com.kotmol.pdbParser.BondInfo.kt Maven / Gradle / Ivy
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/*
* Copyright 2020 James Andreas
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License
*/
@file:Suppress(
"MemberVisibilityCanBePrivate"
)
/*@file:Suppress(
"unused",
"unused_variable",
"unused_parameter",
"deprecation",
"UNUSED_ANONYMOUS_PARAMETER",
"UNUSED_EXPRESSION",
"MemberVisibilityCanBePrivate",
"FunctionWithLambdaExpressionBody",
"UnusedMainParameter",
"JoinDeclarationAndAssignment",
"CanBePrimaryConstructorProperty",
"RemoveEmptyClassBody",
"ASSIGNED_BUT_NEVER_ACCESSED_VARIABLE",
"UNUSED_VALUE",
"ConstantConditionIf",
"ReplaceSingleLineLet",
"ReplaceJavaStaticMethodWithKotlinAnalog",
"NestedLambdaShadowedImplicitParameter",
"ArrayInDataClass" // suppresses complains about overriding equals and hashCode() operations
)*/
package com.kotmol.pdbParser
/**
* bond information
* as extracted from the database at:
* @link: https://www.ebi.ac.uk/pdbe/api/pdb/compound/bonds/
*/
/**
* NOTES:
* from the 1992 PDB file format specification:
*
* PROTEIN DATA BANK
* ATOMIC COORDINATE AND BIBLIOGRAPHIC ENTRY FORMAT DESCRIPTION
* February 1992
*
* Atom names employed for polynucleotides generally follow the precedents set for mononucleotides.
* The following points are worthy of note.
* (i) The prime character (') commonly used to denote atoms of the ribose originally was
* avoided because of non-uniformity of its external representation. An asterisk (*)
* therefore was used in its place, in entries released through January 1992.
* (ii) Of the four characters reserved for atom names the leftmost two are reserved for the
* chemical symbol (right justified) and the remaining two denote the atom's position.
* (iii) Atoms exocyclic to the ring systems have the same position identifier as the atom
* to which they are bonded except if this would result in identical atom names. In this
* case an alphabetic character is used to avoid ambiguity.
* (iv) The ring-oxygen atom of the ribose is denoted O4 rather than O1.
* (v) The extra oxygen atom at the free 5' phosphate terminus is designated OXT. This
* atom will be placed first in the coordinate set.
*/
class BondInfo {
data class KotmolBondRecord(
val atom_1: String,
val atom_2: String,
val bond_order: Float,
val bond_type: String,
val aromatic: Boolean = false,
val length: Float,
var bondRecordCreated: Boolean = false
)
val ala = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.505f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB1", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.468f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.968f
)
)
val arg = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.224f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.36f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.518f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.536f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.096f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.537f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.097f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.098f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "HD2", bond_order = 1f, bond_type = "sing", length = 1.095f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "HD3", bond_order = 1f, bond_type = "sing", length = 1.095f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "NE", bond_order = 1f, bond_type = "sing", length = 1.444f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD", bond_order = 1f, bond_type = "sing", length = 1.527f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG2", bond_order = 1f, bond_type = "sing", length = 1.097f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG3", bond_order = 1f, bond_type = "sing", length = 1.097f),
KotmolBondRecord(atom_1 = "CZ", atom_2 = "NH1", bond_order = 1f, bond_type = "sing", length = 1.391f),
KotmolBondRecord(atom_1 = "CZ", atom_2 = "NH2", bond_order = 2f, bond_type = "doub", length = 1.391f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.462f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 0.997f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 0.996f),
KotmolBondRecord(atom_1 = "NE", atom_2 = "CZ", bond_order = 1f, bond_type = "sing", length = 1.406f),
KotmolBondRecord(atom_1 = "NE", atom_2 = "HE", bond_order = 1f, bond_type = "sing", length = 1.027f),
KotmolBondRecord(atom_1 = "NH1", atom_2 = "HH11", bond_order = 1f, bond_type = "sing", length = 1.018f),
KotmolBondRecord(atom_1 = "NH1", atom_2 = "HH12", bond_order = 1f, bond_type = "sing", length = 1.016f),
KotmolBondRecord(atom_1 = "NH2", atom_2 = "HH21", bond_order = 1f, bond_type = "sing", length = 1.017f),
KotmolBondRecord(atom_1 = "NH2", atom_2 = "HH22", bond_order = 1f, bond_type = "sing", length = 1.017f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.981f
)
)
val asn = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.531f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "ND2", bond_order = 1f, bond_type = "sing", length = 1.348f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "OD1", bond_order = 2f, bond_type = "doub", length = 1.213f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.468f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "ND2", atom_2 = "HD21", bond_order = 1f, bond_type = "sing", length = 0.97f),
KotmolBondRecord(atom_1 = "ND2", atom_2 = "HD22", bond_order = 1f, bond_type = "sing", length = 0.97f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val asp = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.209f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.508f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "OD1", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "OD2", bond_order = 1f, bond_type = "sing", length = 1.341f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "OD2", atom_2 = "HD2", bond_order = 1f, bond_type = "sing", length = 0.966f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val asx = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB1", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "XD1", bond_order = 2f, bond_type = "doub", length = 1.642f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "XD2", bond_order = 1f, bond_type = "sing", length = 1.642f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.008f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val cys = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.343f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.528f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "SG", bond_order = 1f, bond_type = "sing", length = 1.814f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.01f),
