.09716763312559001" k="454823.2121721368"/>
    <Bond class1="[H][O][H]$O1#0" class2="[H][O][H]$H2#2" length="0.09716763312559001" k="454823.2121721368"/>
  </HarmonicBondForce>
  <HarmonicAngleForce>
    <Angle class1="[H][O][H]$H1#1" class2="[H][O][H]$O1#0" class3="[H][O][H]$H2#2" angle="1.9260385591386002" k="544.678275491328"/>
  </HarmonicAngleForce>
  <PeriodicTorsionForce ordering="smirnoff"/>
  <Residues>
    <Residue name="[H][O][H]">
      <Atom name="O1" type="[H][O][H]$O1#0" charge="-0.86"/>
      <Atom name="H1" type="[H][O][H]$H1#1" charge="0.43"/>
      <Atom name="H2" type="[H][O][H]$H2#2" charge="0.43"/>
      <Bond atomName1="O1" atomName2="H1"/>
      <Bond atomName1="O1" atomName2="H2"/>
    </Residue>
  </Residues>
</ForceField>

dict_keys([])
dict_keys([])