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import logging
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from paprika.restraints.utils import get_restraint_values, parse_window
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logger = logging.getLogger(__name__)
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def amber_restraint_line(restraint, window):
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"""Writes an AMBER NMR-style restraint line for a specific window.
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Parameters
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----------
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restraint: :class:`paprika.restraints.DAT_restraint`
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The pAPRika restraint to be used.
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window: str
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The calculation window that will be used to index the restraint values.
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Returns
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-------
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string: str
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A string that can be written to a file that can be read by AMBER.
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Examples
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--------
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.. code-block::
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&rst iat= 3,109, r1= 0.0000, r2= 6.9665, r3= 6.9665, r4= 999.0000,
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rk2= 5.0000000, rk3= 5.0000000, &end
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Or:
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.. code-block::
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&rst iat= -1,-1, igr1=3,4,7,8,21,22,25,26,39,40,43,44,57,58,61,62,75,76,79,
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80,93,94,97,98, igr2=109,113,115,119,
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r1= 0.0000, r2= 5.9665, r3= 5.9665, r4= 999.0000,
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rk2= 5.0000000, rk3= 5.0000000, &end
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"""
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window, phase = parse_window(window)
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if (
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restraint.phase[phase]["force_constants"] is None
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and restraint.phase[phase]["targets"] is None
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):
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return ""
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if not restraint.group1:
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iat1 = "{},".format(restraint.index1[0])
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else:
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iat1 = "-1,"
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igr1 = ""
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for index in restraint.index1:
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igr1 += "{},".format(index)
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if not restraint.group2:
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iat2 = "{},".format(restraint.index2[0])
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else:
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iat2 = "-1,"
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igr2 = ""
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for index in restraint.index2:
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igr2 += "{},".format(index)
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iat3 = ""
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if restraint.index3 and not restraint.group3:
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iat3 = "{},".format(restraint.index3[0])
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elif restraint.group3:
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iat3 = "-1,"
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igr3 = ""
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for index in restraint.index3:
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igr3 += "{},".format(index)
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iat4 = ""
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if restraint.index4 and not restraint.group4:
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iat4 = "{},".format(restraint.index4[0])
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elif restraint.group4:
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iat4 = "-1,"
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igr4 = ""
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for index in restraint.index4:
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igr4 += "{},".format(index)
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# Restraint values - Amber NMR-style
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amber_restraint_values = get_restraint_values(restraint, phase, window)
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# Prepare AMBER NMR-style restraint
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atoms = "".join([iat1, iat2, iat3, iat4])
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string = "&rst iat= {:16s} ".format(atoms)
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string += (
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" r1= {0:10.5f},".format(amber_restraint_values["r1"])
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+ " r2= {0:10.5f},".format(amber_restraint_values["r2"])
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+ " r3= {0:10.5f},".format(amber_restraint_values["r3"])
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+ " r4= {0:10.5f},".format(amber_restraint_values["r4"])
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+ " rk2= {0:10.5f},".format(amber_restraint_values["rk2"])
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+ " rk3= {0:10.5f},".format(amber_restraint_values["rk3"])
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)
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if any([restraint.group1, restraint.group2, restraint.group3, restraint.group4]):
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string += "\n "
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if restraint.group1:
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string += " igr1= {}".format(igr1)
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if restraint.group2:
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string += " igr2= {}".format(igr2)
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if restraint.group3:
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string += " igr3= {}".format(igr3)
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if restraint.group4:
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string += " igr4= {}".format(igr4)
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108
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109
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string += " &end\n"
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return string
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jeff231li