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "SG", atom_2 = "HG", bond_order = 1f, bond_type = "sing", length = 1.344f
)
)
val gln = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.343f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.528f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "NE2", bond_order = 1f, bond_type = "sing", length = 1.347f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "OE1", bond_order = 2f, bond_type = "doub", length = 1.212f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG2", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "NE2", atom_2 = "HE21", bond_order = 1f, bond_type = "sing", length = 0.969f),
KotmolBondRecord(atom_1 = "NE2", atom_2 = "HE22", bond_order = 1f, bond_type = "sing", length = 0.97f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val glu = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.508f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.531f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "OE1", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "OE2", bond_order = 1f, bond_type = "sing", length = 1.343f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD", bond_order = 1f, bond_type = "sing", length = 1.508f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG3", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "OE2", atom_2 = "HE2", bond_order = 1f, bond_type = "sing", length = 0.966f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val glx = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.343f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.531f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB1", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "XE1", bond_order = 2f, bond_type = "doub", length = 1.642f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "XE2", bond_order = 1f, bond_type = "sing", length = 1.642f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG1", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "HXT", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f
)
)
val gly = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.47f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val his = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.227f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.355f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.522f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.534f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.096f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.51f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.099f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.098f),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "HD2", bond_order = 1f, bond_type = "sing", length = 1.072f),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "NE2", bond_order = 1.5f, bond_type = "sing", length = 1.374f, aromatic = true),
KotmolBondRecord(atom_1 = "CE1", atom_2 = "HE1", bond_order = 1f, bond_type = "sing", length = 1.078f),
KotmolBondRecord(atom_1 = "CE1", atom_2 = "NE2", bond_order = 1.5f, bond_type = "sing", length = 1.337f, aromatic = true),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD2", bond_order = 1.5f, bond_type = "doub", length = 1.338f, aromatic = true),
KotmolBondRecord(atom_1 = "CG", atom_2 = "ND1", bond_order = 1.5f, bond_type = "sing", length = 1.351f, aromatic = true),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.441f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.006f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.007f),
KotmolBondRecord(atom_1 = "ND1", atom_2 = "CE1", bond_order = 1.5f, bond_type = "doub", length = 1.337f, aromatic = true),
KotmolBondRecord(atom_1 = "ND1", atom_2 = "HD1", bond_order = 1f, bond_type = "sing", length = 1.016f),
KotmolBondRecord(atom_1 = "NE2", atom_2 = "HE2", bond_order = 1f, bond_type = "sing", length = 1.016f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.98f
)
)
val ile = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG1", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG2", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD11", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD12", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD13", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG1", atom_2 = "CD1", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CG1", atom_2 = "HG12", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG1", atom_2 = "HG13", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG21", bond_order = 1f, bond_type = "sing", length = 1.088f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG22", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG23", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.007f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.008f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val leu = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.343f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD11", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD12", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD13", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "HD21", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "HD22", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "HD23", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD1", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD2", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.008f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.966f
)
)
val lys = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.343f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.531f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "CE", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "HD2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "HD3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CE", atom_2 = "HE2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CE", atom_2 = "HE3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CE", atom_2 = "NZ", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD", bond_order = 1f, bond_type = "sing", length = 1.531f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG2", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "NZ", atom_2 = "HZ1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "NZ", atom_2 = "HZ2", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "NZ", atom_2 = "HZ3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val met = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.343f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.528f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CE", atom_2 = "HE1", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CE", atom_2 = "HE2", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CE", atom_2 = "HE3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "SD", bond_order = 1f, bond_type = "sing", length = 1.814f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.01f),
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "SD", atom_2 = "CE", bond_order = 1f, bond_type = "sing", length = 1.814f
)
)
val phe = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.341f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.505f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "CE1", bond_order = 1.5f, bond_type = "sing", length = 1.382f, aromatic = true),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD1", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "CE2", bond_order = 1.5f, bond_type = "doub", length = 1.382f, aromatic = true),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "HD2", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CE1", atom_2 = "CZ", bond_order = 1.5f, bond_type = "doub", length = 1.381f, aromatic = true),
KotmolBondRecord(atom_1 = "CE1", atom_2 = "HE1", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CE2", atom_2 = "CZ", bond_order = 1.5f, bond_type = "sing", length = 1.382f, aromatic = true),
KotmolBondRecord(atom_1 = "CE2", atom_2 = "HE2", bond_order = 1f, bond_type = "sing", length = 1.081f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD1", bond_order = 1.5f, bond_type = "doub", length = 1.382f, aromatic = true),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD2", bond_order = 1.5f, bond_type = "sing", length = 1.383f, aromatic = true),
KotmolBondRecord(atom_1 = "CZ", atom_2 = "HZ", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.008f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val pro = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.508f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.543f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.543f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "HD2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CD", atom_2 = "HD3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD", bond_order = 1f, bond_type = "sing", length = 1.544f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "HG3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.486f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CD", bond_order = 1f, bond_type = "sing", length = 1.487f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.966f
)
)
val ser = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "OG", bond_order = 1f, bond_type = "sing", length = 1.428f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "OG", atom_2 = "HG", bond_order = 1f, bond_type = "sing", length = 0.967f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val thr = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG2", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "OG1", bond_order = 1f, bond_type = "sing", length = 1.428f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG21", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG22", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG23", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.007f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "OG1", atom_2 = "HG1", bond_order = 1f, bond_type = "sing", length = 0.967f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val trp = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD1", bond_order = 1f, bond_type = "sing", length = 1.079f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "NE1", bond_order = 1.5f, bond_type = "sing", length = 1.369f, aromatic = true),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "CE2", bond_order = 1.5f, bond_type = "doub", length = 1.407f, aromatic = true),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "CE3", bond_order = 1.5f, bond_type = "sing", length = 1.396f, aromatic = true),
KotmolBondRecord(atom_1 = "CE2", atom_2 = "CZ2", bond_order = 1.5f, bond_type = "sing", length = 1.391f, aromatic = true),
KotmolBondRecord(atom_1 = "CE3", atom_2 = "CZ3", bond_order = 1.5f, bond_type = "doub", length = 1.366f, aromatic = true),
KotmolBondRecord(atom_1 = "CE3", atom_2 = "HE3", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD1", bond_order = 1.5f, bond_type = "doub", length = 1.343f, aromatic = true),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD2", bond_order = 1.5f, bond_type = "sing", length = 1.464f, aromatic = true),
KotmolBondRecord(atom_1 = "CH2", atom_2 = "HH2", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CZ2", atom_2 = "CH2", bond_order = 1.5f, bond_type = "doub", length = 1.377f, aromatic = true),
KotmolBondRecord(atom_1 = "CZ2", atom_2 = "HZ2", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CZ3", atom_2 = "CH2", bond_order = 1.5f, bond_type = "sing", length = 1.388f, aromatic = true),
KotmolBondRecord(atom_1 = "CZ3", atom_2 = "HZ3", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.01f),
KotmolBondRecord(atom_1 = "NE1", atom_2 = "CE2", bond_order = 1.5f, bond_type = "sing", length = 1.377f, aromatic = true),
KotmolBondRecord(atom_1 = "NE1", atom_2 = "HE1", bond_order = 1f, bond_type = "sing", length = 0.969f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val tyr = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.207f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.507f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB2", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB3", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "CE1", bond_order = 1.5f, bond_type = "sing", length = 1.381f, aromatic = true),
KotmolBondRecord(atom_1 = "CD1", atom_2 = "HD1", bond_order = 1f, bond_type = "sing", length = 1.079f),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "CE2", bond_order = 1.5f, bond_type = "doub", length = 1.381f, aromatic = true),
KotmolBondRecord(atom_1 = "CD2", atom_2 = "HD2", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CE1", atom_2 = "CZ", bond_order = 1.5f, bond_type = "doub", length = 1.387f, aromatic = true),
KotmolBondRecord(atom_1 = "CE1", atom_2 = "HE1", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CE2", atom_2 = "CZ", bond_order = 1.5f, bond_type = "sing", length = 1.388f, aromatic = true),
KotmolBondRecord(atom_1 = "CE2", atom_2 = "HE2", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD1", bond_order = 1.5f, bond_type = "doub", length = 1.382f, aromatic = true),
KotmolBondRecord(atom_1 = "CG", atom_2 = "CD2", bond_order = 1.5f, bond_type = "sing", length = 1.383f, aromatic = true),
KotmolBondRecord(atom_1 = "CZ", atom_2 = "OH", bond_order = 1f, bond_type = "sing", length = 1.358f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "OH", atom_2 = "HH", bond_order = 1f, bond_type = "sing", length = 0.966f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.968f
)
)
val valine = listOf(
KotmolBondRecord(atom_1 = "C", atom_2 = "O", bond_order = 2f, bond_type = "doub", length = 1.208f),
KotmolBondRecord(atom_1 = "C", atom_2 = "OXT", bond_order = 1f, bond_type = "sing", length = 1.342f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "C", bond_order = 1f, bond_type = "sing", length = 1.506f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "CB", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CA", atom_2 = "HA", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG1", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "CG2", bond_order = 1f, bond_type = "sing", length = 1.529f),
KotmolBondRecord(atom_1 = "CB", atom_2 = "HB", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "CG1", atom_2 = "HG11", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG1", atom_2 = "HG12", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG1", atom_2 = "HG13", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG21", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG22", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "CG2", atom_2 = "HG23", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N", atom_2 = "CA", bond_order = 1f, bond_type = "sing", length = 1.469f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H", bond_order = 1f, bond_type = "sing", length = 1.008f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.009f),
// add H1 and H3 bonds to N
KotmolBondRecord(atom_1 = "N", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 1.009f),
KotmolBondRecord(atom_1 = "N", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.009f),
// end change
KotmolBondRecord(atom_1 = "OXT", atom_2 = "HXT", bond_order = 1f, bond_type = "sing", length = 0.967f
)
)
val da = listOf(
/*
* !!!
* These two records were added to capture the bond between the
* C2' then O2' and HO2'
* this was borrowed from another bond between an OXT and HXT
* SEE: 1A1T.pdb
*/
KotmolBondRecord(atom_1 = "O2'", atom_2 = "HO2'", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "O2'", bond_order = 1f, bond_type = "sing", length = 1.43f),
/*
* End of added record
*/
KotmolBondRecord(atom_1 = "C1'", atom_2 = "H1'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C1'", atom_2 = "N9", bond_order = 1f, bond_type = "sing", length = 1.466f),
KotmolBondRecord(atom_1 = "C2", atom_2 = "H2", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "C2", atom_2 = "N3", bond_order = 1.5f, bond_type = "doub", length = 1.316f, aromatic = true),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.541f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2'", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2''", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "C2'", bond_order = 1f, bond_type = "sing", length = 1.547f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "H3'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "O3'", bond_order = 1f, bond_type = "sing", length = 1.429f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "C3'", bond_order = 1f, bond_type = "sing", length = 1.549f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "H4'", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "O4'", bond_order = 1f, bond_type = "sing", length = 1.446f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C4", bond_order = 1.5f, bond_type = "doub", length = 1.405f, aromatic = true),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C6", bond_order = 1.5f, bond_type = "sing", length = 1.405f, aromatic = true),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "C4'", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5''", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "C6", atom_2 = "N1", bond_order = 1.5f, bond_type = "doub", length = 1.329f, aromatic = true),
KotmolBondRecord(atom_1 = "C6", atom_2 = "N6", bond_order = 1f, bond_type = "sing", length = 1.384f),
KotmolBondRecord(atom_1 = "C8", atom_2 = "H8", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "C8", atom_2 = "N7", bond_order = 1.5f, bond_type = "doub", length = 1.301f, aromatic = true),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C2", bond_order = 1.5f, bond_type = "sing", length = 1.319f, aromatic = true),
KotmolBondRecord(atom_1 = "N3", atom_2 = "C4", bond_order = 1.5f, bond_type = "sing", length = 1.329f, aromatic = true),
KotmolBondRecord(atom_1 = "N6", atom_2 = "H61", bond_order = 1f, bond_type = "sing", length = 0.97f),
KotmolBondRecord(atom_1 = "N6", atom_2 = "H62", bond_order = 1f, bond_type = "sing", length = 0.971f),
KotmolBondRecord(atom_1 = "N7", atom_2 = "C5", bond_order = 1.5f, bond_type = "sing", length = 1.355f, aromatic = true),
KotmolBondRecord(atom_1 = "N9", atom_2 = "C4", bond_order = 1.5f, bond_type = "sing", length = 1.372f, aromatic = true),
KotmolBondRecord(atom_1 = "N9", atom_2 = "C8", bond_order = 1.5f, bond_type = "sing", length = 1.362f, aromatic = true),
KotmolBondRecord(atom_1 = "O3'", atom_2 = "HO3'", bond_order = 1f, bond_type = "sing", length = 0.966f),
KotmolBondRecord(atom_1 = "O4'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.436f),
KotmolBondRecord(atom_1 = "O5'", atom_2 = "C5'", bond_order = 1f, bond_type = "sing", length = 1.428f),
KotmolBondRecord(atom_1 = "OP2", atom_2 = "HOP2", bond_order = 1f, bond_type = "sing", length = 0.966f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "HOP3", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "P", bond_order = 1f, bond_type = "sing", length = 1.61f),
KotmolBondRecord(atom_1 = "P", atom_2 = "O5'", bond_order = 1f, bond_type = "sing", length = 1.609f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP1", bond_order = 2f, bond_type = "doub", length = 1.48f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP2", bond_order = 1f, bond_type = "sing", length = 1.61f
)
)
val dc = listOf(
/*
* !!!
* These two records were added to capture the bond between the
* C2' then O2' and HO2'
* this was borrowed from another bond between an OXT and HXT
* SEE: 1A1T.pdb
*/
KotmolBondRecord(atom_1 = "O2'", atom_2 = "HO2'", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "O2'", bond_order = 1f, bond_type = "sing", length = 1.43f),
/*
* End of added record
*/
KotmolBondRecord(atom_1 = "C1'", atom_2 = "H1'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C1'", atom_2 = "N1", bond_order = 1f, bond_type = "sing", length = 1.465f),
KotmolBondRecord(atom_1 = "C2", atom_2 = "N3", bond_order = 1f, bond_type = "sing", length = 1.332f),
/* BUG should be O2
KotmolBondRecord(atom_1 = "C2", atom_2 = "O2'", bond_order = 2f, bond_type = "doub", length = 1.22f),
*/
KotmolBondRecord(atom_1 = "C2", atom_2 = "O2", bond_order = 2f, bond_type = "doub", length = 1.22f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.541f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2'", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2''", bond_order = 1f, bond_type = "sing", length = 1.091f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "C2'", bond_order = 1f, bond_type = "sing", length = 1.547f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "H3'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "O3'", bond_order = 1f, bond_type = "sing", length = 1.429f),
KotmolBondRecord(atom_1 = "C4", atom_2 = "C5", bond_order = 1f, bond_type = "sing", length = 1.41f),
KotmolBondRecord(atom_1 = "C4", atom_2 = "N4", bond_order = 1f, bond_type = "sing", length = 1.376f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "C3'", bond_order = 1f, bond_type = "sing", length = 1.549f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "H4'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "O4'", bond_order = 1f, bond_type = "sing", length = 1.445f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C6", bond_order = 2f, bond_type = "doub", length = 1.353f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "H5", bond_order = 1f, bond_type = "sing", length = 1.081f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "C4'", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5''", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "C6", atom_2 = "H6", bond_order = 1f, bond_type = "sing", length = 1.08f),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C2", bond_order = 1f, bond_type = "sing", length = 1.344f),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C6", bond_order = 1f, bond_type = "sing", length = 1.362f),
KotmolBondRecord(atom_1 = "N3", atom_2 = "C4", bond_order = 2f, bond_type = "doub", length = 1.326f),
KotmolBondRecord(atom_1 = "N4", atom_2 = "H41", bond_order = 1f, bond_type = "sing", length = 0.97f),
KotmolBondRecord(atom_1 = "N4", atom_2 = "H42", bond_order = 1f, bond_type = "sing", length = 0.97f),
KotmolBondRecord(atom_1 = "O3'", atom_2 = "HO3'", bond_order = 1f, bond_type = "sing", length = 0.968f),
KotmolBondRecord(atom_1 = "O4'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.437f),
KotmolBondRecord(atom_1 = "O5'", atom_2 = "C5'", bond_order = 1f, bond_type = "sing", length = 1.428f),
KotmolBondRecord(atom_1 = "OP2", atom_2 = "HOP2", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "HOP3", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "P", bond_order = 1f, bond_type = "sing", length = 1.61f),
KotmolBondRecord(atom_1 = "P", atom_2 = "O5'", bond_order = 1f, bond_type = "sing", length = 1.611f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP1", bond_order = 2f, bond_type = "doub", length = 1.48f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP2", bond_order = 1f, bond_type = "sing", length = 1.609f
)
)
val dg = listOf(
/*
* !!!
* These two records were added to capture the bond between the
* C2' then O2' and HO2'
* this was borrowed from another bond between an OXT and HXT
* SEE: 1A1T.pdb
*/
KotmolBondRecord(atom_1 = "O2'", atom_2 = "HO2'", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "O2'", bond_order = 1f, bond_type = "sing", length = 1.43f),
/*
* End of added record
*/
KotmolBondRecord(atom_1 = "C1'", atom_2 = "H1'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C1'", atom_2 = "N9", bond_order = 1f, bond_type = "sing", length = 1.464f),
KotmolBondRecord(atom_1 = "C2", atom_2 = "N2", bond_order = 1f, bond_type = "sing", length = 1.372f),
KotmolBondRecord(atom_1 = "C2", atom_2 = "N3", bond_order = 2f, bond_type = "doub", length = 1.314f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.54f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2''", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "C2'", bond_order = 1f, bond_type = "sing", length = 1.547f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "H3'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "O3'", bond_order = 1f, bond_type = "sing", length = 1.43f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "C3'", bond_order = 1f, bond_type = "sing", length = 1.55f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "H4'", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "O4'", bond_order = 1f, bond_type = "sing", length = 1.446f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C4", bond_order = 1.5f, bond_type = "doub", length = 1.4f, aromatic = true),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C6", bond_order = 1f, bond_type = "sing", length = 1.415f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "C4'", bond_order = 1f, bond_type = "sing", length = 1.53f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5'", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5''", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C6", atom_2 = "N1", bond_order = 1f, bond_type = "sing", length = 1.351f),
KotmolBondRecord(atom_1 = "C6", atom_2 = "O6", bond_order = 2f, bond_type = "doub", length = 1.219f),
KotmolBondRecord(atom_1 = "C8", atom_2 = "H8", bond_order = 1f, bond_type = "sing", length = 1.081f),
KotmolBondRecord(atom_1 = "C8", atom_2 = "N7", bond_order = 1.5f, bond_type = "doub", length = 1.302f, aromatic = true),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C2", bond_order = 1f, bond_type = "sing", length = 1.362f),
KotmolBondRecord(atom_1 = "N1", atom_2 = "H1", bond_order = 1f, bond_type = "sing", length = 0.97f),
KotmolBondRecord(atom_1 = "N2", atom_2 = "H21", bond_order = 1f, bond_type = "sing", length = 0.97f),
KotmolBondRecord(atom_1 = "N2", atom_2 = "H22", bond_order = 1f, bond_type = "sing", length = 0.97f),
KotmolBondRecord(atom_1 = "N3", atom_2 = "C4", bond_order = 1f, bond_type = "sing", length = 1.338f),
KotmolBondRecord(atom_1 = "N7", atom_2 = "C5", bond_order = 1.5f, bond_type = "sing", length = 1.355f, aromatic = true),
KotmolBondRecord(atom_1 = "N9", atom_2 = "C4", bond_order = 1.5f, bond_type = "sing", length = 1.368f, aromatic = true),
KotmolBondRecord(atom_1 = "N9", atom_2 = "C8", bond_order = 1.5f, bond_type = "sing", length = 1.364f, aromatic = true),
KotmolBondRecord(atom_1 = "O3'", atom_2 = "HO3'", bond_order = 1f, bond_type = "sing", length = 0.966f),
KotmolBondRecord(atom_1 = "O4'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.437f),
KotmolBondRecord(atom_1 = "O5'", atom_2 = "C5'", bond_order = 1f, bond_type = "sing", length = 1.428f),
KotmolBondRecord(atom_1 = "OP2", atom_2 = "HOP2", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "HOP3", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "P", bond_order = 1f, bond_type = "sing", length = 1.611f),
KotmolBondRecord(atom_1 = "P", atom_2 = "O5'", bond_order = 1f, bond_type = "sing", length = 1.61f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP1", bond_order = 2f, bond_type = "doub", length = 1.479f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP2", bond_order = 1f, bond_type = "sing", length = 1.608f
)
)
val dt = listOf(
KotmolBondRecord(atom_1 = "C1'", atom_2 = "H1'", bond_order = 1f, bond_type = "sing", length = 1.095f),
KotmolBondRecord(atom_1 = "C1'", atom_2 = "N1", bond_order = 1f, bond_type = "sing", length = 1.434f),
KotmolBondRecord(atom_1 = "C2", atom_2 = "N3", bond_order = 1f, bond_type = "sing", length = 1.399f),
/* BUG should be O2
KotmolBondRecord(atom_1 = "C2", atom_2 = "O2'", bond_order = 2f, bond_type = "doub", length = 1.232f),
*/
KotmolBondRecord(atom_1 = "C2", atom_2 = "O2", bond_order = 2f, bond_type = "doub", length = 1.232f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.52f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2'", bond_order = 1f, bond_type = "sing", length = 1.097f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2''", bond_order = 1f, bond_type = "sing", length = 1.095f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "C2'", bond_order = 1f, bond_type = "sing", length = 1.511f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "H3'", bond_order = 1f, bond_type = "sing", length = 1.094f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "O3'", bond_order = 1f, bond_type = "sing", length = 1.426f),
KotmolBondRecord(atom_1 = "C4", atom_2 = "C5", bond_order = 1f, bond_type = "sing", length = 1.487f),
KotmolBondRecord(atom_1 = "C4", atom_2 = "O4", bond_order = 2f, bond_type = "doub", length = 1.228f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "C3'", bond_order = 1f, bond_type = "sing", length = 1.522f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "H4'", bond_order = 1f, bond_type = "sing", length = 1.094f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "O4'", bond_order = 1f, bond_type = "sing", length = 1.441f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C6", bond_order = 2f, bond_type = "doub", length = 1.339f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C7", bond_order = 1f, bond_type = "sing", length = 1.495f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "C4'", bond_order = 1f, bond_type = "sing", length = 1.523f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5'", bond_order = 1f, bond_type = "sing", length = 1.092f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5''", bond_order = 1f, bond_type = "sing", length = 1.093f),
KotmolBondRecord(atom_1 = "C6", atom_2 = "H6", bond_order = 1f, bond_type = "sing", length = 1.086f),
KotmolBondRecord(atom_1 = "C7", atom_2 = "H71", bond_order = 1f, bond_type = "sing", length = 1.089f),
KotmolBondRecord(atom_1 = "C7", atom_2 = "H72", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "C7", atom_2 = "H73", bond_order = 1f, bond_type = "sing", length = 1.09f),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C2", bond_order = 1f, bond_type = "sing", length = 1.411f),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C6", bond_order = 1f, bond_type = "sing", length = 1.389f),
KotmolBondRecord(atom_1 = "N3", atom_2 = "C4", bond_order = 1f, bond_type = "sing", length = 1.387f),
KotmolBondRecord(atom_1 = "N3", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.016f),
KotmolBondRecord(atom_1 = "O3'", atom_2 = "HO3'", bond_order = 1f, bond_type = "sing", length = 0.973f),
KotmolBondRecord(atom_1 = "O4'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.434f),
KotmolBondRecord(atom_1 = "O5'", atom_2 = "C5'", bond_order = 1f, bond_type = "sing", length = 1.418f),
KotmolBondRecord(atom_1 = "OP2", atom_2 = "HOP2", bond_order = 1f, bond_type = "sing", length = 0.981f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "HOP3", bond_order = 1f, bond_type = "sing", length = 0.981f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "P", bond_order = 1f, bond_type = "sing", length = 1.618f),
KotmolBondRecord(atom_1 = "P", atom_2 = "O5'", bond_order = 1f, bond_type = "sing", length = 1.619f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP1", bond_order = 2f, bond_type = "doub", length = 1.501f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP2", bond_order = 1f, bond_type = "sing", length = 1.616f
)
)
val du = listOf(
/*
* !!!
* These two records were added to capture the bond between the
* C2' then O2' and HO2'
* this was borrowed from another bond between an OXT and HXT
* SEE: 1A1T.pdb
*/
KotmolBondRecord(atom_1 = "O2'", atom_2 = "HO2'", bond_order = 1f, bond_type = "sing", length = 0.967f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "O2'", bond_order = 1f, bond_type = "sing", length = 1.43f),
/*
* End of added record
*/
KotmolBondRecord(atom_1 = "C1'", atom_2 = "H1'", bond_order = 1f, bond_type = "sing", length = 1.095f),
KotmolBondRecord(atom_1 = "C1'", atom_2 = "N1", bond_order = 1f, bond_type = "sing", length = 1.434f),
KotmolBondRecord(atom_1 = "C2", atom_2 = "N3", bond_order = 1f, bond_type = "sing", length = 1.402f),
/* BUG should be O2
KotmolBondRecord(atom_1 = "C2", atom_2 = "O2'", bond_order = 2f, bond_type = "doub", length = 1.233f),
*/
KotmolBondRecord(atom_1 = "C2", atom_2 = "O2", bond_order = 2f, bond_type = "doub", length = 1.233f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.52f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2'", bond_order = 1f, bond_type = "sing", length = 1.097f),
KotmolBondRecord(atom_1 = "C2'", atom_2 = "H2''", bond_order = 1f, bond_type = "sing", length = 1.095f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "C2'", bond_order = 1f, bond_type = "sing", length = 1.511f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "H3'", bond_order = 1f, bond_type = "sing", length = 1.094f),
KotmolBondRecord(atom_1 = "C3'", atom_2 = "O3'", bond_order = 1f, bond_type = "sing", length = 1.426f),
KotmolBondRecord(atom_1 = "C4", atom_2 = "C5", bond_order = 1f, bond_type = "sing", length = 1.477f),
KotmolBondRecord(atom_1 = "C4", atom_2 = "O4", bond_order = 2f, bond_type = "doub", length = 1.227f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "C3'", bond_order = 1f, bond_type = "sing", length = 1.522f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "H4'", bond_order = 1f, bond_type = "sing", length = 1.094f),
KotmolBondRecord(atom_1 = "C4'", atom_2 = "O4'", bond_order = 1f, bond_type = "sing", length = 1.441f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "C6", bond_order = 2f, bond_type = "doub", length = 1.336f),
KotmolBondRecord(atom_1 = "C5", atom_2 = "H5", bond_order = 1f, bond_type = "sing", length = 1.083f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "C4'", bond_order = 1f, bond_type = "sing", length = 1.523f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5'", bond_order = 1f, bond_type = "sing", length = 1.092f),
KotmolBondRecord(atom_1 = "C5'", atom_2 = "H5''", bond_order = 1f, bond_type = "sing", length = 1.093f),
KotmolBondRecord(atom_1 = "C6", atom_2 = "H6", bond_order = 1f, bond_type = "sing", length = 1.085f),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C2", bond_order = 1f, bond_type = "sing", length = 1.412f),
KotmolBondRecord(atom_1 = "N1", atom_2 = "C6", bond_order = 1f, bond_type = "sing", length = 1.389f),
KotmolBondRecord(atom_1 = "N3", atom_2 = "C4", bond_order = 1f, bond_type = "sing", length = 1.386f),
KotmolBondRecord(atom_1 = "N3", atom_2 = "H3", bond_order = 1f, bond_type = "sing", length = 1.016f),
KotmolBondRecord(atom_1 = "O3'", atom_2 = "HO3'", bond_order = 1f, bond_type = "sing", length = 0.973f),
KotmolBondRecord(atom_1 = "O4'", atom_2 = "C1'", bond_order = 1f, bond_type = "sing", length = 1.434f),
KotmolBondRecord(atom_1 = "O5'", atom_2 = "C5'", bond_order = 1f, bond_type = "sing", length = 1.418f),
KotmolBondRecord(atom_1 = "OP2", atom_2 = "HOP2", bond_order = 1f, bond_type = "sing", length = 0.981f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "HOP3", bond_order = 1f, bond_type = "sing", length = 0.981f),
KotmolBondRecord(atom_1 = "OP3", atom_2 = "P", bond_order = 1f, bond_type = "sing", length = 1.618f),
KotmolBondRecord(atom_1 = "P", atom_2 = "O5'", bond_order = 1f, bond_type = "sing", length = 1.619f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP1", bond_order = 2f, bond_type = "doub", length = 1.501f),
KotmolBondRecord(atom_1 = "P", atom_2 = "OP2", bond_order = 1f, bond_type = "sing", length = 1.616f
)
)
val kotmolBondLookup = hashMapOf(
"ala" to ala, "arg" to arg, "asn" to asn, "asp" to asp, "asx" to asx, "cys" to cys, "glu" to glu, "gln" to gln, "glx" to glx, "gly" to gly, "his" to his, "ile" to ile, "leu" to leu, "lys" to lys, "met" to met, "phe" to phe, "pro" to pro, "ser" to ser, "thr" to thr, "trp" to trp, "tyr" to tyr, "val" to valine, // nucleic acid bonds
"da" to da, "dc" to dc, "dg" to dg, "dt" to dt, "du" to du, "a" to da, "c" to dc, "g" to dg, "t" to dt, "u" to du
)
}
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